Citrus Sinensis ID: 026341

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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
Protein Sequence
MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYRSRSPVRRSRT
Secondary Structure (PSIPRED)
cccccccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEEEccccccccccccccccccccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEEcEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mcislhyagfafvyfeddrdaadairgldnipfgydrrrLSVEwargergrhrdgsksmanqrptktlfvinfdpirtreRDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYalkddserddrydsprrggygrhspygrspspayrrrpspdygrgrspaydryngpvydqrrspdhgrhrspvpvydrrrspdygrnrspnfgryrsrspvrrsrt
Flexible Loop (DISEMBL)
MCISLHYAGFAFVYFEDDRDAADAIrgldnipfgydrrrlsvewargergrhrdgsksmanqrptktlfvinfdpirtrerdikrhfepygnvlhVRIRRNFAFVQFETQEEatkalestdrsklvdrvisveyalkddserddrydsprrggygrhspygrspspayrrrpspdygrgrspaydryngpvydqrrspdhgrhrspvpvydrrrspdygrnrspnfgryrsrspvrrsrt
Low Complexity Region (SEG)
MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHspygrspspayrrrpspDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGryrsrspvrrsrT
Disordered region (IsUnstruct)
*CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA*********************TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFET***************LVDRVISVEY**********************************************************************************************************
Disordered Region (DISOPRED)
***SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRR*****************************FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVI**************************************************************************************************************
Disordered Region (DISEMBL)
MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA***************NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEE***********KLVDRVISVEYALKD*************GGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRYNGPVYDQ************VPVYDRRRSPDYGRNRSPNFGRY***********
Disordered Region (DISPRO)
MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG**************QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD******************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYRSRSPVRRSRT
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	240	2.2.26 [Sep-21-2011]
P92964	264	Arginine/serine-rich-spli	yes	no	0.920	0.837	0.679	6e-79
P92965	350	Arginine/serine-rich-spli	no	no	0.945	0.648	0.522	5e-50
P92966	356	Arginine/serine-rich-spli	no	no	0.916	0.617	0.512	2e-45
Q66H68	590	RNA-binding protein 47 OS	yes	no	0.654	0.266	0.319	2e-11
Q91WT8	590	RNA-binding protein 47 OS	yes	no	0.654	0.266	0.313	4e-11
Q9XSR3	592	RNA-binding protein 47 OS	yes	no	0.545	0.221	0.328	5e-08
Q5R5P4	593	RNA-binding protein 47 OS	yes	no	0.55	0.222	0.319	1e-07
A0AV96	593	RNA-binding protein 47 OS	yes	no	0.55	0.222	0.319	1e-07
Q09442	388	Splicing factor 3B subuni	yes	no	0.533	0.329	0.286	2e-07
Q6IQ97	419	RNA-binding protein 4.1 O	no	no	0.887	0.508	0.244	6e-07

>sp|P92964|RSP31_ARATH Arginine/serine-rich-splicing factor RSP31 OS=Arabidopsis thaliana GN=RSP31 PE=1 SV=2

 Score =  293 bits (751), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 163/240 (67%), Positives = 187/240 (77%), Gaps = 19/240 (7%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +G+AFVYFED+RDA DAIR LDN PFGY++RRLSVEWA+GERGR R  +K+ +N +PTKT
Sbjct: 35  SGYAFVYFEDERDAEDAIRKLDNFPFGYEKRRLSVEWAKGERGRPRGDAKAPSNLKPTKT 94

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRT+E DI++HFEPYG V +VRIRRNF+FVQFETQE+ATKALE+T RSK++D
Sbjct: 95  LFVINFDPIRTKEHDIEKHFEPYGKVTNVRIRRNFSFVQFETQEDATKALEATQRSKILD 154

Query: 128 RVISVEYALKDDSERDDRYD--SPRRGGYG----RHSP-YGRSPSPAYRRRPSPDYGRGR 180
           RV+SVEYALKDD ERDDR    SPRR        R SP YGR PSP   RRPSPDYGR R
Sbjct: 155 RVVSVEYALKDDDERDDRNGGRSPRRSLSPVYRRRPSPDYGRRPSPGQGRRPSPDYGRAR 214

Query: 181 SPAYDRYNGP-VYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYRSRSPVRRSR 239
           SP YDRY GP  Y++RRSPD+G           RRS DYGR RSP + RYRSRSPV R R
Sbjct: 215 SPEYDRYKGPAAYERRRSPDYG-----------RRSSDYGRQRSPGYDRYRSRSPVPRGR 263

Required for constitutive and alternative pre-mRNA splicing.
Arabidopsis thaliana (taxid: 3702)

>sp|P92965|RSP40_ARATH Arginine/serine-rich-splicing factor RSP40 OS=Arabidopsis thaliana GN=RSP40 PE=1 SV=2

 Score =  197 bits (501), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 126/241 (52%), Positives = 155/241 (64%), Gaps = 14/241 (5%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMAN----QR 63
           AGFAFVY ED+RDA DAIR LD   FG   RRL VEW + ERG  +             R
Sbjct: 35  AGFAFVYMEDERDAEDAIRALDRFEFGRKGRRLRVEWTKSERGGDKRSGGGSRRSSSSMR 94

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRS 123
           P+KTLFVINFD   TR RD+++HFEPYG +++VRIRRNFAF+Q+E QE+AT+AL++++ S
Sbjct: 95  PSKTLFVINFDADNTRTRDLEKHFEPYGKIVNVRIRRNFAFIQYEAQEDATRALDASNNS 154

Query: 124 KLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPA 183
           KL+D+VISVEYA+KDD  R + + SP R          RSPSP  R R SPDYGRG SP 
Sbjct: 155 KLMDKVISVEYAVKDDDARGNGH-SPERRRDRSPERRRRSPSPYKRERGSPDYGRGASPV 213

Query: 184 YDRYNGPVYDQRRSPDHGRHRSPVPVYDRRR-SPDYGRNRSPNFG---RYRSRSPVRRSR 239
                     +R SPD+GR RSP P    RR SP+YGR+R  N     R R  SP + SR
Sbjct: 214 -----AAYRKERTSPDYGRRRSPSPYKKSRRGSPEYGRDRRGNDSPRRRERVASPTKYSR 268

Query: 240 T 240
           +
Sbjct: 269 S 269

Required for constitutive and alternative pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|P92966|RSP41_ARATH Arginine/serine-rich-splicing factor RSP41 OS=Arabidopsis thaliana GN=RSP41 PE=1 SV=2

 Score =  182 bits (462), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 127/248 (51%), Positives = 151/248 (60%), Gaps = 28/248 (11%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPT-- 65
           AGFAFVY ED+RDA DAIR LD   +G   RRL VEW + +RG       S  +      
Sbjct: 35  AGFAFVYMEDERDAEDAIRALDRFEYGRTGRRLRVEWTKNDRGGAGRSGGSRRSSSGLRP 94

Query: 66  -KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSK 124
            KTLFVINFD   TR RD++RHFEPYG +++VRIRRNFAF+Q+E QE+AT+AL++T+ SK
Sbjct: 95  SKTLFVINFDAQNTRTRDLERHFEPYGKIVNVRIRRNFAFIQYEAQEDATRALDATNSSK 154

Query: 125 LVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAY 184
           L+D+VISVEYA+KDD  R + Y SP R          RSPSP  R R SPDYGRG SP  
Sbjct: 155 LMDKVISVEYAVKDDDSRGNGY-SPERRRDRSPDRRRRSPSPYRRERGSPDYGRGASPVA 213

Query: 185 DRYNGPVYDQRRSPDHGR-HRSPVPVYDRRRSPDYG-----------------RNRSPNF 226
            +       +R SPD+GR  RSP P    R SPDY                  RNRSP  
Sbjct: 214 HKR------ERTSPDYGRGRRSPSPYKRARLSPDYKRDDRRRERVASPENGAVRNRSPRK 267

Query: 227 GRYRSRSP 234
           GR  SRSP
Sbjct: 268 GRGESRSP 275

Required for constitutive and alternative pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q66H68|RBM47_RAT RNA-binding protein 47 OS=Rattus norvegicus GN=Rbm47 PE=2 SV=1

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 78/166 (46%), Gaps = 9/166 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++      K L
Sbjct: 195 GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMQTV------KIL 248

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N   I T E  IKR F  +  G V  V+  R++AFV F ++E+A  A+ + + ++L 
Sbjct: 249 YVRNLM-IETTEETIKRSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELE 307

Query: 127 DRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRP 172
              + V  A   D E+  RY    +GG G      + PS  Y   P
Sbjct: 308 GSCLEVTLAKPVDKEQYSRYQKAAKGGGGSAEAVAQQPSYVYSCDP 353

Rattus norvegicus (taxid: 10116)

>sp|Q91WT8|RBM47_MOUSE RNA-binding protein 47 OS=Mus musculus GN=Rbm47 PE=2 SV=1

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 78/166 (46%), Gaps = 9/166 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++      K L
Sbjct: 195 GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMQTV------KIL 248

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N   I T E  IK+ F  +  G V  V+  R++AFV F ++E+A  A+ + + ++L 
Sbjct: 249 YVRNLM-IETTEETIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELE 307

Query: 127 DRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRP 172
              + V  A   D E+  RY    +GG G      + PS  Y   P
Sbjct: 308 GSCLEVTLAKPVDKEQYSRYQKAAKGGGGSAEAVAQQPSYVYSCDP 353

Mus musculus (taxid: 10090)

>sp|Q9XSR3|RBM47_CANFA RNA-binding protein 47 OS=Canis familiaris GN=RBM47 PE=2 SV=1

 Score = 58.2 bits (139), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 46/140 (32%), Positives = 69/140 (49%), Gaps = 9/140 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++      K L
Sbjct: 197 GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV------KIL 250

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N   I T E  IK+ F  +  G V  V+  R++AFV F ++E+A  A+ S + ++L 
Sbjct: 251 YVRNLM-IETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFASREDAVLAMNSLNGTELE 309

Query: 127 DRVISVEYALKDDSERDDRY 146
              + V  A   D E+  RY
Sbjct: 310 GSCLEVTLAKPVDKEQYSRY 329

Canis familiaris (taxid: 9615)

>sp|Q5R5P4|RBM47_PONAB RNA-binding protein 47 OS=Pongo abelii GN=RBM47 PE=2 SV=2

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/141 (31%), Positives = 69/141 (48%), Gaps = 9/141 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++      K L
Sbjct: 195 GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV------KIL 248

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N   I T E  IK+ F  +  G V  V+  R++AFV F ++E+A  A+ + + ++L 
Sbjct: 249 YVRNLM-IETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELE 307

Query: 127 DRVISVEYALKDDSERDDRYD 147
              + V  A   D E+  RY 
Sbjct: 308 GSCLEVTLAKPVDKEQYSRYQ 328

Pongo abelii (taxid: 9601)

>sp|A0AV96|RBM47_HUMAN RNA-binding protein 47 OS=Homo sapiens GN=RBM47 PE=1 SV=2

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/141 (31%), Positives = 69/141 (48%), Gaps = 9/141 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++      K L
Sbjct: 195 GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV------KIL 248

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N   I T E  IK+ F  +  G V  V+  R++AFV F ++E+A  A+ + + ++L 
Sbjct: 249 YVRNLM-IETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELE 307

Query: 127 DRVISVEYALKDDSERDDRYD 147
              + V  A   D E+  RY 
Sbjct: 308 GSCLEVTLAKPVDKEQYSRYQ 328

Homo sapiens (taxid: 9606)

>sp|Q09442|SF3B4_CAEEL Splicing factor 3B subunit 4 OS=Caenorhabditis elegans GN=sap-49 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/150 (28%), Positives = 68/150 (45%), Gaps = 22/150 (14%)

Query: 3   ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ 62
           ++ ++ GF FV F  + DA  AI+ L+ I               G+  +    S    N 
Sbjct: 49  VTANHQGFGFVEFMGEEDADYAIKILNMIKL------------YGKPIKVNKASAHEKNM 96

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV-RIRRN--------FAFVQFETQEEA 113
                +FV N DP    E+ +   F  +G +L V +I R+        FAF+ F + E +
Sbjct: 97  DVGANIFVGNLDP-EVDEKLLYDTFSAFGVILQVPKIMRDVDSGTSKGFAFINFASFEAS 155

Query: 114 TKALESTDRSKLVDRVISVEYALKDDSERD 143
             ALE+ +   L +R I+V YA K DS+ +
Sbjct: 156 DTALEAMNGQFLCNRAITVSYAFKRDSKGE 185

Subunit of the splicing factor SF3B required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Caenorhabditis elegans (taxid: 6239)

>sp|Q6IQ97|RBM41_DANRE RNA-binding protein 4.1 OS=Danio rerio GN=rbm4.1 PE=1 SV=1

 Score = 54.7 bits (130), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 62/254 (24%), Positives = 105/254 (41%), Gaps = 41/254 (16%)

Query: 10  FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLF 69
           F FV+ +   +A +AI+ L +  +  +   ++VE ++G+              + +  L 
Sbjct: 37  FGFVHMDSKSEADEAIQNLHH--YMLNGMAMNVEMSKGK-------------PKTSTKLH 81

Query: 70  VINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRV 129
           V N     T + +++  FE YG V+   I +++AFV  E  E+A +A+   D +    ++
Sbjct: 82  VGNISSSCTNQ-ELRAKFEEYGPVVECDIVKDYAFVHMERVEDAMEAISGLDNTAFQGKL 140

Query: 130 ISVEYALK------DDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSP--------D 175
           +SV+ +           ER   Y   + G + +  P  ++ S  YR  PS         D
Sbjct: 141 MSVKLSTSRLRTAPGMGERTGCYRCGQEGHWSKECPLDQNGS--YREGPSSEGFGPVRFD 198

Query: 176 YGRGRSPAYDR-YNG-PVYDQRRSPDHGRHRS---PVPVYDR----RRSPDYGRNRSPNF 226
            G  R   + R ++G P Y    +P HG  R     VP Y R      +  YG       
Sbjct: 199 SGGDRGRGFHRGFSGEPAYAGSFAPSHGFTRGAGYAVPGYGRGAGFESAMGYGMPAGYGV 258

Query: 227 GRYRSRSPVRRSRT 240
           G   S +PV  S  
Sbjct: 259 GADNSMAPVYGSEA 272

Danio rerio (taxid: 7955)

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	240
356520256	259	PREDICTED: arginine/serine-rich-splicing	0.929	0.861	0.765	1e-88
224068024	236	predicted protein [Populus trichocarpa]	0.833	0.847	0.781	2e-87
255645349	259	unknown [Glycine max]	0.929	0.861	0.757	2e-87
255564609	259	arginine/serine-rich splicing factor, pu	0.837	0.776	0.745	2e-86
356559961	264	PREDICTED: arginine/serine-rich-splicing	0.887	0.806	0.758	7e-86
449432024	253	PREDICTED: arginine/serine-rich-splicing	0.825	0.782	0.827	2e-85
224130604	236	predicted protein [Populus trichocarpa]	0.833	0.847	0.761	1e-84
297745508	224	unnamed protein product [Vitis vinifera]	0.825	0.883	0.786	3e-83
225470972	241	PREDICTED: arginine/serine-rich-splicing	0.795	0.792	0.802	6e-83
357514487	301	Arginine/serine-rich splicing factor [Me	0.85	0.677	0.723	4e-80

>gi|356520256|ref|XP_003528779.1| PREDICTED: arginine/serine-rich-splicing factor RSP31-like [Glycine max]

 Score =  332 bits (850), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 180/235 (76%), Positives = 200/235 (85%), Gaps = 12/235 (5%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVY+ED+RDA +AIR LDN+PFG+++RRLSVEWARGERGRH DGSK  ANQ+PTKT
Sbjct: 35  SGFAFVYYEDERDAEEAIRALDNVPFGHEKRRLSVEWARGERGRHHDGSK--ANQKPTKT 92

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR RDI++HFEPYGNVLHVRIRRNFAFVQFETQE+ATKALE T+ SK++D
Sbjct: 93  LFVINFDPIRTRVRDIEKHFEPYGNVLHVRIRRNFAFVQFETQEDATKALECTNMSKILD 152

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRY 187
           RV+SVEYAL+DD ER D YDSPRR G      Y RSPSP Y RRPSPDYGR RSP YDRY
Sbjct: 153 RVVSVEYALRDDGERGDNYDSPRRRG-----GYERSPSP-YHRRPSPDYGRPRSPVYDRY 206

Query: 188 NGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYR--SRSPVRRSRT 240
           NG   D RRSPD+GRHRS  P Y RRRSPDYG+ RSP +GRYR  SRSPVRRSRT
Sbjct: 207 NGGGPDMRRSPDYGRHRS--PDYGRRRSPDYGKPRSPEYGRYRSCSRSPVRRSRT 259

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068024|ref|XP_002302651.1| predicted protein [Populus trichocarpa] gi|222844377|gb|EEE81924.1| predicted protein [Populus trichocarpa]

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 168/215 (78%), Positives = 183/215 (85%), Gaps = 15/215 (6%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVYFEDDRDAADA+RGLDNIPFGYDRRRLSVEWARGERGRHRDG +S ANQRPTKT
Sbjct: 36  SGFAFVYFEDDRDAADAVRGLDNIPFGYDRRRLSVEWARGERGRHRDGPRSTANQRPTKT 95

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPI TR  DIKRHFE YG VLHVRIRRNFAFVQFETQE+ATKALE T  +K++D
Sbjct: 96  LFVINFDPIHTRVEDIKRHFERYGEVLHVRIRRNFAFVQFETQEDATKALECTHMTKILD 155

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRY 187
           RV+SVEYAL+DDSER DRYDSPRRG Y      GRSPSP YRRRPSPDY R RSP YD+Y
Sbjct: 156 RVVSVEYALRDDSERGDRYDSPRRGSYN-----GRSPSPVYRRRPSPDYVRARSPVYDKY 210

Query: 188 NGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNR 222
           NGPVYD+R+SPD+GR+          RSP+YGRNR
Sbjct: 211 NGPVYDRRQSPDYGRN----------RSPEYGRNR 235

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645349|gb|ACU23171.1| unknown [Glycine max]

 Score =  327 bits (839), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 178/235 (75%), Positives = 199/235 (84%), Gaps = 12/235 (5%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFV++ED+RDA +AIR LDN+PFG+++RRLSVEWARGERGRH DGSK  ANQ+PTKT
Sbjct: 35  SGFAFVFYEDERDAEEAIRALDNVPFGHEKRRLSVEWARGERGRHHDGSK--ANQKPTKT 92

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR RDI++HFEPYGNVLHVRIRRNFAFVQFETQE+ATKALE T+ SK++D
Sbjct: 93  LFVINFDPIRTRVRDIEKHFEPYGNVLHVRIRRNFAFVQFETQEDATKALECTNMSKILD 152

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRY 187
           RV+SVEYAL+DD ER D YDSPRR G      Y RSPSP Y RRPSPDYGR RSP YDRY
Sbjct: 153 RVVSVEYALRDDGERGDNYDSPRRRG-----GYERSPSP-YHRRPSPDYGRPRSPVYDRY 206

Query: 188 NGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYR--SRSPVRRSRT 240
           NG   D RRSPD+GRHRS  P Y RRRSPDYG+ RSP +GRYR  SRS VRRSRT
Sbjct: 207 NGGGPDMRRSPDYGRHRS--PDYGRRRSPDYGKPRSPEYGRYRSCSRSLVRRSRT 259

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564609|ref|XP_002523299.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223537387|gb|EEF39015.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  324 bits (830), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 167/224 (74%), Positives = 184/224 (82%), Gaps = 23/224 (10%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVYFED+RDAADAIRGLDNI FGYDRR+LSVEWARGERGRHRDGS+SMANQRPTKT
Sbjct: 36  SGFAFVYFEDERDAADAIRGLDNISFGYDRRKLSVEWARGERGRHRDGSRSMANQRPTKT 95

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPI TR  DIKRHFE YG VLHVRIRRNFAFVQFETQE+ATKALE T  +K++D
Sbjct: 96  LFVINFDPIHTRVEDIKRHFERYGEVLHVRIRRNFAFVQFETQEDATKALECTHMTKILD 155

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRY 187
           RV+SVEYAL+DDSER D+ DSPRRG     S YGRSPSP YRRRPSPDYGR RSP YD+Y
Sbjct: 156 RVVSVEYALRDDSERGDKSDSPRRG-----SHYGRSPSPVYRRRPSPDYGRARSPVYDKY 210

Query: 188 NGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYRS 231
           NGP YD+RR                  SP+YGR++SP +GRYRS
Sbjct: 211 NGPSYDRRR------------------SPEYGRDQSPEYGRYRS 236

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559961|ref|XP_003548264.1| PREDICTED: arginine/serine-rich-splicing factor RSP31-like [Glycine max]

 Score =  322 bits (826), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 170/224 (75%), Positives = 194/224 (86%), Gaps = 11/224 (4%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVY+ED+RDA +AIR LDN+PFG+++RRLSVEWARGERGRHRDGSK  ANQ+PTKT
Sbjct: 35  SGFAFVYYEDERDAEEAIRALDNVPFGHEKRRLSVEWARGERGRHRDGSK--ANQKPTKT 92

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR RDI++HFEPYGNVLHVRIRRNFAFVQFETQE+ATKA+E T+ SK++D
Sbjct: 93  LFVINFDPIRTRVRDIEKHFEPYGNVLHVRIRRNFAFVQFETQEDATKAIECTNMSKILD 152

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRY 187
           RV+SVEYAL+DD ER D YDSPRRGG      Y RSPSP Y RRPSPDYGR RSP YDRY
Sbjct: 153 RVVSVEYALRDDGERGDNYDSPRRGG------YERSPSP-YHRRPSPDYGRPRSPVYDRY 205

Query: 188 NGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYRS 231
           NG   D+RRSPD+GRHRS  P Y RRRSPDYGR +SP++G+ RS
Sbjct: 206 NGGGPDRRRSPDYGRHRS--PDYGRRRSPDYGRRKSPDYGKPRS 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432024|ref|XP_004133800.1| PREDICTED: arginine/serine-rich-splicing factor RSP31-like [Cucumis sativus] gi|449477961|ref|XP_004155176.1| PREDICTED: arginine/serine-rich-splicing factor RSP31-like [Cucumis sativus]

 Score =  321 bits (822), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/203 (82%), Positives = 184/203 (90%), Gaps = 5/203 (2%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVYFED+RDA DAIRGLDN+PFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT
Sbjct: 35  SGFAFVYFEDERDAEDAIRGLDNLPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 94

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR RDI+RHFEPYG VL+VRIRRNFAFVQFETQE+ATKALE T  SK++D
Sbjct: 95  LFVINFDPIRTRVRDIERHFEPYGKVLNVRIRRNFAFVQFETQEDATKALECTHMSKILD 154

Query: 128 RVISVEYALKDDSERDDRYD-SPRR-GGYGR--HSPYGRSPSPAYRRRPSPDYGRGRSPA 183
           RV+SVEYAL+DD ER D +D SPRR GGYGR   SPY RSPSP +RRRPSPDYGR  SPA
Sbjct: 155 RVVSVEYALRDDGERGDPFDESPRRAGGYGRPGDSPYRRSPSPVFRRRPSPDYGRAHSPA 214

Query: 184 YDRYNGPVYDQRRSPDHGRHRSP 206
           YDRYNGP Y++RRSPD+GR+RSP
Sbjct: 215 YDRYNGP-YERRRSPDYGRNRSP 236

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130604|ref|XP_002320882.1| predicted protein [Populus trichocarpa] gi|222861655|gb|EEE99197.1| predicted protein [Populus trichocarpa]

 Score =  318 bits (815), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 166/218 (76%), Positives = 184/218 (84%), Gaps = 18/218 (8%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR---GERGRHRDGSKSMANQRP 64
           +GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   GERGRHRDG +S  NQRP
Sbjct: 34  SGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARVYAGERGRHRDGPRSTVNQRP 93

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSK 124
           TKTLFVINFDPI TR  DIKRHFE YG VLHVRIRRNFAFVQFETQE+ATKAL+ T  +K
Sbjct: 94  TKTLFVINFDPIHTRVEDIKRHFERYGEVLHVRIRRNFAFVQFETQEDATKALQRTHMTK 153

Query: 125 LVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAY 184
           ++DRV+SVEYAL+DDSER DRYDSPRRG Y     YGRSPSPA+ RRP+PDYGRG SP Y
Sbjct: 154 ILDRVVSVEYALRDDSERGDRYDSPRRGSY-----YGRSPSPAHHRRPNPDYGRGHSPVY 208

Query: 185 DRYNGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNR 222
           D+YNGPV+D+RRSPD+GR+          RSP+YGR+R
Sbjct: 209 DKYNGPVHDRRRSPDYGRN----------RSPEYGRHR 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745508|emb|CBI40588.3| unnamed protein product [Vitis vinifera]

 Score =  313 bits (803), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 162/206 (78%), Positives = 180/206 (87%), Gaps = 8/206 (3%)

Query: 1   MCIS-LHYA-GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
            C S LH + GFAFVYFED+ DA DAIRGLDNIPFGYDRRRLSVEWA+GERGRHR+GS+S
Sbjct: 9   FCASALHISSGFAFVYFEDEHDADDAIRGLDNIPFGYDRRRLSVEWAKGERGRHREGSRS 68

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
           MANQRPTKTLFVINFDPIRTR RDI+RHFEPYG VLHVRIRRNFAFVQ+ETQE+ATKALE
Sbjct: 69  MANQRPTKTLFVINFDPIRTRIRDIERHFEPYGKVLHVRIRRNFAFVQYETQEDATKALE 128

Query: 119 STDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGR--HSPYGRSPSPAYRR-RPSPD 175
            T  SK++DRV+SVEYAL+DDS   D+YDSPRRGGY R   SPYGRSPSP  RR RPSPD
Sbjct: 129 CTHMSKILDRVVSVEYALRDDS---DKYDSPRRGGYSRRGESPYGRSPSPVNRRGRPSPD 185

Query: 176 YGRGRSPAYDRYNGPVYDQRRSPDHG 201
           YGR +SP YDRYNGP Y++ RSP++G
Sbjct: 186 YGRAQSPVYDRYNGPAYERNRSPEYG 211

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225470972|ref|XP_002267297.1| PREDICTED: arginine/serine-rich-splicing factor RSP31-like [Vitis vinifera]

 Score =  312 bits (800), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 158/197 (80%), Positives = 176/197 (89%), Gaps = 6/197 (3%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVYFED+ DA DAIRGLDNIPFGYDRRRLSVEWA+GERGRHR+GS+SMANQRPTKT
Sbjct: 35  SGFAFVYFEDEHDADDAIRGLDNIPFGYDRRRLSVEWAKGERGRHREGSRSMANQRPTKT 94

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR RDI+RHFEPYG VLHVRIRRNFAFVQ+ETQE+ATKALE T  SK++D
Sbjct: 95  LFVINFDPIRTRIRDIERHFEPYGKVLHVRIRRNFAFVQYETQEDATKALECTHMSKILD 154

Query: 128 RVISVEYALKDDSERDDRYDSPRRGGYGR--HSPYGRSPSPAYRR-RPSPDYGRGRSPAY 184
           RV+SVEYAL+DDS   D+YDSPRRGGY R   SPYGRSPSP  RR RPSPDYGR +SP Y
Sbjct: 155 RVVSVEYALRDDS---DKYDSPRRGGYSRRGESPYGRSPSPVNRRGRPSPDYGRAQSPVY 211

Query: 185 DRYNGPVYDQRRSPDHG 201
           DRYNGP Y++ RSP++G
Sbjct: 212 DRYNGPAYERNRSPEYG 228

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357514487|ref|XP_003627532.1| Arginine/serine-rich splicing factor [Medicago truncatula] gi|355521554|gb|AET02008.1| Arginine/serine-rich splicing factor [Medicago truncatula]

 Score =  303 bits (776), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 162/224 (72%), Positives = 184/224 (82%), Gaps = 20/224 (8%)

Query: 8   AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
           +GFAFVY+ED+RDA +AIR LDNIPFG+D+RRLSVEWARGERGRHRDGSK   NQ+PTKT
Sbjct: 35  SGFAFVYYEDERDAEEAIRALDNIPFGHDKRRLSVEWARGERGRHRDGSK--PNQKPTKT 92

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFVINFDPIRTR  DI+RHF+PYG + HVRIRRNFAFVQ+ETQE+ATKALE T+ SK++D
Sbjct: 93  LFVINFDPIRTRVSDIERHFKPYGPLHHVRIRRNFAFVQYETQEDATKALECTNMSKILD 152

Query: 128 RVISVEYALKDDSERDDRY-DSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDR 186
           RV+SVEYAL+DDS+R D Y  SPRRGG        RSPSP YRRRPSPDYGR RSP YDR
Sbjct: 153 RVVSVEYALRDDSDRVDNYGGSPRRGG-----GLARSPSPGYRRRPSPDYGRPRSPVYDR 207

Query: 187 YNGPVYDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSPNFGRYR 230
           Y GP  D+RRSPD+GR+          RSPDYGRNRSP +GRYR
Sbjct: 208 YTGP--DRRRSPDYGRN----------RSPDYGRNRSPEYGRYR 239

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	240
TAIR|locus:2079502	264	RS31 "arginine/serine-rich spl	0.887	0.806	0.633	1.7e-68
TAIR|locus:2039975	250	RS31a "arginine/serine-rich sp	0.858	0.824	0.610	1.2e-63
TAIR|locus:2131864	350	RS40 "arginine/serine-rich spl	0.883	0.605	0.520	2.4e-51
TAIR|locus:2173088	357	RS41 "arginine/serine-rich spl	0.858	0.577	0.520	1.5e-49
DICTYBASE|DDB_G0275409	737	DDB_G0275409 "RNA-binding regi	0.554	0.180	0.307	1.6e-14
UNIPROTKB|F1NPM7	277	TRA2A "Uncharacterized protein	0.720	0.624	0.321	3.8e-12
MGI|MGI:1933972	281	Tra2a "transformer 2 alpha hom	0.745	0.637	0.318	9.2e-12
ZFIN|ZDB-GENE-040426-1415	248	zgc:65772 "zgc:65772" [Danio r	0.662	0.641	0.290	1.8e-11
ZFIN|ZDB-GENE-040426-1467	258	srsf1b "serine/arginine-rich s	0.75	0.697	0.287	3e-11
UNIPROTKB|Q06AA6	279	TRA2A "Uncharacterized protein	0.737	0.634	0.316	3.4e-11

TAIR|locus:2079502 RS31 "arginine/serine-rich splicing factor 31" [Arabidopsis thaliana (taxid:3702)]

 Score = 695 (249.7 bits), Expect = 1.7e-68, P = 1.7e-68
 Identities = 142/224 (63%), Positives = 166/224 (74%)

Query:     8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT 67
             +G+AFVYFED+RDA DAIR LDN PFGY++RRLSVEWA+GERGR R  +K+ +N +PTKT
Sbjct:    35 SGYAFVYFEDERDAEDAIRKLDNFPFGYEKRRLSVEWAKGERGRPRGDAKAPSNLKPTKT 94

Query:    68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
             LFVINFDPIRT+E DI++HFEPYG V +VRIRRNF+FVQFETQE+ATKALE+T RSK++D
Sbjct:    95 LFVINFDPIRTKEHDIEKHFEPYGKVTNVRIRRNFSFVQFETQEDATKALEATQRSKILD 154

Query:   128 RVISVEYALKDDSERDDRYD--SPRRG---GYGRHXXXXXXXXXXXXXXX--XXDYGRGR 180
             RV+SVEYALKDD ERDDR    SPRR     Y R                    DYGR R
Sbjct:   155 RVVSVEYALKDDDERDDRNGGRSPRRSLSPVYRRRPSPDYGRRPSPGQGRRPSPDYGRAR 214

Query:   181 SPAYDRYNGPV-YDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRS 223
             SP YDRY GP  Y++RRSPD+GR  S    Y R+RSP Y R RS
Sbjct:   215 SPEYDRYKGPAAYERRRSPDYGRRSSD---YGRQRSPGYDRYRS 255

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:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IDA;RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0005681 "spliceosomal complex" evidence=TAS

TAIR|locus:2039975 RS31a "arginine/serine-rich splicing factor 31a" [Arabidopsis thaliana (taxid:3702)]

 Score = 649 (233.5 bits), Expect = 1.2e-63, P = 1.2e-63
 Identities = 135/221 (61%), Positives = 161/221 (72%)

Query:     8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR---GERGRHRDGSKSMANQRP 64
             +G+AFVYFED+RDA DAIR  DN  FGY RR+LSVEWA+   GERG+ RDG K+++NQRP
Sbjct:    35 SGYAFVYFEDERDAEDAIRRTDNTTFGYGRRKLSVEWAKDFQGERGKPRDG-KAVSNQRP 93

Query:    65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSK 124
             TKTLFVINFDPIRTRERD++RHFEPYG VL+VR+RRNFAFVQF TQE+ATKAL+ST  SK
Sbjct:    94 TKTLFVINFDPIRTRERDMERHFEPYGKVLNVRMRRNFAFVQFATQEDATKALDSTHNSK 153

Query:   125 LVDRVISVEYALKDDSERDDRYDSPRRGGYGRHXXXXXXXXXXXXXXXXXDYGRGRSPAY 184
             L+D+V+SVEYAL++  ER+DRY   RR                       DY R RSP Y
Sbjct:   154 LLDKVVSVEYALREAGEREDRYAGSRR---------RRSPSPVYRRRPSPDYTRRRSPEY 204

Query:   185 DRYNGPV-YDQRRSPDHGRHRSPVPVYDRRRSPDYGRNRSP 224
             DRY GP  Y++R+SPD+GR  S      R RSP Y R+RSP
Sbjct:   205 DRYKGPAPYERRKSPDYGRRSSDYG-RARARSPGYDRSRSP 244

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

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

TAIR|locus:2131864 RS40 "arginine/serine-rich splicing factor 40" [Arabidopsis thaliana (taxid:3702)]

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 116/223 (52%), Positives = 145/223 (65%)

Query:     8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG---RHRDGSK-SMANQR 63
             AGFAFVY ED+RDA DAIR LD   FG   RRL VEW + ERG   R   GS+ S ++ R
Sbjct:    35 AGFAFVYMEDERDAEDAIRALDRFEFGRKGRRLRVEWTKSERGGDKRSGGGSRRSSSSMR 94

Query:    64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRS 123
             P+KTLFVINFD   TR RD+++HFEPYG +++VRIRRNFAF+Q+E QE+AT+AL++++ S
Sbjct:    95 PSKTLFVINFDADNTRTRDLEKHFEPYGKIVNVRIRRNFAFIQYEAQEDATRALDASNNS 154

Query:   124 KLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHXXXXXXXXXXXXXXXXXDYGRGRSPA 183
             KL+D+VISVEYA+KDD  R + + SP R                       DYGRG SP 
Sbjct:   155 KLMDKVISVEYAVKDDDARGNGH-SPERRRDRSPERRRRSPSPYKRERGSPDYGRGASPV 213

Query:   184 YDRYNGPVYDQRRSPDHGRHRSPVPVYDRRR-SPDYGRNRSPN 225
                Y      +R SPD+GR RSP P    RR SP+YGR+R  N
Sbjct:   214 A-AYR----KERTSPDYGRRRSPSPYKKSRRGSPEYGRDRRGN 251

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:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS;RCA

GO:0005681 "spliceosomal complex" evidence=ISS

TAIR|locus:2173088 RS41 "arginine/serine-rich splicing factor 41" [Arabidopsis thaliana (taxid:3702)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 114/219 (52%), Positives = 141/219 (64%)

Query:     8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG-RHRDGS--KSMANQRP 64
             AGFAFVY ED+RDA DAIR LD   +G   RRL VEW + +RG   R G   +S +  RP
Sbjct:    35 AGFAFVYMEDERDAEDAIRALDRFEYGRTGRRLRVEWTKNDRGGAGRSGGSRRSSSGLRP 94

Query:    65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSK 124
             +KTLFVINFD   TR RD++RHFEPYG +++VRIRRNFAF+Q+E QE+AT+AL++T+ SK
Sbjct:    95 SKTLFVINFDAQNTRTRDLERHFEPYGKIVNVRIRRNFAFIQYEAQEDATRALDATNSSK 154

Query:   125 LVDRVISVEYALKDDSERDDRYDSPRRGGYGRHXXXXXXXXXXXXXXXXXDYGRGRSP-A 183
             L+D+VISVEYA+KDD  R + Y SP R                       DYGRG SP A
Sbjct:   155 LMDKVISVEYAVKDDDSRGNGY-SPERRRDRSPDRRRRSPSPYRRERGSPDYGRGASPVA 213

Query:   184 YDRYNGPVYDQRRSPDHGR-HRSPVPVYDRRRSPDYGRN 221
             + R       +R SPD+GR  RSP P    R SPDY R+
Sbjct:   214 HKR-------ERTSPDYGRGRRSPSPYKRARLSPDYKRD 245

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:0008380 "RNA splicing" evidence=NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS;RCA

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0005681 "spliceosomal complex" evidence=ISS

DICTYBASE|DDB_G0275409 DDB_G0275409 "RNA-binding region RNP-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 173 (66.0 bits), Expect = 1.6e-14, Sum P(2) = 1.6e-14
 Identities = 44/143 (30%), Positives = 81/143 (56%)

Query:     9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
             G+AFV    + D    ++ L    F    + L+V+ A+ E  + ++ S+ +   +P++ +
Sbjct:   175 GYAFVIVSTN-DPDIVVKELHRKEFL--NKSLTVQIAKSE-SKKKEESEEV---KPSRAI 227

Query:    69 FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDR 128
             F++N++  +T   DI     PYGNV  V++ +NF FV+FET ++A+KAL++ D       
Sbjct:   228 FIVNYNVSKTTTNDIADWCSPYGNVNRVQMVKNFCFVEFETIDQASKALKALDLKSFDGH 287

Query:   129 VISVEY---ALKDDSERDDRYDS 148
              ++VEY   ++  D+ + DRY S
Sbjct:   288 SLTVEYVNGSIDRDNYQRDRYGS 310

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1NPM7 TRA2A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 165 (63.1 bits), Expect = 3.8e-12, P = 3.8e-12
 Identities = 64/199 (32%), Positives = 82/199 (41%)

Query:    35 YDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL 94
             Y RRR         R RH  GS+  AN  P   L V     + T ERD++  F  YG + 
Sbjct:    93 YRRRRSRSHSPMSNRRRHT-GSR--ANPDPNTCLGVFGLS-LYTTERDLREVFSRYGPLT 148

Query:    95 HVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
              V +         R FAFV FE  +++ +A+E  +  +L  R I V+Y++        R 
Sbjct:   149 GVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDYSITK------RA 202

Query:   147 DSPRRGGY-GRHXXXXXXXXXXXXXXXXXDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRS 205
              +P  G Y GR                   Y RG    YDRY    YD R      R RS
Sbjct:   203 HTPTPGIYMGRPTHSGGGGGGGAGRRRDSYYDRGYDRGYDRYEE--YDYRY-----RRRS 255

Query:   206 PVPVYDRRRSPDYGRNRSP 224
             P P Y R RS    R+ SP
Sbjct:   256 PSPYYSRYRSRSRSRSYSP 274

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1933972 Tra2a "transformer 2 alpha homolog (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 162 (62.1 bits), Expect = 9.2e-12, P = 9.2e-12
 Identities = 64/201 (31%), Positives = 84/201 (41%)

Query:    35 YDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL 94
             Y RRR         R RH  GS+  AN  P   L V     + T ERD++  F  YG + 
Sbjct:    89 YRRRRSRSHSPMSNRRRHT-GSR--ANPDPNTCLGVFGLS-LYTTERDLREVFSRYGPLS 144

Query:    95 HVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
              V +         R FAFV FE  +++ +A+E  +  +L  R I V+Y++        R 
Sbjct:   145 GVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITK------RA 198

Query:   147 DSPRRGGY-GR--HXXXXXXXXXXXXXXXXXDYGRGRSPAYDRYNGPVYDQRRSPDHGRH 203
              +P  G Y GR  H                   GR R   YDR     YD+    D+ R 
Sbjct:   199 HTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGGGGRRRDSYYDRGYDRGYDRYEDYDY-RR 257

Query:   204 RSPVPVYDRRRSPDYGRNRSP 224
             RSP P Y R RS    R+ SP
Sbjct:   258 RSPSPYYSRYRSRSRSRSYSP 278

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0042802 "identical protein binding" evidence=IPI

ZFIN|ZDB-GENE-040426-1415 zgc:65772 "zgc:65772" [Danio rerio (taxid:7955)]

 Score = 157 (60.3 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 52/179 (29%), Positives = 78/179 (43%)

Query:    64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATK 115
             P  +LFV N     +R  D++R F  YG ++ V I         R FA++QFE   +A  
Sbjct:     8 PNSSLFVRNISD-ESRPEDLRREFGRYGPIVDVYIPLDFYSRRPRGFAYIQFEDVRDAED 66

Query:   116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHXXXXXXXXXXXXXXXXXD 175
             AL + DR  +  R I +++A + D +   +  +  R    R                  D
Sbjct:    67 ALHNLDRKWVCGRQIEIQFA-QGDRKTPGQMKNKERSS-PRSSRYEDSDRRRRSRSRSYD 124

Query:   176 YGRGRSPAYDRY----NGPVYDQ-----RRSPDHGRHRSPVPVYDRRRSPDYGRNRSPN 225
               R RSP+YDR     + P   +     RRS +H RHR     + R R+    R+RSP+
Sbjct:   125 RRRSRSPSYDRRRRRSDSPRESRGRTHSRRSREHDRHRGSTRDHHRSRTDAASRSRSPS 183

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ZFIN|ZDB-GENE-040426-1467 srsf1b "serine/arginine-rich splicing factor 1b" [Danio rerio (taxid:7955)]

 Score = 156 (60.0 bits), Expect = 3.0e-11, P = 3.0e-11
 Identities = 60/209 (28%), Positives = 81/209 (38%)

Query:    10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS----------KSM 59
             FAFV FED RDA DA+ G D   + YD  RL VE+ R  RG  R G           +  
Sbjct:    55 FAFVEFEDPRDAEDAVYGRDG--YDYDGYRLRVEFPRSGRGGGRGGGGGGGVGAPRGRYG 112

Query:    60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-FAFVQFETQEEATKALE 118
                R ++   +++  P     +D+K H    G+V +  + R+    V+F  +E+ T A+ 
Sbjct:   113 PPSRRSEYRVIVSGLPPSGSWQDLKDHMREAGDVCYADVFRDGTGVVEFVRKEDMTYAVR 172

Query:   119 STDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHXXXXXXXXXXXXXXXXXDYGR 178
               D +K         Y          + D PR   YGR                   Y  
Sbjct:   173 KLDNTKFRSHEGETAYIRV-------KVDGPRSPSYGRSRSRSRSRSRSRSNSRSRSYSP 225

Query:   179 GRSPAYDRYNGPVYDQRRSPDHGRHRSPV 207
              RS    RY         SP H R RSPV
Sbjct:   226 RRSRGSPRY---------SPRHSRSRSPV 245

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q06AA6 TRA2A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 157 (60.3 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 63/199 (31%), Positives = 83/199 (41%)

Query:    35 YDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL 94
             Y RRR         R RH  GS+  AN  P   L V     + T ERD++  F  YG + 
Sbjct:    91 YRRRRSRSHSPMSNRRRHT-GSR--ANPDPNTCLGVFGLS-LYTTERDLREVFSRYGPLS 146

Query:    95 HVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
              V +         R FAFV FE  +++ +A+E  +  +L  R I V+Y++        R 
Sbjct:   147 GVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITK------RA 200

Query:   147 DSPRRGGY-GRHXXXXXXXXXXXXXXXXXDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRS 205
              +P  G Y GR                    GR R   YDR     YD+    D+ R RS
Sbjct:   201 HTPTPGIYMGRPTHSGGGGGGGGGGGGGG--GRRRDSYYDRGYDRGYDRYEDYDY-RRRS 257

Query:   206 PVPVYDRRRSPDYGRNRSP 224
             P P Y R RS    R+ SP
Sbjct:   258 PSPYYSRYRSRSRSRSYSP 276

GO:0005634 "nucleus" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P92964	RSP31_ARATH	No assigned EC number	0.6791	0.9208	0.8371	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00021623 hypothetical protein (236 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	240
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	4e-38
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	9e-28
smart00360	73	smart00360, RRM, RNA recognition motif	2e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-15
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	1e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-13
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-12
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-11
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-10
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	6e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-09
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-08
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	3e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-08
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	4e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	9e-08
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	9e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-07
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-07
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	2e-07
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	3e-06
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	4e-06
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	1e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	2e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-05
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	2e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	4e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	4e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-05
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	7e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	8e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	8e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	9e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-04
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	1e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-04
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	2e-04
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	3e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	3e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	4e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	5e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	5e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	6e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	8e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	8e-04
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	9e-04
smart00360	73	smart00360, RRM, RNA recognition motif	0.001
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.001
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.001
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.001
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.001
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.001
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.001
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.001
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.002
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.002
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.002
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.002
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.002
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.002
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.002
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.002
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.002
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.002
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.002
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.002
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.003
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.003
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	0.003
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.003
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.003
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.003
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	0.003
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.004
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.004
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.004
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.004

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score =  127 bits (320), Expect = 4e-38
 Identities = 55/70 (78%), Positives = 65/70 (92%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           TLFVINFDPI TR RD++RHFEPYG +++VRIRRNFAFVQ+ETQE+ATKALEST+ SK++
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQEDATKALESTNMSKVL 60

Query: 127 DRVISVEYAL 136
           DRVISVEYA 
Sbjct: 61  DRVISVEYAA 70

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

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

 Score =  100 bits (251), Expect = 9e-28
 Identities = 35/70 (50%), Positives = 50/70 (71%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           TLFV+ FDP  TRE DI++ FEP+G ++   IR+ FAFV+FE  E+ATKALE+   S++ 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRID 60

Query: 127 DRVISVEYAL 136
             V++VE+  
Sbjct: 61  GSVLTVEFVK 70

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

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

 Score = 68.4 bits (168), Expect = 2e-15
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 9/74 (12%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           TLFV N  P  T E +++  F  +G V  VR+ R+        FAFV+FE++E+A KALE
Sbjct: 1   TLFVGNLPP-DTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59

Query: 119 STDRSKLVDRVISV 132
           + +  +L  R + V
Sbjct: 60  ALNGKELDGRPLKV 73

Length = 73

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

 Score = 66.9 bits (164), Expect = 7e-15
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALEST 120
           LFV N  P  T E D++  F  +G +  VRI        + FAFV+FE+ E+A KALE+ 
Sbjct: 1   LFVGNLPP-DTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 121 DRSKLVDRVISVE 133
           +  +L  R + V 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 63.7 bits (155), Expect = 1e-13
 Identities = 29/39 (74%), Positives = 32/39 (82%)

Query: 8  AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          +GFAFVY ED+RDA DAIRGLDN  FG  RRRL VEWA+
Sbjct: 34 SGFAFVYMEDERDAEDAIRGLDNFEFGRQRRRLRVEWAK 72

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

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

 Score = 63.0 bits (154), Expect = 2e-13
 Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 8/70 (11%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALEST 120
           LFV N  P  T E D+K  F  +G +  +RI        + FAFV+FE +E+A KALE+ 
Sbjct: 1   LFVGNLPPD-TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 121 DRSKLVDRVI 130
           +  +L  R +
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 67.9 bits (166), Expect = 3e-13
 Identities = 45/183 (24%), Positives = 69/183 (37%), Gaps = 22/183 (12%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDR--RRLSVEWA--RGERGRHRDGSKSMANQRP 64
           GFAFV FE   DAA A+  ++    G  +  ++L V  A  R ER            Q  
Sbjct: 220 GFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQER 279

Query: 65  TK-----TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEE 112
                   L+V N D   T E+ ++  F   G +   ++  +       F FV F   EE
Sbjct: 280 KMKAQGVNLYVKNLDDTVTDEK-LRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEE 338

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSER---DDRYDSPRRGGYGRHSPYGRSPSPAYR 169
           A +A+       L  + + V  A + +  R    D++   +     R  P G     A  
Sbjct: 339 ANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPR--MRQLPMGSPMGGAMG 396

Query: 170 RRP 172
           + P
Sbjct: 397 QPP 399

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|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 = 59.5 bits (145), Expect = 4e-12
 Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
            LFV      RT E++++  F  +G V  V +         R F FV FE+ E+A  A+ 
Sbjct: 3   KLFVSGLST-RTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 119 STDRSKLVDRVISVEYALK 137
             +  +L  RVI VE A +
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 57.1 bits (139), Expect = 2e-11
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 3/56 (5%)

Query: 83  IKRHFEPYGNVLHVRIRR---NFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           + + F P+GNV  +++ +    FAFV+F T+E A KA++  +      R + V+Y+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 56.4 bits (137), Expect = 5e-11
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTD 121
           L+V N  P    E D++  F PYG V  VR+       R FAFV+F + E+A  AL+  +
Sbjct: 1   LYVRNLPP-SVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLN 59

Query: 122 RSKLVDRVI 130
              L  R +
Sbjct: 60  GLVLDGRTL 68

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

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

 Score = 56.9 bits (138), Expect = 5e-11
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 7/69 (10%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVD 127
           P +  E D+K+ F P+G V  V I R        FAFVQF ++ +A KA++  +  K+  
Sbjct: 8   PFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67

Query: 128 RVISVEYAL 136
           R ++V++A+
Sbjct: 68  RPVAVDWAV 76

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

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

 Score = 54.2 bits (131), Expect = 4e-10
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKL 125
           K L+V N  P+ T E  ++  F  YG V  V+  +++AFV FE +++A KA+E  +  +L
Sbjct: 2   KVLYVRNL-PLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKEL 60

Query: 126 VDRVISVEYA 135
               I V  A
Sbjct: 61  EGSPIEVSLA 70

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

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

 Score = 53.8 bits (130), Expect = 5e-10
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFV N     T   +++  FE YG V    + +N+ FV  E +E+A  A+++ +  + + 
Sbjct: 2   LFVGNLPD-ATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDAEDAIKALNGYEFMG 60

Query: 128 RVISVE 133
           + I+VE
Sbjct: 61  KRINVE 66

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

 Score = 53.6 bits (129), Expect = 6e-10
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNV--LHV--RIRRNFAFVQFETQEEATKALESTDR 122
           T++   F P      D+KR FE  G V  + +  R  +  AF+ FE  E A  A+E+ + 
Sbjct: 1   TVYAGPF-PTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNG 59

Query: 123 SKLVDRVISVEY 134
           + +    I V+ 
Sbjct: 60  ASVDGNCIKVQR 71

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

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 12/80 (15%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATK 115
            L++ N D  R  E  + + F  YG +                 R + FV FET+EEA K
Sbjct: 1   RLWIGNLDS-RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEK 59

Query: 116 ALESTDRSKLVDRVISVEYA 135
           AL+S +    + + + V +A
Sbjct: 60  ALKSLNGKTALGKKLVVRWA 79

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

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

 Score = 56.2 bits (135), Expect = 3e-09
 Identities = 58/226 (25%), Positives = 79/226 (34%), Gaps = 13/226 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E  R AA A R L           ++V+WA  E     D    +      K L
Sbjct: 183 GFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKV------KIL 236

Query: 69  FVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           +V N     T E  I++ F  +  G V  V+  R++AFV FE +E+A KA++  +  +L 
Sbjct: 237 YVRNL-MTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELE 295

Query: 127 DRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDR 186
              I V  A   D +   RY   R  G           S      P+          Y  
Sbjct: 296 GSEIEVTLAKPVDKKSYVRYT--RGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHP 353

Query: 187 YNGPVYDQRRSPDHGRHRSPVPVYDRRRSP--DYGRNRSPNFGRYR 230
              P     R P   R R       R               +G Y 
Sbjct: 354 PYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPYGYEAYYGDYY 399

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

>gnl|CDD|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 = 51.5 bits (124), Expect = 4e-09
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--NFAFVQFETQEEATKA 116
           T++V N       E +++R F P+G +  VR+ +   +AFV+F+T E A  A
Sbjct: 2   TVYVGNLPH-GLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATA 52

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

 Score = 51.1 bits (123), Expect = 6e-09
 Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 18/85 (21%)

Query: 66  KTLFVIN--FDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           +T+F+ N  FD     E ++K  F  +G V + RI ++         AFV+F+T+E A K
Sbjct: 1   RTVFIRNLPFD---ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57

Query: 116 ALESTDRS-----KLVDRVISVEYA 135
            LE+ D +      L  R + V  A
Sbjct: 58  CLEAADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 8/64 (12%)

Query: 78  TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 129
           T+  D+K+ F  YG V+  +I  N        F FV   + EEA K ++   R++L  RV
Sbjct: 11  TKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRV 70

Query: 130 ISVE 133
           ISVE
Sbjct: 71  ISVE 74

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

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 18/68 (26%)

Query: 66  KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------------FAFVQFETQ 110
            TLFV  +NF    T E  +K+HFE  G V  V I +              + FV+F+++
Sbjct: 1   TTLFVKNLNFK---TTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSK 57

Query: 111 EEATKALE 118
           E A KAL+
Sbjct: 58  EAAQKALK 65

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

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALES 119
           LFV N  P    E ++K  F+ +GNVL VRI          NF FV F+  E   K L +
Sbjct: 6   LFVGNL-PHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 120 TDRSKLVDRVISVE 133
                  D  ++VE
Sbjct: 65  KPIYFRGDHRLNVE 78

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

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

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALEST 120
           ++FV    P  T+E ++   F  +G +L V +         FAF++FE ++ A +A+ES 
Sbjct: 5   SIFVGQLSPDVTKE-ELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 121 DRSKLVDRVISVEY 134
           + S L ++ + V+Y
Sbjct: 64  NHSMLKNKTMHVQY 77

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALES 119
           TL+V NF P    + DI+  FE YG +L +R         R F +VQF + E A  A+  
Sbjct: 2   TLWVTNF-PPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 120 TDRSKLVDRVISVEY 134
            +        + V+ 
Sbjct: 61  LNGKLGEGYKLVVKI 75

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 14/85 (16%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGN--VLHVRIRRN--------FAFVQFETQEEA 113
           PT TL +   D + T E DI +      +  +  VR+ R+        FAFV+F + E+A
Sbjct: 1   PTNTLILRGLDLL-TTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59

Query: 114 TKALEST---DRSKLVDRVISVEYA 135
           T+ +++    D   +  RV+ V YA
Sbjct: 60  TQWMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

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

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTD 121
            TL V N  P       +  HF  +G ++++++      A VQF T EEA KA  S +
Sbjct: 2   TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRSPE 59

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

 Score = 48.4 bits (116), Expect = 6e-08
 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
            L+V N  P    E D+K  F  +G V   R+         R F FV+ ET EEA  A+E
Sbjct: 1   NLYVGNL-PYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59

Query: 119 STDRSKLVDRVISVEYA 135
             + +    R ++V  A
Sbjct: 60  KLNGTDFGGRTLTVNEA 76

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|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 = 48.0 bits (115), Expect = 8e-08
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 7/68 (10%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVD 127
           P    +++++  F P+G V  VR+        R FAFV+F T++EA  A+E+   + L  
Sbjct: 9   PFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYG 68

Query: 128 RVISVEYA 135
           R + +EYA
Sbjct: 69  RHLVLEYA 76

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

 Score = 48.1 bits (115), Expect = 9e-08
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALES 119
           TLFV N       + D++  F+  G V+ VRI ++       F  V+F T+E A KALE 
Sbjct: 1   TLFVGNL-SWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK 59

Query: 120 TDRSKLVDRVISVEYA 135
           +    L+ R I V+ A
Sbjct: 60  SGEE-LLGREIRVDLA 74

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|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 47.9 bits (114), Expect = 9e-08
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI----RRNFAFVQFETQEEATKALES 119
           PTK + V N  P    E D+  H   +G +++V++     +  A V+F T+E+AT+AL  
Sbjct: 6   PTKMIHVSNL-PSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALAC 64

Query: 120 TDRSKL 125
              S L
Sbjct: 65  KHASSL 70

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 9/73 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNV--LHV------RIRRNFAFVQFETQEEATKALES 119
           LFV N  P  T E +++  FE +G +  +H+      +  + FAFV F   E A KA   
Sbjct: 2   LFVRNL-PFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 120 TDRSKLVDRVISV 132
            D S    R++ V
Sbjct: 61  LDGSIFQGRLLHV 73

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 8/59 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN----F---AFVQFETQEEATKALE 118
           T++V  F    T + DI+  FE +G V ++R+RR+    F    FV+F+T+E+A K LE
Sbjct: 1   TVYVKGFPKDATLD-DIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLE 58

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

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

 Score = 50.7 bits (120), Expect = 2e-07
 Identities = 38/198 (19%), Positives = 65/198 (32%), Gaps = 14/198 (7%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQF 107
                ++    TLFV N       E D++  F+ +G V  VR+         R FAFV+F
Sbjct: 106 KSRQKSKEENNTLFVGNLPYD-VTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPA 167
           E++E A KA+E  +  +L  R + V+ A      R +  ++       + S         
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEK 224

Query: 168 ----YRRRPSPDYGRGRSPAYDRYNGPVYDQRRSPDH-GRHRSPVPVYDRRRSPDYGRNR 222
               Y                 +  G +      P   G+            S D   + 
Sbjct: 225 SDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESN 284

Query: 223 SPNFGRYRSRSPVRRSRT 240
           S    +       R++ +
Sbjct: 285 SRGNKKKILGRGPRKAFS 302

Length = 306

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 17/66 (25%), Positives = 31/66 (46%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LF+ N    R  + D+ R F  YG +  + ++  + FVQF++ E    A+       +  
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFVQFDSPESCANAINCEQGKMIRG 61

Query: 128 RVISVE 133
           R + +E
Sbjct: 62  RKLHLE 67

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALE 118
           P K LF+ N     T +  ++  F  +     VR+  RR  AFV+FET+E+AT AL+
Sbjct: 1   PNKILFLQNLPE-ETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQ 56

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALES 119
           L+V         E+ +   F P+G++  ++I         R FAFV+FE  E+A  A+++
Sbjct: 1   LYVGGLAEEVD-EKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 120 TDRSKLVDRVISV 132
            + S+L  R I V
Sbjct: 60  MNESELFGRTIRV 72

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

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 27/67 (40%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           L+V  F P  T E  I+  F PYG V  V++  NFAFV+FE+ E A +A +S     L +
Sbjct: 2   LYVRPF-PPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAIRAKDSVHGKVLNN 60

Query: 128 RVISVEY 134
             + V Y
Sbjct: 61  NPLYVTY 67

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

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

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 15/54 (27%), Positives = 31/54 (57%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD 121
           +FV N +  +  + D++  F  YG +L + + + + FVQF+ +E+A  A+   +
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGEN 56

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

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

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNV--LHVRI-RRN-----FAFVQFETQEEATKALES 119
           +FV        +E D+   F  +G +  LH+ + RR      +A +++ET++EA  A+E 
Sbjct: 9   IFVTGVHE-EAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 120 TDRSKLVDRVISVEYA 135
            +  +L+ + ISV++A
Sbjct: 68  LNGKELLGQTISVDWA 83

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

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

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 13/77 (16%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI-----------RRNFAFVQFETQEEATKA 116
           ++V N D  +  E D++  F  +G V  +RI              FAFV F+    A  A
Sbjct: 3   IYVRNLD-FKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 117 LESTDRSKLVDRVISVE 133
           L+  + ++L  R ISV 
Sbjct: 62  LQ-LNGTELGGRKISVS 77

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

 Score = 45.5 bits (108), Expect = 8e-07
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALE 118
             LFV    P    + ++++ F+ +G V  VR+  N        A+V++E +  A++A+ 
Sbjct: 3   HKLFVSGL-PFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVL 61

Query: 119 STDRSKLVDRVISV 132
             D +++ ++ ISV
Sbjct: 62  KMDGTEIKEKTISV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 21/38 (55%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          GFAFV F    DA  AI  L+   FGYD   LSVEWA+
Sbjct: 42 GFAFVTFHTREDAERAIEKLNG--FGYDNLILSVEWAK 77

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

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 21/39 (53%), Positives = 24/39 (61%), Gaps = 2/39 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG 47
          GFAFV FED RDA DA+R LD         R+ VE +RG
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRI--CGNRVRVELSRG 73

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

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFV N  P    E++I+  FE YG VL   I +N+ FV  + +  A +A+ +    KL  
Sbjct: 3   LFVGNLPP-EATEQEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAADEAIRNLHHYKLHG 61

Query: 128 RVISVE 133
             I+VE
Sbjct: 62  VAINVE 67

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

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRVIS 131
           E D++  FEP+G +  V+++R+        + F+QF   E+A KALE  +  +L  R I 
Sbjct: 12  EDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIK 71

Query: 132 V 132
           V
Sbjct: 72  V 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           +FV N D   T + +++  FE YG VL   + R FAFV    +  A +A+E  +  +L  
Sbjct: 3   IFVGNVD-EDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAADRAIEELNGRELHG 61

Query: 128 RVISVE 133
           R + VE
Sbjct: 62  RKLVVE 67

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

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 76  IRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVD 127
           + T ERD++  F  YG +  V++         R F FV FE+ E+A +A E  +  ++  
Sbjct: 9   LYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDG 68

Query: 128 RVISVEYAL 136
           R I V+Y++
Sbjct: 69  RRIRVDYSI 77

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

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKALES 119
           P       +K  F  YG V++V + R         FAF++FET EEA KA + 
Sbjct: 8   PKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------FAFVQFETQEEATKALES 119
           K L V N  P R R+ D+++ F  +G +L V I  N      F FV F    +A +A E 
Sbjct: 1   KRLHVSNI-PFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREK 59

Query: 120 TDRSKLVDRVISVEYA 135
              + +  R I V  A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVL-HVRIRRN--------FAFVQFETQEEATKALE 118
           LF+ N DP    E+ +   F  +G +L   +I R+        FAF+ +++ E +  A+E
Sbjct: 4   LFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 119 STDRSKLVDRVISVEYALKDD 139
           + +   L +R I+V YA K D
Sbjct: 63  AMNGQYLCNRPITVSYAFKKD 83

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALEST 120
           TL+V      R  E+D++ HF  +G +  + +  R+  AFV F T+E A KA E  
Sbjct: 3   TLYVGGLGE-RVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERL 57

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 64  PTKTLFVINFDPIRTRER---DIKRHFEPYGNVLHVRIRRN-----FAFVQFETQEEATK 115
           P+  +FV +    ++ +     +  HF  YG ++ V++ R+     +AFVQF   ++A  
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKN 60

Query: 116 ALESTDRSKLVDRVISVEYA 135
           AL     + L  R I  E A
Sbjct: 61  ALAKGQGTILDGRHIRCERA 80

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 57  KSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEAT 114
           KSM    PT  +++   D   T E+ + RHF  YG V+HV I R    A V F+  E A 
Sbjct: 3   KSM----PTNCVWLDGLDESVT-EQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQ 57

Query: 115 KALESTDRSKLVDRVISVEY 134
            A+      KL  R + V++
Sbjct: 58  AAVNEMKGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALEST 120
           +FV N  P     +D+K  F   GNVL   ++       + F  V FE+ E+A +A+E  
Sbjct: 1   IFVRNL-PFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 121 DRSKLVDRVISV 132
           +   L  R + V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 42.8 bits (101), Expect = 6e-06
 Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 12/76 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALES 119
           LFV N     T E +++ HF   G +  VR+         + FAFV FE  E AT AL+ 
Sbjct: 1   LFVGNLS-FETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59

Query: 120 TDRSKLVDRVISVEYA 135
                L  R + VEY 
Sbjct: 60  ---KHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 42.5 bits (101), Expect = 7e-06
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 8/48 (16%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALES 119
           E D++  FE YGN+  V I R+         AFV+F ++EEA KA+E+
Sbjct: 13  EEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 9/79 (11%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           P   LFV   +P+ T + D++  F  +G +    + R+        +AF++FET+E+  +
Sbjct: 2   PENVLFVCKLNPV-TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 116 ALESTDRSKLVDRVISVEY 134
           A    D   + DR I V++
Sbjct: 61  AYFKMDNVLIDDRRIHVDF 79

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

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

 Score = 42.5 bits (101), Expect = 9e-06
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 10/78 (12%)

Query: 67  TLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEATKAL 117
           TL++ N    + ++ ++KR     F  +G VL +   +       AFV F+  E AT AL
Sbjct: 1   TLYINNL-NEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNAL 59

Query: 118 ESTDRSKLVDRVISVEYA 135
            +       D+ + ++YA
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

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

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSK 124
           ++V N  P R  +R+++  FE YG +  V + RN   FAFV+FE   +A  A+ + D  +
Sbjct: 2   VYVGNLGP-RATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 125 LVDRVISVEYA 135
           +    + VE +
Sbjct: 61  ICGNRVRVELS 71

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|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 = 1e-05
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 9/61 (14%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           TL++ + +P    E  I   F   G V  V+I RN        + FV+F T E A +AL+
Sbjct: 1   TLWMGDLEPWMD-EAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQ 59

Query: 119 S 119
           S
Sbjct: 60  S 60

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

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 21/61 (34%), Positives = 35/61 (57%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY 134
           P R RERD++R F+ YG +  + ++  F FV+FE   +A  A+   +  +L    + VE+
Sbjct: 8   PYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEH 67

Query: 135 A 135
           A
Sbjct: 68  A 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 8/59 (13%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-------NFAFVQFETQEEATKA 116
           T+TLFV N +   T E +++R FE YG V  V I+R        +AFV+F   + A +A
Sbjct: 2   TRTLFVGNLEITITEE-ELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
           ++V N       E+ +K  F  YG +   ++ ++       F FV FE  E A KA+E  
Sbjct: 4   VYVKNLGEDMDDEK-LKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 121 DRSKLVDRVISVEYALK 137
           +  ++  + + V  A K
Sbjct: 63  NGKEVNGKKLYVGRAQK 79

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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 16/68 (23%), Positives = 35/68 (51%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           +F+ N + +  ++ D++  F  YG ++   + + FAFVQ+  +  A  A+   D   +  
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 63

Query: 128 RVISVEYA 135
           +V+ +  A
Sbjct: 64  QVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 68  LFVINFDP-IRTRERDIKRHFEPYGNVL-------HVRIRRNFAFVQFETQEEATKALES 119
           +F+ N D  I  +   +   F  +GN+L            + + FV FET+E A +A+E 
Sbjct: 5   IFIKNLDKSIDNKA--LYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEK 62

Query: 120 TDRSKLVDRVISV 132
            +   L D+ + V
Sbjct: 63  VNGMLLNDKKVFV 75

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

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 8/62 (12%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRVIS 131
           E +++++F  +G V  +R+ R+        +AFV+FE+ E A    E+ +   L +R++ 
Sbjct: 13  EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72

Query: 132 VE 133
            +
Sbjct: 73  CK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 78  TRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           TRE DIK  F  +G V +V         +++F+T E A KA E+            ++ +
Sbjct: 14  TRE-DIKAVFAQFGEVKYVDFTEGADTGYIRFKTPEAAQKAREAFVEKGEGLLGKEIKLS 72

Query: 136 L 136
            
Sbjct: 73  A 73

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 9/67 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRN--FAFVQFETQEEATKALE 118
           T+FV+     + RERD+   F   G V  VRI      RR+   A+V+F  +E    AL 
Sbjct: 1   TVFVMQLSL-KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59

Query: 119 STDRSKL 125
            T +  L
Sbjct: 60  LTGQRLL 66

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

 Score = 44.4 bits (105), Expect = 3e-05
 Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 18/125 (14%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKT- 67
           G+ FV+FE +  A  AI+ ++ +    + + + V       GR     +  A      T 
Sbjct: 130 GYGFVHFEKEESAKAAIQKVNGMLL--NDKEVYV-------GRFIKKHEREAAPLKKFTN 180

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
           L+V N DP    ++ ++  F  +G +    + ++       FAFV FE  E+A KA+E  
Sbjct: 181 LYVKNLDPSVNEDK-LRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 121 DRSKL 125
           +  K+
Sbjct: 240 NGKKI 244

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 9/76 (11%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKA 116
           T  LFV N  P   +E D+++ F  +G +  +HV I +       FA+V F   E+A KA
Sbjct: 2   TGRLFVRNL-PYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 117 LESTDRSKLVDRVISV 132
            +  D      R+I +
Sbjct: 61  YKELDGKVFQGRLIHI 76

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

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 8/62 (12%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALES 119
            +FV    P  T E +++  F  +G+V  V+I        + + FV FETQE+A K L  
Sbjct: 4   RIFVGGI-PPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 120 TD 121
            +
Sbjct: 63  GN 64

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

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 8/75 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALEST 120
           TL V +  P  + E D +   + +G    VR+       +N AF  F+ ++ A++AL   
Sbjct: 1   TLLVRHLPPELS-EDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRL 58

Query: 121 DRSKLVDRVISVEYA 135
            + K++ + + VEYA
Sbjct: 59  HQLKILGKRLVVEYA 73

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALEST 120
           +FV   D  +T E D+++ F  YG V  V+I        + + FV FETQE+A K L+  
Sbjct: 5   IFVGGID-FKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63

Query: 121 DRSKLVDRVISVEYALK 137
           +R    D+ +++  A++
Sbjct: 64  NRLCFRDKKLNIGQAIR 80

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

>gnl|CDD|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 = 40.4 bits (95), Expect = 4e-05
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALE 118
           T+FV   DP  T E +++  F P+G +++V+I   +   FVQF  +  A  A++
Sbjct: 3   TVFVGGLDPAVT-EDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQ 55

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|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           L V N     T + +++  FE YG V+   I +++AFV  E  E+A +A+   D ++   
Sbjct: 3   LHVGNISSSCTNQ-ELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQG 61

Query: 128 RVISVE 133
           + + V+
Sbjct: 62  KRMHVQ 67

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 10/75 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALE 118
            LFV N  P  T   D+  HF+  G    VR+         +  AFV+F+T E  TKAL 
Sbjct: 2   ILFVGNL-PYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL- 59

Query: 119 STDRSKLVDRVISVE 133
               + L  R I+VE
Sbjct: 60  KLHHTLLKGRKINVE 74

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

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

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 78  TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 129
           TR  D+K  F  YG V+  ++  N        + FV   T EEATK +    R++L  R+
Sbjct: 13  TRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRM 72

Query: 130 ISVE 133
           ISVE
Sbjct: 73  ISVE 76

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

>gnl|CDD|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 = 40.3 bits (95), Expect = 5e-05
 Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          GF FV FE   DA  AIR L+      + R + VE A+
Sbjct: 44 GFGFVTFESVEDADAAIRDLNGKEL--EGRVIKVEKAK 79

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 8/56 (14%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKA 116
           L+V N D     ER ++  F P+G +   ++  +       F FV F + EEATKA
Sbjct: 4   LYVKNLDDSIDDER-LREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKA 58

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|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 = 5e-05
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALES 119
           T+FV N D     E ++++ F   G +  VR+ +N       +A+V+FE +E   +AL  
Sbjct: 1   TVFVSNLD-YSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-K 58

Query: 120 TDRSKLVDRVISV 132
            DR  +  R + V
Sbjct: 59  LDRELIKGRPMFV 71

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLH---VRIR-----RNFAFVQFETQEEATKALE 118
           TLFV N  P  T +  ++  F   G +     V+ +     R F +V F  +E+A +ALE
Sbjct: 1   TLFVRNL-PYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59

Query: 119 STDRSKLVDRVISVEYALK 137
              ++K   R I VE+A K
Sbjct: 60  EKKKTKFGGRKIHVEFAKK 78

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|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.5 bits (93), Expect = 7e-05
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVL-HVRIRRNF--AFVQFETQEEATKALESTDR 122
           +T+ + N       E+ IK  FE  G  +  + +  +   A V+FE+  +A KA  S + 
Sbjct: 1   RTIGLFNVSDTVNEEQ-IKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNG 59

Query: 123 SKLVDRVI 130
           S+   + I
Sbjct: 60  SQFGGKTI 67

This subfamily corresponds to the RRM4 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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 11/79 (13%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATK 115
           R  +TLFV N  P      ++K  FE   + + +R+        +  A+++F+T+ EA K
Sbjct: 1   RDARTLFVKNL-PYNITVDELKEVFE---DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEK 56

Query: 116 ALESTDRSKLVDRVISVEY 134
           ALE    +++  R I V+Y
Sbjct: 57  ALEEKQGAEVDGRSIVVDY 75

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

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

 Score = 39.6 bits (92), Expect = 8e-05
 Identities = 18/57 (31%), Positives = 36/57 (63%)

Query: 79  RERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           RE+D++R F+ YG +  + ++R F FV+F+   +A  A+   D  +L +  +++E+A
Sbjct: 12  REKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERVTIEHA 68

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

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

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 9/66 (13%)

Query: 75  PIRTRERDIKRHFEPYG-NVLHVRIRRNF-------AFVQFETQEEATKALESTDRSKLV 126
           P    E DI+  F         + I  +        A+V+F + E+A +AL     +K+ 
Sbjct: 8   PFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRAL-RKHNNKMG 66

Query: 127 DRVISV 132
            R I V
Sbjct: 67  GRYIEV 72

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

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 9/81 (11%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
            +L+V N     TR  D++R F  YG ++ V I         R FA+VQFE   +A  AL
Sbjct: 1   TSLYVRNV-ADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 118 ESTDRSKLVDRVISVEYALKD 138
              DR++ + R I +++A  D
Sbjct: 60  YYLDRTRFLGREIEIQFAQGD 80

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

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           P  TLFV      +T E  ++  F  YG++  +R+ R+        +AFV++E + +A +
Sbjct: 2   PYLTLFVGRLSL-QTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 116 ALESTDRSKLVDRVISVEY 134
           A     +  +    I V++
Sbjct: 61  AYRDAHKLVIDGSEIFVDF 79

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

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSK 124
           L V N +        +   F  YG+V+ V+I   +++ A +Q    ++A  AL   +  +
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIR 61

Query: 125 LVDRVISVEY 134
           L  + + V  
Sbjct: 62  LHGKKLRVTL 71

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDR 122
           + TL++ +    +  E D+K  FE YG +  + +   R  A+V  ET+++A +AL+    
Sbjct: 2   STTLWIGHLSK-KVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 123 SKLVDRVISVEYAL 136
            KL  + I V +A 
Sbjct: 61  VKLAGKKIKVAWAP 74

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

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 8/61 (13%)

Query: 83  IKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY 134
           +K  FE +G V+  R+         R F +V FE+ E+A KA+E+ D  +L  R I+V++
Sbjct: 16  LKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDF 75

Query: 135 A 135
           +
Sbjct: 76  S 76

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

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

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 71  INFDPIRTRERDIKRHFEPYGNVLHVRI----RRNFAFVQFETQEEATKAL 117
              D  R  E D+  +F  +G VL VRI    +R F FV FE  E   + L
Sbjct: 5   FPADS-RFTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVKRIL 54

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

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 78  TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 129
             E D++  F P+G +  V + ++        FAFV F T+E+A +A+E  +     + +
Sbjct: 11  ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLI 70

Query: 130 ISVEYA 135
           +SVE+A
Sbjct: 71  LSVEWA 76

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

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVD 127
           P    ++D++  F  YG +  VR+        R FAFV+F T +EA  A+ +   + L+ 
Sbjct: 9   PFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLG 68

Query: 128 RVISVEYA 135
           R + ++YA
Sbjct: 69  RRLVLQYA 76

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

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           ++FV N  P    E ++++HFE  G+V  VRI R+        F +V F+T++    AL 
Sbjct: 1   SVFVGNL-PFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL- 58

Query: 119 STDRSKLVDRVISVE 133
             +  KL  R I V+
Sbjct: 59  KLNGIKLKGRKIRVK 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|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 78  TRERDIKRHFEPYGNV--LHVRIRRNFAFVQFETQEEATKALE 118
           +RE ++ R FE YG V  L +   + + FV + + E+A  A +
Sbjct: 16  SRE-ELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYD 57

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVD 127
           P    E  ++ HFE  G V  V++ R        F FV F+++E+A +A++  +++ +  
Sbjct: 9   PKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDT 68

Query: 128 RVISVEYA 135
             ISVE A
Sbjct: 69  SKISVELA 76

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           T++V N  P      D+ + F  YG V+ V I ++         AF+ F  +E+A K ++
Sbjct: 3   TVYVSNL-PFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 119 STDRSKLVDRVISVEYA 135
           + +  +L  R +    A
Sbjct: 62  ALNNKELFGRTLKCSIA 78

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

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-----FAFVQFETQEEATKALES 119
           T+TLF+ N +   T   D++  FE +G ++ + I++      +AF+Q+       KA+  
Sbjct: 2   TRTLFIGNLEKTTTYS-DLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRK 60

Query: 120 TDRSKL 125
            D   L
Sbjct: 61  MDGEYL 66

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV--RIRRNFAFVQFETQEEATKALEST 120
           R   TL+V  +      E  +K+ F P+GN++++     +N  FV FE  E A +A+   
Sbjct: 2   RKGNTLYVHGYG---LTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAEL 58

Query: 121 DRSKLVDRVISVEYALK 137
           + + +    + V  A K
Sbjct: 59  NGTTVQGVQLKVSLARK 75

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 13/26 (50%), Positives = 16/26 (61%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFG 34
          GFAFV FED+ DA  A+  L+    G
Sbjct: 40 GFAFVEFEDEEDAEKALEALNGKELG 65

(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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 79  RERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           RE+DI+R F  YG +L + ++  + FV+FE   +A  A+   +   L    + VE+A
Sbjct: 12  REKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKAL 117
           KT  ++N+ P    + +I+  F   G +   ++ R+        + FV +   E+A KA+
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 118 ESTDRSKLVDRVISVEYA 135
            + +  +L ++ I V YA
Sbjct: 61  NTLNGLRLQNKTIKVSYA 78

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

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

 Score = 37.9 bits (88), Expect = 3e-04
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 82  DIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVE 133
           +++  FE +G V+     +++AFV  E +EEA  A+E+ +  ++  R I+VE
Sbjct: 16  ELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVE 67

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 68  LFVINFDPIRTRERDIKRHF-EPYGNVLHVRIRRN-------FAFVQFETQEEATKALES 119
           L V N  P    E ++K HF +  G +  V++ R         AF+ ++T+EEA KA + 
Sbjct: 3   LIVKNL-PASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 120 TDRSKLVDRVISVEYA 135
            + + +    ISVE+A
Sbjct: 62  FNNTYINTSKISVEFA 77

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

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDR 122
            K+ F+   +     E  I+ +FE +G    V +  R    FV+FET+E A K   +   
Sbjct: 2   IKSFFLFGVED-DLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISE 60

Query: 123 SKL 125
           + L
Sbjct: 61  NGL 63

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALEST 120
           L V N       ++ +++ FE +G +  V+++       R F FV ++T+EEA KAL+  
Sbjct: 3   LIVKNLPKGIKEDK-LRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61

Query: 121 DRSKLVDRVISVE 133
           + S +    I+VE
Sbjct: 62  NNSFIDTSKITVE 74

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 24/92 (26%), Positives = 43/92 (46%), Gaps = 27/92 (29%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------------RNF------ 102
           +T+FV N  P+ T+++D+K+ F+ +G +  VR R                 + F      
Sbjct: 1   RTVFVGNL-PLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDN 59

Query: 103 --AFVQFETQEEATKALESTDRSKLVDRVISV 132
             A+V F+ +E A KAL+  + ++     I V
Sbjct: 60  VNAYVVFKEEESAEKALKL-NGTEFEGHHIRV 90

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

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKL 125
           LFV N     T E + K  F  YG V  V +   + F F++ +T+  A KA    D    
Sbjct: 4   LFVGNLPNDIT-EEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMR 62

Query: 126 VDRVISVEY 134
             R + V +
Sbjct: 63  KGRQLRVRF 71

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

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 10/78 (12%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALES 119
           TL+V  F    TR RD+   FE YG ++   I        R FAFV++E+  +A  A E 
Sbjct: 1   TLYVTGF-GAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEE 59

Query: 120 TDRSKLVDR--VISVEYA 135
               +  D    + V++A
Sbjct: 60  MHGRRFPDTGDTLHVQWA 77

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 37.3 bits (86), Expect = 5e-04
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKL 125
           K LFV N     T E  +++ F  +G +  V+  +++AF+ F+ ++ A KA+E  +  +L
Sbjct: 2   KVLFVRNLANTVTEEI-LEKAFGQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 126 VDRVISVEYA 135
               I + +A
Sbjct: 61  EGENIEIVFA 70

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

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 21/35 (60%), Positives = 24/35 (68%), Gaps = 2/35 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE 43
          G+AF+ FED RDA DAIRG D   F  D +RL VE
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDF--DGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 9/59 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           LF+ +  P    ++D+ + F P+GNV+  ++  +        F FV ++  E A  A++
Sbjct: 1   LFIYHL-PNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIK 58

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

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

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 9/60 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALES 119
           +FV    P  T E  I+ +F  +GN++ + +        RR F F+ F+++E   K LE+
Sbjct: 2   IFVGGLSP-ETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

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

>gnl|CDD|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 = 37.1 bits (87), Expect = 8e-04
 Identities = 17/27 (62%), Positives = 20/27 (74%), Gaps = 2/27 (7%)

Query: 93  VLHVRIR--RNFAFVQFETQEEATKAL 117
           VL V+I   +NFAFV+F T EEAT AL
Sbjct: 39  VLSVQINPEKNFAFVEFRTVEEATAAL 65

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 13/79 (16%)

Query: 66  KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           KTLFV  +N+D   T E  ++R FE YG +  +R+ R+        +AF++FE + +   
Sbjct: 2   KTLFVARLNYD---TTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKA 58

Query: 116 ALESTDRSKLVDRVISVEY 134
           A +  D  K+  R + V+ 
Sbjct: 59  AYKYADGKKIDGRRVLVDV 77

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

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 36.7 bits (85), Expect = 9e-04
 Identities = 15/37 (40%), Positives = 19/37 (51%)

Query: 10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          FAFV +E  RDA DA   +    F      L V+WA+
Sbjct: 42 FAFVEYESHRDAEDAYEEMHGRRFPDTGDTLHVQWAK 78

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSV 42
          GFAFV FE + DA  A+  L+      D R L V
Sbjct: 42 GFAFVEFESEEDAEKALEALNGKEL--DGRPLKV 73

Length = 73

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

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
          + +     GFAFV F  +  A  A++ L+ + FG   R L V+++
Sbjct: 14 IKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGG--RPLRVDYS 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALES 119
           +FV N  P    E  + + F P+G V +V++ R+F         FV     +EA  A+ S
Sbjct: 6   IFVYNLAP-DADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 120 TDRSKLVDRVISVEY 134
            +  +L DRV+ V +
Sbjct: 65  LNGYRLGDRVLQVSF 79

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

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 7/65 (10%)

Query: 83  IKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           +K+ F  YG V    I R        FAFV  + ++ A  ALE+T+  ++  R ++V++A
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77

Query: 136 LKDDS 140
           ++ + 
Sbjct: 78  VQKNR 82

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

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 20/35 (57%), Positives = 23/35 (65%), Gaps = 2/35 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE 43
           FAFV FED RDA DA+RG D   + +D  RL VE
Sbjct: 39 PFAFVEFEDPRDAEDAVRGRDG--YDFDGYRLRVE 71

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
           T  ++N+ P    + +++  FE  G +   +I R+        + FV +  + +A KA+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 119 STDRSKLVDRVISVEYA 135
           + +  ++ ++ + V YA
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 65  TKTLFV----INFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALE 118
            +TL+V          +  E  ++RHF  +G++  +R+   +  AFV+++ +  A  A E
Sbjct: 1   NRTLYVGGIKAGSALKQIEEI-LRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKE 59

Query: 119 STDRSKLVDR-VISVEYA 135
           +     L    V++V +A
Sbjct: 60  AMADQSLDGGEVLNVRWA 77

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 18/27 (66%), Positives = 21/27 (77%)

Query: 3  ISLHYAGFAFVYFEDDRDAADAIRGLD 29
          I+ +  GFAFV FED RDA DA+RGLD
Sbjct: 31 IARNPPGFAFVEFEDPRDAEDAVRGLD 57

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that 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. 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. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, 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 = 77

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 71  INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDR 122
           I+F+     E  I++ F P+G +  + +         + FAFV++E  E A  ALE  + 
Sbjct: 8   ISFE---LGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNG 64

Query: 123 SKLVDRVISV 132
             L  R I V
Sbjct: 65  VMLGGRNIKV 74

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

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

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 13/64 (20%)

Query: 68  LFV--INFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKAL 117
           LF+  +++D   T E  ++ +F  YG V+   I         R F FV F       K L
Sbjct: 1   LFIGGLSWD---TTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL 57

Query: 118 ESTD 121
            +  
Sbjct: 58  AAKP 61

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE 43
          GFAFV FE   DA  A+  L+      D R+L V 
Sbjct: 40 GFAFVEFESPEDAEKALEALNGKEL--DGRKLKVS 72

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

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALES 119
           +FV N  P  + E  + + F P+G V +V++ R+F         FV     +EA  A+ S
Sbjct: 6   IFVYNLSP-DSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64

Query: 120 TDRSKLVDRVISVEY 134
            +  +L DRV+ V +
Sbjct: 65  LNGYRLGDRVLQVSF 79

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

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALES 119
           +FV N  P    E  + + F P+G V +V++ R+F         FV     +EA  A+ S
Sbjct: 4   IFVYNLSP-EADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS 62

Query: 120 TDRSKLVDRVISVEY 134
            +  +L DRV+ V +
Sbjct: 63  LNGYRLGDRVLQVSF 77

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

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 9/59 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVL--------HVRIRRNFAFVQFETQEEATKALE 118
           LFV   + ++T +  ++RHF  YG +         + +  R F F+ F + +EA +A+E
Sbjct: 5   LFVGGLN-LKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

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

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 4/45 (8%)

Query: 85  RHFEPYGNVLHVRIRRNF----AFVQFETQEEATKALESTDRSKL 125
           + F PYG V  + I        A VQF++ E A  A ++ +   +
Sbjct: 20  QVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNI 64

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 8/63 (12%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRVIS 131
           E+++K++F  +G V +VR+ R+        + F+QF   E A  A +S +   L+ +V+ 
Sbjct: 13  EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

Query: 132 VEY 134
           V  
Sbjct: 73  VHV 75

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 13/83 (15%)

Query: 65  TKTLFVINFDPIRTRERDIK----RHFEPY---GNVLHVRI----R-RNFAFVQFETQEE 112
           +K L+V N    R  E D+     R  +      N+  +R+    R +  AFV F ++E 
Sbjct: 1   SKRLYVKNLSK-RVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEI 59

Query: 113 ATKALESTDRSKLVDRVISVEYA 135
           ATKAL   +   L  + + +++ 
Sbjct: 60  ATKALNLVNGYVLKGKPMVIQFG 82

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>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 = 35.7 bits (83), Expect = 0.002
 Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
          G+ F  FED   AA AIR L+   F    R L V++A
Sbjct: 41 GYGFCEFEDIETAASAIRNLNGYEFN--GRALRVDFA 75

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKAL 117
           T++V N  P  T + D+   F+ +G +L  R +  R FAFV+ +T E+A  A+
Sbjct: 2   TVYVGNIPPYTT-QADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAI 53

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 9/76 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
            +FV N  P    E  + + F P+G V +V++ R+        + FV     EEA  A+ 
Sbjct: 3   CIFVYNLPP-DADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 119 STDRSKLVDRVISVEY 134
           S +  +L  RV+ V +
Sbjct: 62  SLNGYRLGGRVLQVSF 77

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 18/37 (48%), Positives = 23/37 (62%)

Query: 99  RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           R++FAFV F ++EE  KALE  D  K   RV+S   A
Sbjct: 41  RQDFAFVTFRSEEERQKALEILDGFKWKGRVLSARLA 77

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

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

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 10/64 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           LFV+   P    E D++  F+ +G++ +V I ++        F +V+F    +A  ALE+
Sbjct: 4   LFVVI--PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61

Query: 120 TDRS 123
            D+S
Sbjct: 62  CDKS 65

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

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

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 68  LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
           LF+  ++FD   T E+ +++ F  YG +  V +         R F FV FE  ++A  A+
Sbjct: 3   LFIGGLSFD---TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM 59

Query: 118 ESTDRSKLVDRVISVEYALK 137
            + +   +  R I V+ A K
Sbjct: 60  MAMNGKSVDGRQIRVDQAGK 79

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

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR----NFAFVQFETQEEATKALESTDR 122
           T+ V N  P  T E  I++ F+  G +  V+I        A ++FET++EA  AL + D 
Sbjct: 2   TVKVKNL-PKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAAL-TKDH 59

Query: 123 SKLVDRVISVE 133
            +L    ISV 
Sbjct: 60  KRLGGNEISVS 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 78  TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 129
           T E  I   F   G++  + +  +        F FV++ T+E+A  A++  + +KL DR+
Sbjct: 10  TTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRI 69

Query: 130 ISVE 133
           I V+
Sbjct: 70  IRVD 73

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

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRS 123
             + V N  P  T E +++  FE +G++  + +   R  A V+F    +A KA +S    
Sbjct: 1   TVILVKNL-PFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYK 59

Query: 124 KLVDRVISVEYA 135
           +     + +E+A
Sbjct: 60  RFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues 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. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 31/132 (23%), Positives = 55/132 (41%), Gaps = 19/132 (14%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G+ +V F++  DA  A+  ++    G    R+   W+       RD S   +       +
Sbjct: 43  GYGYVNFQNPADAERALETMNFKRLGGKPIRIM--WS------QRDPSLRRSG---VGNI 91

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTD 121
           FV N D      + +   F  +GN+L  ++        R + FV FE +E A  A++  +
Sbjct: 92  FVKNLDKSVD-NKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 122 RSKLVDRVISVE 133
              L D+ + V 
Sbjct: 151 GMLLNDKEVYVG 162

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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 18/58 (31%), Positives = 33/58 (56%)

Query: 77  RTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY 134
           + RERD++R F+ YG +L V ++  + FV+F+   +A  A+   +   L    + VE+
Sbjct: 10  QARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEH 67

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 23/41 (56%), Positives = 26/41 (63%), Gaps = 2/41 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
          GFAFV FED RDAADA+R LD       R R  VE + GE+
Sbjct: 42 GFAFVEFEDPRDAADAVRELDGRTLCGCRVR--VELSNGEK 80

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that 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. SRSF3 can shuttle between the nucleus and cytoplasm. It contains 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 = 81

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 8/25 (32%), Positives = 14/25 (56%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPF 33
          G+AFV F    +A +A++ L+    
Sbjct: 51 GYAFVEFATPEEAKEAVKALNGYKL 75

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

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

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 14/53 (26%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 80  ERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVI 130
           E+ +++ F P+G ++ VR+   + ++FV+F + E A  A+ S + + +   V+
Sbjct: 14  EQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTIEGHVV 66

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

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 9/80 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHV--------RIRRNFAFVQFETQEEATKALE 118
           +LFV N     TR  D++R F  YG ++ V        R  R FA+VQFE   +A  AL 
Sbjct: 2   SLFVRNIAD-DTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 119 STDRSKLVDRVISVEYALKD 138
           + DR  +  R I +++A  D
Sbjct: 61  NLDRKWICGRQIEIQFAQGD 80

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRS 123
           TL V N DP  + + D+ + F  YG +  +R    +R+  F++F     A  AL++ +RS
Sbjct: 3   TLVVFNLDPSVSND-DLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRS 61

Query: 124 KLVDRVISVE 133
           ++  + I +E
Sbjct: 62  EIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 90  YGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEY 134
           YGNVL ++  ++    A VQ    + A +A+E  +   L  + + V +
Sbjct: 24  YGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEVNF 71

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 8/49 (16%)

Query: 78  TRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
           T E D+K++F  +G V    +         R F FV FE+++   K  E
Sbjct: 11  TTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59

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

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

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 9/63 (14%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
           P K +FV   +P  T E+ I+ +F  +G +  + +        RR F F+ F+ ++   K
Sbjct: 3   PVKKIFVGGLNPEATEEK-IREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61

Query: 116 ALE 118
            LE
Sbjct: 62  VLE 64

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKL 125
           K LFV N     T E  +++ F  +G +  V+  +++AFV FE ++ A +A++  +  ++
Sbjct: 2   KVLFVRNLATTVTEEI-LEKSFSEFGKLERVKKLKDYAFVHFEERDAAVRAMDEMNGKEI 60

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 13/53 (24%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 80  ERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVI 130
           E+ +++ F P+G ++ +R+   + ++F++F T E A  A+ S + + +   V+
Sbjct: 14  EQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTIEGHVV 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	240
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.91
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.91
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.89
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.87
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.87
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.87
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.86
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.86
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.86
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.85
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.85
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.85
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.84
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.84
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.84
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.82
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.81
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.81
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.8
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.8
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.79
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.78
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.76
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.76
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.68
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.68
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.67
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.67
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.63
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.62
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.57
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.57
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.56
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.56
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.55
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.54
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.53
PLN03120	260	nucleic acid binding protein; Provisional	99.52
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.51
KOG0122	270	consensus Translation initiation factor 3, subunit	99.48
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.47
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.46
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.45
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.44
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.43
PLN03213	759	repressor of silencing 3; Provisional	99.43
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.43
PLN03121	243	nucleic acid binding protein; Provisional	99.4
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.39
smart00362	72	RRM_2 RNA recognition motif.	99.38
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.36
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.36
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.34
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.34
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.33
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.31
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.31
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.3
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.29
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.28
smart00360	71	RRM RNA recognition motif.	99.28
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.27
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.26
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.25
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.23
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.2
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.18
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.18
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.15
smart00361	70	RRM_1 RNA recognition motif.	99.1
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.09
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.08
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.07
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.06
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.03
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.99
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.99
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.96
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.92
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.91
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.87
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.84
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.82
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.8
smart00361	70	RRM_1 RNA recognition motif.	98.79
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.79
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.76
KOG4210	285	consensus Nuclear localization sequence binding pr	98.72
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.69
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.66
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.58
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.57
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.56
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.54
KOG0226	290	consensus RNA-binding proteins [General function p	98.54
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.53
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.53
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.53
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.51
KOG0151	877	consensus Predicted splicing regulator, contains R	98.51
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.48
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.46
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.43
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.42
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.42
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.42
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.4
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.4
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.33
smart00360	71	RRM RNA recognition motif.	98.29
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.19
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.18
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.16
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.13
smart00362	72	RRM_2 RNA recognition motif.	98.09
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.04
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.94
PLN03120	260	nucleic acid binding protein; Provisional	97.93
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.92
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	97.9
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.9
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.9
PLN03213	759	repressor of silencing 3; Provisional	97.87
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.86
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.86
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.84
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.78
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	97.76
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	97.75
KOG0226	290	consensus RNA-binding proteins [General function p	97.72
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.71
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.69
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.68
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.66
PLN03121	243	nucleic acid binding protein; Provisional	97.64
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.5
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.48
KOG2314	698	consensus Translation initiation factor 3, subunit	97.39
KOG3152	278	consensus TBP-binding protein, activator of basal	97.36
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.32
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.29
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.17
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.16
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.14
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.08
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.91
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.88
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.76
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.74
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.72
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	96.64
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.57
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	96.55
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.38
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	96.27
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	96.21
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.89
KOG2314	698	consensus Translation initiation factor 3, subunit	95.83
KOG0533	243	consensus RRM motif-containing protein [RNA proces	95.69
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.65
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	95.65
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.61
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.6
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	95.58
KOG2135	526	consensus Proteins containing the RNA recognition	95.53
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.45
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.44
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.95
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.88
KOG1995	351	consensus Conserved Zn-finger protein [General fun	94.2
KOG0151	877	consensus Predicted splicing regulator, contains R	94.18
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.08
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	93.9
KOG2318	650	consensus Uncharacterized conserved protein [Funct	93.24
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	93.14
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	92.72
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.12
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.76
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	91.0
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.21
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	87.38
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	87.23
COG5175	480	MOT2 Transcriptional repressor [Transcription]	86.39
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.88
KOG2888	453	consensus Putative RNA binding protein [General fu	85.43
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	85.38
KOG4210	285	consensus Nuclear localization sequence binding pr	85.35
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	84.23
KOG2891	445	consensus Surface glycoprotein [General function p	83.25
KOG0835	367	consensus Cyclin L [General function prediction on	81.17

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=4.5e-26  Score=193.13  Aligned_cols=125  Identities=27%  Similarity=0.446  Sum_probs=109.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      +|++++|||||+|.++++|++||+.||+..|  .+++|+|.|+.+....           ...++|||+|| |..+++++
T Consensus       144 ~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l--~gr~i~V~~a~p~~~~-----------~~~~~lfV~nL-p~~vtee~  209 (346)
T TIGR01659       144 KTGYSFGYAFVDFGSEADSQRAIKNLNGITV--RNKRLKVSYARPGGES-----------IKDTNLYVTNL-PRTITDDQ  209 (346)
T ss_pred             CCCccCcEEEEEEccHHHHHHHHHHcCCCcc--CCceeeeecccccccc-----------cccceeEEeCC-CCcccHHH
Confidence            4778899999999999999999999999999  6999999998754321           23568999999 89999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCCCC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDDSE  141 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~~  141 (240)
                      |+++|++||+|..|.|.        ++||||+|++.++|++||+.||+..|.+  ++|.|.++......
T Consensus       210 L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       210 LDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             HHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            99999999999999884        4799999999999999999999998876  78999998865443

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).

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

Probab=99.95  E-value=1.3e-26  Score=182.35  Aligned_cols=135  Identities=22%  Similarity=0.437  Sum_probs=118.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCC-----CCCCCCCCCEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSK-----SMANQRPTKTLFVINFDPIR   77 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~-----~~~~~~~~~~l~v~nl~~~~   77 (240)
                      .|+++||||||.|.+.++|+.||..|||..|  +++.|..+||..+......+..     -.+..+.+++|||+|+ +..
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl--G~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I-~~~  175 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWL--GRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNI-ASG  175 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeee--ccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCc-Ccc
Confidence            4889999999999999999999999999999  7999999999977632222211     1346677899999999 668


Q ss_pred             CCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           78 TRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        78 ~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      +++++|++.|..||.|..|.+.  +||+||.|++.|.|..||..||+++|.|+.|+|.|.+....
T Consensus       176 lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  176 LTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             ccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            9999999999999999999995  79999999999999999999999999999999999886554

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

Probab=99.93  E-value=5.7e-25  Score=195.66  Aligned_cols=131  Identities=32%  Similarity=0.425  Sum_probs=113.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      +++++|||||+|.++++|+.|+..|+...+.+.|+.|.|+|+.++.....      .......+|||+|| ++.+++++|
T Consensus       178 kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~------~~~~~~k~LfVgNL-~~~~tee~L  250 (578)
T TIGR01648       178 KKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE------DVMAKVKILYVRNL-MTTTTEEII  250 (578)
T ss_pred             cCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccc------cccccccEEEEeCC-CCCCCHHHH
Confidence            35679999999999999999999887543323699999999987654321      12334678999999 899999999


Q ss_pred             HHhhccC--CCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCC
Q 026341           84 KRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSE  141 (240)
Q Consensus        84 ~~~f~~~--G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  141 (240)
                      +++|++|  |+|..|.+.++||||+|++.++|++||+.||+.+|+|+.|.|.|+++....
T Consensus       251 ~~~F~~f~~G~I~rV~~~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       251 EKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHHHHhcCCCceEEEEeecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            9999999  999999999999999999999999999999999999999999999886554

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.

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

Probab=99.92  E-value=1.8e-24  Score=192.80  Aligned_cols=134  Identities=17%  Similarity=0.287  Sum_probs=112.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .|++++|||||+|.++++|+.||+.|||..|  +|+.|.|.++.....................+|||+|| +..+++++
T Consensus       144 ~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i--~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnL-p~~vteed  220 (612)
T TIGR01645       144 ATGKHKGFAFVEYEVPEAAQLALEQMNGQML--GGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASV-HPDLSETD  220 (612)
T ss_pred             CCCCcCCeEEEEeCcHHHHHHHHHhcCCeEE--ecceeeecccccccccccccccccccccccceEEeecC-CCCCCHHH
Confidence            4788999999999999999999999999999  69999999765432211110111112334679999999 88999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      |+++|+.||.|..|.|.        +|||||+|.+.++|.+||..||+..|+|+.|.|.++....
T Consensus       221 Lk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       221 IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            99999999999999883        6899999999999999999999999999999999988643

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.91  E-value=2.7e-23  Score=178.39  Aligned_cols=135  Identities=23%  Similarity=0.359  Sum_probs=109.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC--------------CC-------------
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD--------------GS-------------   56 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~--------------~~-------------   56 (240)
                      ++.++|||||+|.+.++|+.|++.|||..+...+.+|.|.|+.........              ..             
T Consensus       127 ~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  206 (352)
T TIGR01661       127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIG  206 (352)
T ss_pred             CCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCC
Confidence            456799999999999999999999999988533478999998644311000              00             


Q ss_pred             -----------------------------------C-------------------CCCCCCCCCEEEEeccCCCCCCHHH
Q 026341           57 -----------------------------------K-------------------SMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus        57 -----------------------------------~-------------------~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                                                         .                   .+.....+.+|||+|| |..+++++
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL-~~~~~e~~  285 (352)
T TIGR01661       207 PMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNL-SPDTDETV  285 (352)
T ss_pred             CccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCC-CCCCCHHH
Confidence                                               0                   0000122347999999 88999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      |.++|++||.|..|.|.        +|||||+|.+.++|..||..|||..|+|+.|.|.|+..+.
T Consensus       286 L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       286 LWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999984        7999999999999999999999999999999999988764

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

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

Probab=99.91  E-value=4.1e-24  Score=178.50  Aligned_cols=132  Identities=33%  Similarity=0.462  Sum_probs=117.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      .++++|||||+|++...|..|..+|-.-.|.+-|..++|.||.+......+      .....+.|||.|| +..+|++.|
T Consensus       204 k~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded------~ms~VKvLYVRNL-~~~tTeE~l  276 (506)
T KOG0117|consen  204 KTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDED------TMSKVKVLYVRNL-MESTTEETL  276 (506)
T ss_pred             cccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChh------hhhheeeeeeecc-chhhhHHHH
Confidence            567899999999999999999988755444447999999999987765432      4455789999999 999999999


Q ss_pred             HHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCCC
Q 026341           84 KRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSER  142 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  142 (240)
                      +++|++||.|..|+.++.||||.|.+.++|.+||+.|||++|+|..|.|.+|++..++.
T Consensus       277 k~~F~~~G~veRVkk~rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  277 KKLFNEFGKVERVKKPRDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             HHHHHhccceEEeecccceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            99999999999999999999999999999999999999999999999999999877654

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

Probab=99.90  E-value=2.4e-22  Score=148.86  Aligned_cols=78  Identities=27%  Similarity=0.443  Sum_probs=72.4

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      -.+.|||+|| +..+++.||+.+|..||+|..|+|   +.|||||||++..+|+.|+..|+|..|+|..|.|+++.....
T Consensus         9 ~~~kVYVGnL-~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    9 GNTKVYVGNL-GSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCceEEeccC-CCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            3789999999 889999999999999999999999   579999999999999999999999999999999999987665


Q ss_pred             CC
Q 026341          141 ER  142 (240)
Q Consensus       141 ~~  142 (240)
                      ..
T Consensus        88 ~~   89 (195)
T KOG0107|consen   88 GS   89 (195)
T ss_pred             cc
Confidence            33

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

Probab=99.90  E-value=6e-23  Score=182.06  Aligned_cols=132  Identities=28%  Similarity=0.441  Sum_probs=110.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC-CCCCCCCCCCCCEEEEeccCCCCCCHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD-GSKSMANQRPTKTLFVINFDPIRTRER   81 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~-~~~~~~~~~~~~~l~v~nl~~~~~~~~   81 (240)
                      .+++++|||||+|.+.++|++||. |+|..|  .|++|.|.++......... ........+...+|||+|| |..++++
T Consensus       126 ~~~~skg~afVeF~~~e~A~~Al~-l~g~~~--~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl-~~~~te~  201 (457)
T TIGR01622       126 NSRRSKGVAYVEFYDVESVIKALA-LTGQML--LGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNL-HFNITEQ  201 (457)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHH-hCCCEE--CCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCC-CCCCCHH
Confidence            467889999999999999999997 999999  5999999987654332211 1111112234789999999 8899999


Q ss_pred             HHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           82 DIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        82 ~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +|+++|.+||.|..|.|.        +|||||+|.+.++|+.|+..|||..|.|++|.|.|+...
T Consensus       202 ~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       202 ELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             HHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            999999999999999884        589999999999999999999999999999999998743

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.89  E-value=1.4e-22  Score=173.94  Aligned_cols=123  Identities=21%  Similarity=0.497  Sum_probs=108.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .+++++|||||+|.++++|++||+.|||..|  .|+.|.|+|+.+...           .....+|||+|| |..+++++
T Consensus        40 ~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l--~g~~i~v~~a~~~~~-----------~~~~~~l~v~~l-~~~~~~~~  105 (352)
T TIGR01661        40 VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL--QNKTIKVSYARPSSD-----------SIKGANLYVSGL-PKTMTQHE  105 (352)
T ss_pred             CCCccceEEEEEECcHHHHHHHHhhcccEEE--CCeeEEEEeeccccc-----------ccccceEEECCc-cccCCHHH
Confidence            3678899999999999999999999999999  699999999976442           123568999999 89999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDD  139 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~  139 (240)
                      |+++|.+||.|..+.+.        +|||||+|++.++|+.||+.|||..+.|  .+|.|.++....
T Consensus       106 l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       106 LESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            99999999999988873        6899999999999999999999999887  678888886554

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

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

Probab=99.88  E-value=5.8e-22  Score=177.99  Aligned_cols=130  Identities=18%  Similarity=0.295  Sum_probs=105.9

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC------C-C---C--------CCCCCCCCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR------D-G---S--------KSMANQRPTK   66 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~------~-~---~--------~~~~~~~~~~   66 (240)
                      .+.+|||||+|.+.++|+.||+ |||+.|  .|.+|.|.........+.      . .   .        ..........
T Consensus       220 ~~~kg~afVeF~~~e~A~~Al~-l~g~~~--~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (509)
T TIGR01642       220 NKEKNFAFLEFRTVEEATFAMA-LDSIIY--SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKD  296 (509)
T ss_pred             CCCCCEEEEEeCCHHHHhhhhc-CCCeEe--eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCC
Confidence            3568999999999999999995 999998  599999976543221110      0 0   0        0011234467


Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +|||+|| |..+++++|+++|+.||.|..+.|.        +|||||+|.+.++|+.||..|||..|.|+.|.|.++...
T Consensus       297 ~l~v~nl-p~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       297 RIYIGNL-PLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            9999999 9999999999999999999998873        689999999999999999999999999999999998754

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

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

Probab=99.87  E-value=3.7e-21  Score=146.17  Aligned_cols=79  Identities=35%  Similarity=0.497  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .......|.|.|| .+.++.++|..+|++||.|..|.|+        +|||||.|....+|++|+++|+|.+|+|+.|.|
T Consensus         9 dv~gm~SLkVdNL-TyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    9 DVEGMTSLKVDNL-TYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CcccceeEEecce-eccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            4445688999999 9999999999999999999999995        699999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      ++|+-...
T Consensus        88 q~arygr~   95 (256)
T KOG4207|consen   88 QMARYGRP   95 (256)
T ss_pred             hhhhcCCC
Confidence            99985443

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

Probab=99.87  E-value=1.8e-21  Score=176.70  Aligned_cols=133  Identities=25%  Similarity=0.385  Sum_probs=112.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCC----CceEEEEeccCCCCCCCC-------CCCCCCCCCCCCEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYD----RRRLSVEWARGERGRHRD-------GSKSMANQRPTKTLFVIN   72 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~----g~~l~v~~a~~~~~~~~~-------~~~~~~~~~~~~~l~v~n   72 (240)
                      +++++|||||+|.+.++|.+|++.|||..|  .    |..|.|.++..+.+....       ............+|||+|
T Consensus       215 ~g~~~G~afV~F~~~e~A~~Av~~l~g~~i--~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~n  292 (562)
T TIGR01628       215 SGRSRGFAFVNFEKHEDAAKAVEEMNGKKI--GLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKN  292 (562)
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCcEe--cccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeC
Confidence            567799999999999999999999999998  6    899999988755433110       000111234577899999


Q ss_pred             cCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           73 FDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        73 l~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      | +..+++++|+++|++||.|..|.+.       +|||||+|.+.++|++|+..|||..|.|++|.|.+|..+.
T Consensus       293 l-~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       293 L-DDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             C-CCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            9 8899999999999999999999884       6899999999999999999999999999999999998654

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

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

Probab=99.87  E-value=7.2e-22  Score=157.09  Aligned_cols=127  Identities=24%  Similarity=0.428  Sum_probs=114.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHh
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRH   86 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~   86 (240)
                      -|.||||..+++..|+.||..|+|..|  +|..|.|+-++.+.+             +.++|+|+|| ...++.++|+..
T Consensus        35 vKNYgFVHiEdktaaedairNLhgYtL--hg~nInVeaSksKsk-------------~stkl~vgNi-s~tctn~ElRa~   98 (346)
T KOG0109|consen   35 VKNYGFVHIEDKTAAEDAIRNLHGYTL--HGVNINVEASKSKSK-------------ASTKLHVGNI-SPTCTNQELRAK   98 (346)
T ss_pred             ecccceEEeecccccHHHHhhccccee--cceEEEEEeccccCC-------------CccccccCCC-CccccCHHHhhh
Confidence            389999999999999999999999999  799999999887532             4789999999 778999999999


Q ss_pred             hccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCCCCCCCCCC
Q 026341           87 FEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSP  149 (240)
Q Consensus        87 f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~  149 (240)
                      |++||+|..|+|.++|+||.|+-.++|..|+..||+.+|+|+.++|+++...-....+..+..
T Consensus        99 fe~ygpviecdivkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtapgmgDq~  161 (346)
T KOG0109|consen   99 FEKYGPVIECDIVKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPGMGDQS  161 (346)
T ss_pred             hcccCCceeeeeecceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCCCCCCHH
Confidence            999999999999999999999999999999999999999999999999987766555444433

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

Probab=99.86  E-value=8.3e-21  Score=168.95  Aligned_cols=131  Identities=20%  Similarity=0.214  Sum_probs=105.0

Q ss_pred             CccceEEEEeCChhHHHHHHHhh--CCCcccCCCceEEEEeccCCCCCCCCCCC-CCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGL--DNIPFGYDRRRLSVEWARGERGRHRDGSK-SMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l--~g~~~~~~g~~l~v~~a~~~~~~~~~~~~-~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      +.+|||||+|+++++|++||+.|  ++..|  +|++|.|+|+............ .........+|+|.|| ++.+++++
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l--~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl-~~~vt~~~  112 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYI--RGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENP-MYPITLDV  112 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceE--cCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCC-CCCCCHHH
Confidence            46899999999999999999875  66777  7999999999754322111000 1111223457999999 88999999


Q ss_pred             HHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCC
Q 026341           83 IKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDD  139 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~  139 (240)
                      |+++|+.||.|..|.|.    .++|||+|.+.++|.+|++.|||..|.|  +.|.|+|++...
T Consensus       113 L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       113 LYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTR  175 (481)
T ss_pred             HHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCC
Confidence            99999999999999884    2589999999999999999999999965  589999998643

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=99.86  E-value=6.6e-21  Score=169.58  Aligned_cols=129  Identities=22%  Similarity=0.319  Sum_probs=106.0

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC------CCC---C-----------------CCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR------DGS---K-----------------SMA   60 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~------~~~---~-----------------~~~   60 (240)
                      .+|||||+|.+.++|+.||..|||..|  .|++|.|.+++.......      .+.   .                 ...
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l--~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~  389 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKL--FGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNN  389 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEE--CCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccc
Confidence            379999999999999999999999999  699999999875421110      000   0                 001


Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCC--eEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcE---
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGN--VLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRV---  129 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~--i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~---  129 (240)
                      ..+++.+|||+|| |..+++++|+++|+.||.  |..+.+.      +++|||+|++.++|.+||..||+..|.+..   
T Consensus       390 ~~~ps~~L~v~NL-p~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~  468 (481)
T TIGR01649       390 IQPPSATLHLSNI-PLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSA  468 (481)
T ss_pred             cCCCCcEEEEecC-CCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCc
Confidence            2356789999999 889999999999999997  7888773      589999999999999999999999999874   


Q ss_pred             ---EEEEEeecC
Q 026341          130 ---ISVEYALKD  138 (240)
Q Consensus       130 ---l~v~~a~~~  138 (240)
                         |+|.|+++.
T Consensus       469 ~~~lkv~fs~~~  480 (481)
T TIGR01649       469 PYHLKVSFSTSR  480 (481)
T ss_pred             cceEEEEeccCC
Confidence               999988753

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

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

Probab=99.86  E-value=8.6e-21  Score=170.44  Aligned_cols=131  Identities=22%  Similarity=0.308  Sum_probs=105.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCC-----------------CCCCCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSK-----------------SMANQRPTK   66 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~-----------------~~~~~~~~~   66 (240)
                      ++.++|||||+|.+.++|+.||+.|||+.|  +|+.|.|+++............                 ......++.
T Consensus       333 ~g~~~g~afv~f~~~~~a~~A~~~l~g~~~--~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~  410 (509)
T TIGR01642       333 TGLSKGYAFCEYKDPSVTDVAIAALNGKDT--GDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTK  410 (509)
T ss_pred             CCCcCeEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCce
Confidence            678899999999999999999999999999  6999999998744322110000                 011234678


Q ss_pred             EEEEeccCCCC--C--------CHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcc
Q 026341           67 TLFVINFDPIR--T--------RERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKL  125 (240)
Q Consensus        67 ~l~v~nl~~~~--~--------~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~  125 (240)
                      +|+|.|| ...  +        ..++|+++|.+||.|+.|.|+           .|+|||+|++.++|++||..|||..|
T Consensus       411 v~~l~N~-~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~  489 (509)
T TIGR01642       411 VVQLTNL-VTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKF  489 (509)
T ss_pred             EEEeccC-CchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEE
Confidence            8999998 421  1        126789999999999999985           37899999999999999999999999


Q ss_pred             cCcEEEEEEeec
Q 026341          126 VDRVISVEYALK  137 (240)
Q Consensus       126 ~g~~l~v~~a~~  137 (240)
                      +|+.|.|.|...
T Consensus       490 ~gr~v~~~~~~~  501 (509)
T TIGR01642       490 NDRVVVAAFYGE  501 (509)
T ss_pred             CCeEEEEEEeCH
Confidence            999999999754

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

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

Probab=99.85  E-value=6.2e-21  Score=173.23  Aligned_cols=123  Identities=21%  Similarity=0.453  Sum_probs=107.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      |++++|||||+|.++++|++|++.||+..|  .|++|.|.|+.......         .....+|||+|| +..+++++|
T Consensus        38 t~~s~G~afV~F~~~~~A~~Al~~ln~~~i--~gk~i~i~~s~~~~~~~---------~~~~~~vfV~nL-p~~~~~~~L  105 (562)
T TIGR01628        38 TRRSLGYGYVNFQNPADAERALETMNFKRL--GGKPIRIMWSQRDPSLR---------RSGVGNIFVKNL-DKSVDNKAL  105 (562)
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCeeEEeeccccccccc---------ccCCCceEEcCC-CccCCHHHH
Confidence            577899999999999999999999999988  59999999986433221         122457999999 899999999


Q ss_pred             HHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           84 KRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +++|+.||.|..|.|.       +|||||+|++.++|++|++.|||..+.|+.|.|......
T Consensus       106 ~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       106 FDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             HHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            9999999999999883       689999999999999999999999999999999776543

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

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

Probab=99.85  E-value=5.4e-21  Score=142.60  Aligned_cols=126  Identities=26%  Similarity=0.432  Sum_probs=108.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      |...+|||||||.++|+|+.|++.||...|+  |++|+|..+..-.+          +...+..|||+|| ...+++..|
T Consensus        47 ~~~~qGygF~Ef~~eedadYAikiln~VkLY--grpIrv~kas~~~~----------nl~vganlfvgNL-d~~vDe~~L  113 (203)
T KOG0131|consen   47 TQKHQGYGFAEFRTEEDADYAIKILNMVKLY--GRPIRVNKASAHQK----------NLDVGANLFVGNL-DPEVDEKLL  113 (203)
T ss_pred             cccccceeEEEEechhhhHHHHHHHHHHHhc--CceeEEEecccccc----------ccccccccccccc-CcchhHHHH
Confidence            4567999999999999999999999988885  99999998882211          3344689999999 558999999


Q ss_pred             HHhhccCCCeEEE-EE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCCC
Q 026341           84 KRHFEPYGNVLHV-RI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSER  142 (240)
Q Consensus        84 ~~~f~~~G~i~~~-~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  142 (240)
                      .++|+.||.+... .+        +++||||.|.+.+.+.+|+..|||+.+++++|.|.++..+..+.
T Consensus       114 ~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  114 YDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             HHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            9999999987651 22        36899999999999999999999999999999999999887655

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

Probab=99.85  E-value=3.2e-21  Score=160.65  Aligned_cols=129  Identities=25%  Similarity=0.384  Sum_probs=111.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcc-cCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPF-GYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRER   81 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~-~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~   81 (240)
                      .|+.++|||||.|.+.++|.+|+..|+++.. .+...+|.|.||..+++..          .....|||+-| +..++|.
T Consensus        71 ~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~----------~~e~KLFvg~l-sK~~te~  139 (510)
T KOG0144|consen   71 STGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERI----------VEERKLFVGML-SKQCTEN  139 (510)
T ss_pred             ccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhcc----------ccchhhhhhhc-cccccHH
Confidence            4778899999999999999999999988644 3345789999999877542          34678999999 8999999


Q ss_pred             HHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCC-cccC--cEEEEEEeecCCCCC
Q 026341           82 DIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRS-KLVD--RVISVEYALKDDSER  142 (240)
Q Consensus        82 ~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~-~~~g--~~l~v~~a~~~~~~~  142 (240)
                      +|+++|.+||.|++|.|.       +|||||.|.+.+.|..||+.|||. .+.|  .+|.|.||..++.+.
T Consensus       140 evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  140 EVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             HHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCch
Confidence            999999999999999983       799999999999999999999997 4555  799999998877644

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

Probab=99.84  E-value=7.5e-21  Score=149.23  Aligned_cols=124  Identities=24%  Similarity=0.505  Sum_probs=110.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      -+|++.|||||.|-+++||++||..|||..|  ..+.|+|.||.+....           .....|||.+| |..++..+
T Consensus        78 itGqSLGYGFVNYv~p~DAe~AintlNGLrL--Q~KTIKVSyARPSs~~-----------Ik~aNLYvSGl-PktMtqke  143 (360)
T KOG0145|consen   78 ITGQSLGYGFVNYVRPKDAEKAINTLNGLRL--QNKTIKVSYARPSSDS-----------IKDANLYVSGL-PKTMTQKE  143 (360)
T ss_pred             ccccccccceeeecChHHHHHHHhhhcceee--ccceEEEEeccCChhh-----------hcccceEEecC-CccchHHH
Confidence            4788999999999999999999999999999  6999999999976532           34678999999 99999999


Q ss_pred             HHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCCC
Q 026341           83 IKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDDS  140 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~  140 (240)
                      |+++|++||.|....|        .+|.+||.|+...+|++||..|||..-.|  .+|.|.||..+..
T Consensus       144 lE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  144 LEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             HHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            9999999998876554        58999999999999999999999998876  6899999986644

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

Probab=99.84  E-value=2e-20  Score=156.53  Aligned_cols=119  Identities=28%  Similarity=0.411  Sum_probs=105.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      -+|.++|||||+|.+.++|++||+.||+.+|- .|+.|.|+.+..                 ++.|||+|| |.+.++++
T Consensus       120 ~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir-~GK~igvc~Sva-----------------n~RLFiG~I-PK~k~kee  180 (506)
T KOG0117|consen  120 FSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR-PGKLLGVCVSVA-----------------NCRLFIGNI-PKTKKKEE  180 (506)
T ss_pred             cCCCCcceEEEEeecHHHHHHHHHHhhCcccc-CCCEeEEEEeee-----------------cceeEeccC-CccccHHH
Confidence            37889999999999999999999999999997 699999998773                 789999999 99999999


Q ss_pred             HHHhhccCC-CeEEEEE---------eCCeEEEEecCHHHHHHHHHhcC-C-CcccCcEEEEEEeecCCC
Q 026341           83 IKRHFEPYG-NVLHVRI---------RRNFAFVQFETQEEATKALESTD-R-SKLVDRVISVEYALKDDS  140 (240)
Q Consensus        83 l~~~f~~~G-~i~~~~~---------~kg~afV~f~~~~~a~~A~~~l~-g-~~~~g~~l~v~~a~~~~~  140 (240)
                      |.+.|.+.+ .|+.|.|         .+|||||+|+++..|..|-..|- + .++.|..+.|.||.+...
T Consensus       181 Ilee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e  250 (506)
T KOG0117|consen  181 ILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEE  250 (506)
T ss_pred             HHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccC
Confidence            999999988 5667766         36999999999999999988773 3 467899999999998765

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

Probab=99.84  E-value=2e-20  Score=159.97  Aligned_cols=133  Identities=29%  Similarity=0.512  Sum_probs=112.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC-C-C----CC---------CCCCCCCCCEEE
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR-D-G----SK---------SMANQRPTKTLF   69 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~-~-~----~~---------~~~~~~~~~~l~   69 (240)
                      ..++|||||.|.-++|++.|++.+++..|  +|+.|.|.++........ . +    ..         ......+-..|+
T Consensus        44 ~~~RGfgfVtFam~ED~qrA~~e~~~~kf--~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLI  121 (678)
T KOG0127|consen   44 SEKRGFGFVTFAMEEDVQRALAETEQSKF--EGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLI  121 (678)
T ss_pred             ccccCccceeeehHhHHHHHHHHhhcCcc--cceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEE
Confidence            35699999999999999999999999999  799999999985432220 0 0    00         011123468899


Q ss_pred             EeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           70 VINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        70 v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      |.|| |+.|...+|+.+|+.||.|..|.|+       .|||||.|.+..+|..||+.||+.+|+|++|-|.||.++..
T Consensus       122 IRNL-Pf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  122 IRNL-PFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             eecC-CcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            9999 9999999999999999999999996       48999999999999999999999999999999999987653

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

Probab=99.82  E-value=4.6e-20  Score=162.15  Aligned_cols=128  Identities=27%  Similarity=0.529  Sum_probs=110.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHh
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRH   86 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~   86 (240)
                      +.|||||+|.++++|+.|+..|+|+.|  +|..|.|.++........ + +.......++.|+|.|| |+..+..+|+++
T Consensus       559 SmGfgFVEF~~~e~A~~a~k~lqgtvl--dGH~l~lk~S~~k~~~~~-g-K~~~~kk~~tKIlVRNi-pFeAt~rEVr~L  633 (725)
T KOG0110|consen  559 SMGFGFVEFAKPESAQAALKALQGTVL--DGHKLELKISENKPASTV-G-KKKSKKKKGTKILVRNI-PFEATKREVRKL  633 (725)
T ss_pred             ccceeEEEecCHHHHHHHHHHhcCcee--cCceEEEEeccCcccccc-c-cccccccccceeeeecc-chHHHHHHHHHH
Confidence            469999999999999999999999999  899999999993332221 1 22223344789999999 999999999999


Q ss_pred             hccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           87 FEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        87 f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      |..||.|..|.|+        +|||||+|-++.+|..|+.+|..+.+.|+.|.++||....
T Consensus       634 F~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  634 FTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            9999999999995        5899999999999999999999999999999999998543

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

Probab=99.81  E-value=8.4e-19  Score=137.76  Aligned_cols=134  Identities=23%  Similarity=0.373  Sum_probs=111.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCC---------------CC-----------
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDG---------------SK-----------   57 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~---------------~~-----------   57 (240)
                      |+.++|-|||.|...++|+.||..|||..-.....+|.|+|+..........               ..           
T Consensus       165 tg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~  244 (360)
T KOG0145|consen  165 TGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDN  244 (360)
T ss_pred             cceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhcccc
Confidence            6788999999999999999999999998775557899999998654221100               00           


Q ss_pred             --------------------------CCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeE
Q 026341           58 --------------------------SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFA  103 (240)
Q Consensus        58 --------------------------~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~a  103 (240)
                                                .+.....+.+|||.|| ..++++.-|+++|.+||.|..|+|.        |||+
T Consensus       245 ~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL-spd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfg  323 (360)
T KOG0145|consen  245 LLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL-SPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFG  323 (360)
T ss_pred             ccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEec-CCCchHhHHHHHhCcccceeeEEEEecCCccccccee
Confidence                                      1112234689999999 6689999999999999999999984        7999


Q ss_pred             EEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341          104 FVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus       104 fV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ||.+.+-++|..||..|||..+.++.|.|.|...+
T Consensus       324 FVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  324 FVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             EEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            99999999999999999999999999999996543

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

Probab=99.81  E-value=2.6e-20  Score=152.45  Aligned_cols=131  Identities=18%  Similarity=0.302  Sum_probs=109.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      |+++||||||||+-+|.|..|++.|||..+  +|+.|+|....+.......-............|||..+ ..+.+++||
T Consensus       151 T~kHKgFAFVEYEvPEaAqLAlEqMNg~ml--GGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSv-HpDLSe~Di  227 (544)
T KOG0124|consen  151 TGKHKGFAFVEYEVPEAAQLALEQMNGQML--GGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASV-HPDLSETDI  227 (544)
T ss_pred             cccccceEEEEEeCcHHHHHHHHHhccccc--cCccccccCCCCCcccchHHHHHHHHHHhhheEEeeec-CCCccHHHH
Confidence            789999999999999999999999999999  79999999665433221110001113344789999999 668999999


Q ss_pred             HHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           84 KRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      +.+|+.||+|..|.+        .+||+||+|.+.....+||..||-..++|+-|.|-.+..
T Consensus       228 KSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  228 KSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             HHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            999999999999999        379999999999999999999999999999999877653

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

Probab=99.80  E-value=5.1e-19  Score=151.44  Aligned_cols=134  Identities=33%  Similarity=0.529  Sum_probs=108.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC-----------------------------
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR-----------------------------   53 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~-----------------------------   53 (240)
                      ..+++-|||||+|.+..+|++||+.||+..|  +|++|.|.||..+..-..                             
T Consensus       153 ~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i--~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~  230 (678)
T KOG0127|consen  153 KDGKLCGFAFVQFKEKKDAEKALEFFNGNKI--DGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDF  230 (678)
T ss_pred             CCCCccceEEEEEeeHHHHHHHHHhccCcee--cCceeEEeeecccccccccchhhhhhhhhccchhhhccccccccccc
Confidence            3566789999999999999999999999999  799999999984431000                             


Q ss_pred             ---------------CC---------CC--------------------------CCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341           54 ---------------DG---------SK--------------------------SMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus        54 ---------------~~---------~~--------------------------~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                                     .+         ..                          .........+|||.|| |+++++++|
T Consensus       231 ~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL-~fD~tEEel  309 (678)
T KOG0127|consen  231 DEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNL-PFDTTEEEL  309 (678)
T ss_pred             chhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecC-CccccHHHH
Confidence                           00         00                          0011223479999999 999999999


Q ss_pred             HHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhc-----CC-CcccCcEEEEEEeecCC
Q 026341           84 KRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST-----DR-SKLVDRVISVEYALKDD  139 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l-----~g-~~~~g~~l~v~~a~~~~  139 (240)
                      .++|++||+|.++.|        ++|.|||.|.+..+|++||...     .| ..|+|+.|.|..|....
T Consensus       310 ~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  310 KEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             HHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchH
Confidence            999999999999887        4799999999999999999976     23 57899999999987543

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

Probab=99.80  E-value=3.4e-19  Score=158.91  Aligned_cols=118  Identities=29%  Similarity=0.417  Sum_probs=99.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .+++++|||||+|.++++|++||+.||+..|. .|+.|.|.++.                 ..++|||+|| |..+++++
T Consensus        94 ~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~-~Gr~l~V~~S~-----------------~~~rLFVgNL-P~~~Teee  154 (578)
T TIGR01648        94 FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIR-PGRLLGVCISV-----------------DNCRLFVGGI-PKNKKREE  154 (578)
T ss_pred             CCCCccceEEEEeCCHHHHHHHHHHcCCCeec-CCccccccccc-----------------cCceeEeecC-CcchhhHH
Confidence            46789999999999999999999999999885 57888776653                 2578999999 89999999


Q ss_pred             HHHhhccCCC-eEEEEE---------eCCeEEEEecCHHHHHHHHHhcCC--CcccCcEEEEEEeecCC
Q 026341           83 IKRHFEPYGN-VLHVRI---------RRNFAFVQFETQEEATKALESTDR--SKLVDRVISVEYALKDD  139 (240)
Q Consensus        83 l~~~f~~~G~-i~~~~~---------~kg~afV~f~~~~~a~~A~~~l~g--~~~~g~~l~v~~a~~~~  139 (240)
                      |.++|.+++. ++.+.+         .++||||+|.++++|+.|+..|+.  ..+.|+.|.|+|+.+..
T Consensus       155 L~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       155 ILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             HHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccc
Confidence            9999999863 444433         268999999999999999998864  35789999999998654

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

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

Probab=99.79  E-value=4.2e-18  Score=151.11  Aligned_cols=131  Identities=21%  Similarity=0.361  Sum_probs=103.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC------------------------------
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR------------------------------   53 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~------------------------------   53 (240)
                      +++++|||||+|.+.++|.+|+..|||..|  .|++|.|.|+........                              
T Consensus       224 ~g~~~g~afV~f~~~e~A~~A~~~l~g~~i--~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  301 (457)
T TIGR01622       224 TGRSKGFGFIQFHDAEEAKEALEVMNGFEL--AGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKL  301 (457)
T ss_pred             CCccceEEEEEECCHHHHHHHHHhcCCcEE--CCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhh
Confidence            567899999999999999999999999988  699999999652110000                              


Q ss_pred             --CC-----------C-------------C-----------------------CCCCCCCCCEEEEeccCCCCCC-----
Q 026341           54 --DG-----------S-------------K-----------------------SMANQRPTKTLFVINFDPIRTR-----   79 (240)
Q Consensus        54 --~~-----------~-------------~-----------------------~~~~~~~~~~l~v~nl~~~~~~-----   79 (240)
                        ..           .             .                       ......+..+|+|.|| ....+     
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~-~~~~~~~~~~  380 (457)
T TIGR01622       302 DRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNM-FDPATEEEPN  380 (457)
T ss_pred             ccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecC-CCCcccccch
Confidence              00           0             0                       0002245678999998 32222     


Q ss_pred             -----HHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           80 -----ERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        80 -----~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                           .+||++.|.+||.|+.|.|.    .|++||+|.+.++|++|++.|||..|+|+.|.|.+...
T Consensus       381 ~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       381 FDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             HHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence                 36899999999999999885    68999999999999999999999999999999999754

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.

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

Probab=99.78  E-value=7.7e-18  Score=126.02  Aligned_cols=79  Identities=27%  Similarity=0.427  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .....++|||+|| ++.+++++|+++|.+||.|..|.|+        ++||||+|.+.++|+.||+.||+..|+|+.|.|
T Consensus        30 ~~~~~~~lfVgnL-~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V  108 (144)
T PLN03134         30 LRLMSTKLFIGGL-SWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV  108 (144)
T ss_pred             ccCCCCEEEEeCC-CCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3445789999999 8999999999999999999999884        689999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.....
T Consensus       109 ~~a~~~~~  116 (144)
T PLN03134        109 NPANDRPS  116 (144)
T ss_pred             EeCCcCCC
Confidence            99986544

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

Probab=99.76  E-value=4.6e-18  Score=145.20  Aligned_cols=114  Identities=24%  Similarity=0.485  Sum_probs=104.8

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHh
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRH   86 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~   86 (240)
                      +-|||||.|.++++|++||.+||...|  .|++|.|-|+.....                .|||.|| +..++..+|.++
T Consensus        36 slgy~yvnf~~~~da~~A~~~~n~~~~--~~~~~rim~s~rd~~----------------~~~i~nl-~~~~~~~~~~d~   96 (369)
T KOG0123|consen   36 SLGYAYVNFQQPADAERALDTMNFDVL--KGKPIRIMWSQRDPS----------------LVFIKNL-DESIDNKSLYDT   96 (369)
T ss_pred             ccceEEEecCCHHHHHHHHHHcCCccc--CCcEEEeehhccCCc----------------eeeecCC-CcccCcHHHHHH
Confidence            789999999999999999999999999  699999999985431                2999999 789999999999


Q ss_pred             hccCCCeEEEEE------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           87 FEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        87 f~~~G~i~~~~~------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      |+.||+|+.|++      .+|| ||+|+++++|.+||..|||..+.|+.|.|.....+..
T Consensus        97 f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   97 FSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             HHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            999999999999      3789 9999999999999999999999999999988876554

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

Probab=99.76  E-value=2.5e-18  Score=134.22  Aligned_cols=122  Identities=47%  Similarity=0.665  Sum_probs=101.9

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC---CC------CCCCCCCCCCCEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR---DG------SKSMANQRPTKTLFVINFDPIRT   78 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~---~~------~~~~~~~~~~~~l~v~nl~~~~~   78 (240)
                      .|||||+|+++.+|+.||..||+.+|+  |..+.|+|+........   .+      ..-.......+.|+|.|+ +..+
T Consensus        35 ~gf~fv~fed~rda~Dav~~l~~~~l~--~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~-~~r~  111 (216)
T KOG0106|consen   35 NGFGFVEFEDPRDADDAVHDLDGKELC--GERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNL-SLRV  111 (216)
T ss_pred             cccceeccCchhhhhcccchhcCceec--ceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccc-hhhh
Confidence            799999999999999999999999995  66699999995422110   00      011122345678889999 7789


Q ss_pred             CHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           79 RERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        79 ~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .+++|.++|.++|.+....+..+++||+|++.++|..|+..|++..+.++.|.+
T Consensus       112 ~~qdl~d~~~~~g~~~~~~~~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  112 SWQDLKDHFRPAGEVTYVDARRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hHHHHhhhhcccCCCchhhhhccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            999999999999999887778999999999999999999999999999999999

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

Probab=99.68  E-value=2.1e-15  Score=120.84  Aligned_cols=80  Identities=30%  Similarity=0.518  Sum_probs=73.4

Q ss_pred             CCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           59 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        59 ~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      .+...|.+||||+-| ++.+++..|+..|+.||+|..|.|        ++|||||+|+++.+...|.+..+|.+|+|+.|
T Consensus        95 ~a~gDPy~TLFv~RL-nydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   95 NAIGDPYKTLFVARL-NYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             cccCCccceeeeeec-cccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            346688999999999 999999999999999999999998        47999999999999999999999999999999


Q ss_pred             EEEEeecCC
Q 026341          131 SVEYALKDD  139 (240)
Q Consensus       131 ~v~~a~~~~  139 (240)
                      .|.+-....
T Consensus       174 ~VDvERgRT  182 (335)
T KOG0113|consen  174 LVDVERGRT  182 (335)
T ss_pred             EEEeccccc
Confidence            999876543

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

Probab=99.68  E-value=6.5e-16  Score=119.68  Aligned_cols=133  Identities=22%  Similarity=0.422  Sum_probs=109.9

Q ss_pred             CcccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC-------------------------C
Q 026341            1 MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD-------------------------G   55 (240)
Q Consensus         1 ~~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~-------------------------~   55 (240)
                      +++|.+++|.|||.|.+.+.|..|+..|+|..|+  |++|.|+||..+...-..                         .
T Consensus        45 a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFy--gK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~  122 (221)
T KOG4206|consen   45 AFKTPKMRGQAFVVFKETEAASAALRALQGFPFY--GKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDT  122 (221)
T ss_pred             ecCCCCccCceEEEecChhHHHHHHHHhcCCccc--CchhheecccCccchhhccCceeccccCccccccccccCCcccc
Confidence            4689999999999999999999999999999996  999999999854321100                         0


Q ss_pred             CCC--------------CCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHH
Q 026341           56 SKS--------------MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALE  118 (240)
Q Consensus        56 ~~~--------------~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~  118 (240)
                      +..              ....++...|++.|| |..++.+.|..+|.+|.....+.+   ..+.|||+|.+...|..|..
T Consensus       123 ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~ni-P~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~  201 (221)
T KOG4206|consen  123 NGHFYNMNRMNLPPPFLAQMAPPNNILFLTNI-PSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQ  201 (221)
T ss_pred             cccccccccccCCCCccccCCCCceEEEEecC-CcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhh
Confidence            000              123677889999999 889999999999999987777776   46899999999999999999


Q ss_pred             hcCCCccc-CcEEEEEEee
Q 026341          119 STDRSKLV-DRVISVEYAL  136 (240)
Q Consensus       119 ~l~g~~~~-g~~l~v~~a~  136 (240)
                      .|++..|- ..++.|.++.
T Consensus       202 ~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  202 ALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hhccceeccCceEEecccC
Confidence            99998886 7888887764

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

Probab=99.67  E-value=8.7e-17  Score=126.96  Aligned_cols=80  Identities=18%  Similarity=0.431  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..+.+|.|||.+| |....+.+|.++|-.||.|...++        .|+|+||.|++..+|+.||..|||..|+-+.|+|
T Consensus       281 eGPeGCNlFIYHL-PQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  281 EGPEGCNLFIYHL-PQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             cCCCcceEEEEeC-chhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            4566899999999 889999999999999999988777        4899999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      .+.++++..
T Consensus       360 QLKRPkdan  368 (371)
T KOG0146|consen  360 QLKRPKDAN  368 (371)
T ss_pred             hhcCccccC
Confidence            998877643

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

Probab=99.67  E-value=1.2e-16  Score=137.43  Aligned_cols=132  Identities=27%  Similarity=0.429  Sum_probs=108.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCC---CCCCCCCCEEEEeccCCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS---MANQRPTKTLFVINFDPIRTR   79 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~---~~~~~~~~~l~v~nl~~~~~~   79 (240)
                      .++.+||.|||+|.|.+..-.||. |.|..++  |.+|.|+.....+.........   .....|...|||+|| .++++
T Consensus       216 ~s~rskgi~Yvef~D~~sVp~aia-LsGqrll--g~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnL-HfNit  291 (549)
T KOG0147|consen  216 NSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLL--GVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNL-HFNIT  291 (549)
T ss_pred             cchhhcceeEEEEecccchhhHhh-hcCCccc--CceeEecccHHHHHHHHhccccccccccccchhhhhhccc-ccCch
Confidence            356689999999999999999996 9999884  9999999877554432111110   111233444999999 89999


Q ss_pred             HHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           80 ERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        80 ~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +++|+.+|+.||.|..|.++        +||+||+|.+.++|.+|++.|||.+|.|+.|+|......
T Consensus       292 e~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  292 EDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            99999999999999999884        799999999999999999999999999999998887643

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

Probab=99.63  E-value=3.3e-14  Score=106.72  Aligned_cols=125  Identities=30%  Similarity=0.451  Sum_probs=99.7

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCC---------------CCCCCCCCCCCEEEEe
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDG---------------SKSMANQRPTKTLFVI   71 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~---------------~~~~~~~~~~~~l~v~   71 (240)
                      ..+||||+|+++.+|+.||..-+|..+  +|..|.|+|+..-.......               ..-+..-.....|.|.
T Consensus        44 ~ppfafVeFEd~RDAeDAiygRdGYdy--dg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVs  121 (241)
T KOG0105|consen   44 PPPFAFVEFEDPRDAEDAIYGRDGYDY--DGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVS  121 (241)
T ss_pred             CCCeeEEEecCccchhhhhhccccccc--CcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEe
Confidence            368999999999999999999999999  79999999998654221110               0012223335679999


Q ss_pred             ccCCCCCCHHHHHHhhccCCCeEEEEEeC-CeEEEEecCHHHHHHHHHhcCCCccc--CcEEEEEE
Q 026341           72 NFDPIRTRERDIKRHFEPYGNVLHVRIRR-NFAFVQFETQEEATKALESTDRSKLV--DRVISVEY  134 (240)
Q Consensus        72 nl~~~~~~~~~l~~~f~~~G~i~~~~~~k-g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~  134 (240)
                      +| |...+|+||++++.+.|.|.+..+.+ +++.|+|...|+.+-|+..|+.+.+.  |.+..+.+
T Consensus       122 GL-p~SgSWQDLKDHmReaGdvCfadv~rDg~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  122 GL-PPSGSWQDLKDHMREAGDVCFADVQRDGVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             cC-CCCCchHHHHHHHHhhCCeeeeeeecccceeeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            99 77899999999999999999999864 89999999999999999999887664  44444433

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

Probab=99.62  E-value=2.5e-15  Score=112.73  Aligned_cols=76  Identities=28%  Similarity=0.499  Sum_probs=70.4

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...+.|||+|| |.++.+.+|+++|.+||.|..|.|.     ..||||+|++..+|+.||..-+|..++|+.|.|+|+..
T Consensus         4 r~~~~iyvGNL-P~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    4 RNSRRIYVGNL-PGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cccceEEecCC-CcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            34789999999 8899999999999999999999994     47999999999999999999999999999999999986


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      -.
T Consensus        83 gr   84 (241)
T KOG0105|consen   83 GR   84 (241)
T ss_pred             CC
Confidence            54

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

Probab=99.62  E-value=2.1e-15  Score=128.97  Aligned_cols=124  Identities=26%  Similarity=0.450  Sum_probs=108.0

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHh
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRH   86 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~   86 (240)
                      ++|| ||+|+++++|.+||..|||..+  .+++|.|..+..+........  . .....+.++|.|+ +..+++++|.++
T Consensus       115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll--~~kki~vg~~~~~~er~~~~~--~-~~~~~t~v~vk~~-~~~~~~~~l~~~  187 (369)
T KOG0123|consen  115 SKGY-FVQFESEESAKKAIEKLNGMLL--NGKKIYVGLFERKEEREAPLG--E-YKKRFTNVYVKNL-EEDSTDEELKDL  187 (369)
T ss_pred             ceee-EEEeCCHHHHHHHHHHhcCccc--CCCeeEEeeccchhhhccccc--c-hhhhhhhhheecc-ccccchHHHHHh
Confidence            7999 9999999999999999999999  699999998887655432111  1 3345678999999 889999999999


Q ss_pred             hccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           87 FEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        87 f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      |..+|.|..+.++       ++|+||+|++.++|..|+..||+..+.+..+.|.-+..
T Consensus       188 f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  188 FSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             hcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            9999999999884       68999999999999999999999999999999888776

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.57  E-value=1.2e-14  Score=123.55  Aligned_cols=77  Identities=21%  Similarity=0.408  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .....++|||+|| |+++++++|+++|+.||+|+.|.|.        ++||||+|.++++|++||+.||+..|.+++|+|
T Consensus       103 ~~~~~~~LfVgnL-p~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       103 TNNSGTNLIVNYL-PQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            4556789999999 9999999999999999999999884        489999999999999999999999999999999


Q ss_pred             EEeecC
Q 026341          133 EYALKD  138 (240)
Q Consensus       133 ~~a~~~  138 (240)
                      .++.+.
T Consensus       182 ~~a~p~  187 (346)
T TIGR01659       182 SYARPG  187 (346)
T ss_pred             eccccc
Confidence            998753

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>PF00076 RRM_1: RNA recognition motif

Probab=99.57  E-value=1e-14  Score=95.49  Aligned_cols=63  Identities=33%  Similarity=0.667  Sum_probs=59.2

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      |||+|| |..+++++|+++|.+||.|..+.+.       +++|||+|.+.++|+.|++.|||..|.|+.|+
T Consensus         1 l~v~nl-p~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNL-PPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESE-TTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCC-CCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999 8999999999999999999998883       57999999999999999999999999999874

(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 ....

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

Probab=99.56  E-value=1.3e-14  Score=103.39  Aligned_cols=81  Identities=22%  Similarity=0.454  Sum_probs=73.6

Q ss_pred             CCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           59 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        59 ~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      ++....+..|||.++ ...+++++|.+.|..||+|+.+.|        .||||+|+|++.++|++||..|||..|.|+.|
T Consensus        66 PqrSVEGwIi~Vtgv-HeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGV-HEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             CccceeeEEEEEecc-CcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            345556889999999 788999999999999999999988        38999999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 026341          131 SVEYALKDDS  140 (240)
Q Consensus       131 ~v~~a~~~~~  140 (240)
                      .|.|+..+..
T Consensus       145 ~VDw~Fv~gp  154 (170)
T KOG0130|consen  145 SVDWCFVKGP  154 (170)
T ss_pred             eEEEEEecCC
Confidence            9999987643

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

Probab=99.56  E-value=1.9e-14  Score=120.54  Aligned_cols=77  Identities=21%  Similarity=0.487  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..+.+..|||.+| |...-+.+|-..|..||.|+..++        .+.|+||.|++..+|.+||..|||..|+.+.|+|
T Consensus       420 eGpeGanlfiyhl-Pqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkV  498 (510)
T KOG0144|consen  420 EGPEGANLFIYHL-PQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKV  498 (510)
T ss_pred             cCCCccceeeeeC-chhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceE
Confidence            4556788999999 989999999999999999988776        3789999999999999999999999999999999


Q ss_pred             EEeecC
Q 026341          133 EYALKD  138 (240)
Q Consensus       133 ~~a~~~  138 (240)
                      ......
T Consensus       499 Qlk~~~  504 (510)
T KOG0144|consen  499 QLKRDR  504 (510)
T ss_pred             Eeeecc
Confidence            987654

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

Probab=99.55  E-value=1.6e-14  Score=102.16  Aligned_cols=77  Identities=25%  Similarity=0.404  Sum_probs=70.3

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ....++|||+|| .+.++|++|.++|+++|+|..|.|        +-|||||+|.+.++|+.|+..++|+.++.++|.|.
T Consensus        33 ~r~S~tvyVgNl-SfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   33 LRKSCTVYVGNL-SFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HhhcceEEEeee-eeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            345899999999 889999999999999999999988        35899999999999999999999999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      |...-.
T Consensus       112 ~D~GF~  117 (153)
T KOG0121|consen  112 WDAGFV  117 (153)
T ss_pred             ccccch
Confidence            976543

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

Probab=99.54  E-value=1.6e-14  Score=117.24  Aligned_cols=73  Identities=34%  Similarity=0.552  Sum_probs=69.2

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ..+.|+|+|| |+...+.||..+|.+||+|.+|.|      .|||+||+|++.++|++|-++|||..|.|++|+|..|..
T Consensus        95 ~pkRLhVSNI-PFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   95 TPKRLHVSNI-PFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCceeEeecC-CccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            3578999999 999999999999999999999999      489999999999999999999999999999999999875

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

Probab=99.53  E-value=2.4e-13  Score=112.18  Aligned_cols=130  Identities=20%  Similarity=0.204  Sum_probs=109.5

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC---------------------------C--------
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR---------------------------D--------   54 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~---------------------------~--------   54 (240)
                      .|.|||++.+.|++|.+.|||..|+-+...|+|+||++.+-.-.                           .        
T Consensus       161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~  240 (494)
T KOG1456|consen  161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGY  240 (494)
T ss_pred             eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCC
Confidence            79999999999999999999999987778999999996541000                           0        


Q ss_pred             ------C------------------------------CCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE
Q 026341           55 ------G------------------------------SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI   98 (240)
Q Consensus        55 ------~------------------------------~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~   98 (240)
                            +                              ...+....+++++.|.+|....++.+.|.++|..||.|..|++
T Consensus       241 ~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkF  320 (494)
T KOG1456|consen  241 HPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKF  320 (494)
T ss_pred             ChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEE
Confidence                  0                              0012345668899999997677889999999999999999999


Q ss_pred             eC---CeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           99 RR---NFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        99 ~k---g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      +|   |-|+||+.+..+.+.|+..||+..+-|.+|.|.+++..-
T Consensus       321 mkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~  364 (494)
T KOG1456|consen  321 MKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNF  364 (494)
T ss_pred             eecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccc
Confidence            64   899999999999999999999999999999999987654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.52  E-value=6.9e-14  Score=112.23  Aligned_cols=72  Identities=28%  Similarity=0.427  Sum_probs=67.2

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      .++|||+|| ++.+++++|+++|+.||+|..|.|.     ++||||+|.++++|+.||. |||..|.|+.|.|.++...
T Consensus         4 ~rtVfVgNL-s~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNV-SLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            579999999 8899999999999999999999994     6899999999999999996 9999999999999998654

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

Probab=99.51  E-value=1e-13  Score=119.46  Aligned_cols=133  Identities=21%  Similarity=0.340  Sum_probs=99.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC-------------C------C--------
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD-------------G------S--------   56 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~-------------~------~--------   56 (240)
                      ||.+||||||+|.+.++|.+|++.|||.+|  .|+.|+|..-.........             +      .        
T Consensus       316 tG~skgfGfi~f~~~~~ar~a~e~lngfel--AGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kl  393 (549)
T KOG0147|consen  316 TGRSKGFGFITFVNKEDARKALEQLNGFEL--AGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKL  393 (549)
T ss_pred             cccccCcceEEEecHHHHHHHHHHhcccee--cCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHH
Confidence            899999999999999999999999999777  7999998755421111000             0      0        


Q ss_pred             ----C------------------------------CCCCC-------CCCCEEEEeccC-CCCCC--------HHHHHHh
Q 026341           57 ----K------------------------------SMANQ-------RPTKTLFVINFD-PIRTR--------ERDIKRH   86 (240)
Q Consensus        57 ----~------------------------------~~~~~-------~~~~~l~v~nl~-~~~~~--------~~~l~~~   86 (240)
                          .                              .....       .++.++.+.|+- |...|        .++|.+.
T Consensus       394 a~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Ee  473 (549)
T KOG0147|consen  394 AEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEE  473 (549)
T ss_pred             hccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHH
Confidence                0                              00011       345566777761 11111        2677888


Q ss_pred             hccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           87 FEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        87 f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +.+||+|..|.|-   -|+.||.|.+.+.|..|+.+|||..|.|+.|++.|....
T Consensus       474 c~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  474 CGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLE  528 (549)
T ss_pred             HHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehh
Confidence            8999999999983   389999999999999999999999999999999997643

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

Probab=99.48  E-value=1.5e-13  Score=107.53  Aligned_cols=74  Identities=27%  Similarity=0.523  Sum_probs=69.7

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|-|.|| +.++++.+|+++|.+||.|..|.|        .+|||||.|.+.++|++||..|||.-+++-.|.|+|+
T Consensus       188 D~~tvRvtNL-sed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  188 DEATVRVTNL-SEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             ccceeEEecC-ccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            4578999999 899999999999999999999988        4799999999999999999999999999999999999


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

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

Probab=99.47  E-value=1e-13  Score=114.98  Aligned_cols=130  Identities=25%  Similarity=0.402  Sum_probs=106.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++||+||+|++++....+|.....+ |  +|+.|.+.-|.+........     .......|||++| +..+++++|
T Consensus        44 t~rsrgFgfv~f~~~~~v~~vl~~~~h~-~--dgr~ve~k~av~r~~~~~~~-----~~~~tkkiFvGG~-~~~~~e~~~  114 (311)
T KOG4205|consen   44 TGRSRGFGFVTFATPEGVDAVLNARTHK-L--DGRSVEPKRAVSREDQTKVG-----RHLRTKKIFVGGL-PPDTTEEDF  114 (311)
T ss_pred             CCCcccccceecCCCcchheeecccccc-c--CCccccceeccCcccccccc-----cccceeEEEecCc-CCCCchHHH
Confidence            6788999999999999988888643333 4  69999999888766543221     2225789999999 899999999


Q ss_pred             HHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCCCC
Q 026341           84 KRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERD  143 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~  143 (240)
                      ++.|.+||.|..+.+        +++|+||.|.+++.+.+++. .+-+.|+|+.|.|..|.++.....
T Consensus       115 r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  115 KDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             hhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhccc
Confidence            999999998888877        37999999999999999886 577899999999999998776543

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

Probab=99.46  E-value=4e-13  Score=91.60  Aligned_cols=76  Identities=25%  Similarity=0.448  Sum_probs=69.9

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-----eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-----RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-----~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ...+..|||.|| |+.+|.+++.++|.+||.|..|.|     .+|-|||.|++..+|.+|+..|+|..++++.|.|-+-.
T Consensus        15 pevnriLyirNL-p~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   15 PEVNRILYIRNL-PFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hhhheeEEEecC-CccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            344688999999 999999999999999999999999     47999999999999999999999999999999998866


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      +.
T Consensus        94 ~~   95 (124)
T KOG0114|consen   94 PE   95 (124)
T ss_pred             HH
Confidence            54

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.45  E-value=4e-13  Score=88.12  Aligned_cols=63  Identities=35%  Similarity=0.664  Sum_probs=56.7

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      |||+|| |..+++++|.++|..||.|..+.+.       +++|||+|.++++|+.|++.+++..|+|+.|.
T Consensus         1 v~i~nl-p~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNL-PPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESS-TTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999 8899999999999999999998883       47999999999999999999999999999874

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 ....

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

Probab=99.44  E-value=1.3e-13  Score=110.35  Aligned_cols=73  Identities=30%  Similarity=0.499  Sum_probs=70.0

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ..|||+|| |..+++.+|+.+|++||+|+.|.|.|.||||..++...|+.||..|||..|+|..|.|+-++.+.
T Consensus         3 ~KLFIGNL-p~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNL-PREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCC-CcccchHHHHHHHHhhCceEeeeeecccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            46999999 99999999999999999999999999999999999999999999999999999999999998773

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

Probab=99.43  E-value=7.4e-13  Score=102.33  Aligned_cols=117  Identities=26%  Similarity=0.389  Sum_probs=90.0

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccC-CCceEEEEeccCCCCCCCCC--C----C-----------------------
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGY-DRRRLSVEWARGERGRHRDG--S----K-----------------------   57 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~-~g~~l~v~~a~~~~~~~~~~--~----~-----------------------   57 (240)
                      +-+|||+|.+..+|.+|+..|||+.|.. -+..|.|++++...+.....  .    .                       
T Consensus        77 ~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~  156 (284)
T KOG1457|consen   77 KPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEG  156 (284)
T ss_pred             cceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhcccc
Confidence            5799999999999999999999998832 37889999998543221100  0    0                       


Q ss_pred             ----------------------------------------------CCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCC
Q 026341           58 ----------------------------------------------SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYG   91 (240)
Q Consensus        58 ----------------------------------------------~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G   91 (240)
                                                                    -......+.+|||.|| ..++++++|+++|..|-
T Consensus       157 l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl-~~~~~ed~l~~~~~~~~  235 (284)
T KOG1457|consen  157 LSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANL-GPNCTEDELKQLLSRYP  235 (284)
T ss_pred             ccCccccCCccccccCCCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhcc-CCCCCHHHHHHHHHhCC
Confidence                                                          0011223578999999 66899999999999997


Q ss_pred             CeEEEEEe--C--CeEEEEecCHHHHHHHHHhcCCCcc
Q 026341           92 NVLHVRIR--R--NFAFVQFETQEEATKALESTDRSKL  125 (240)
Q Consensus        92 ~i~~~~~~--k--g~afV~f~~~~~a~~A~~~l~g~~~  125 (240)
                      ....++|.  .  .+|||+|++.+.|..||..|+|..|
T Consensus       236 gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  236 GFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             CceEEEEecCCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            66666663  2  3899999999999999999998765

>PLN03213 repressor of silencing 3; Provisional

Probab=99.43  E-value=5.4e-13  Score=113.75  Aligned_cols=74  Identities=22%  Similarity=0.284  Sum_probs=69.1

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCH--HHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQ--EEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~--~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+..|||||| ++.+++++|..+|..||.|..|.|+    +|||||+|.+.  .++.+||..|||..+.|+.|+|+.|+
T Consensus         8 ~~gMRIYVGNL-SydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          8 GGGVRLHVGGL-GESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CcceEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            44689999999 9999999999999999999999997    68999999987  78999999999999999999999998


Q ss_pred             c
Q 026341          137 K  137 (240)
Q Consensus       137 ~  137 (240)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            4

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

Probab=99.43  E-value=7.1e-13  Score=115.36  Aligned_cols=131  Identities=24%  Similarity=0.367  Sum_probs=99.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCC-------------CCCCCCCCCEEEE
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSK-------------SMANQRPTKTLFV   70 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~-------------~~~~~~~~~~l~v   70 (240)
                      ++.++||||.+|.++..+..|++.|||+.+  ++++|.|+.|............             ......++.+|.+
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnGm~l--gd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L  404 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNGMQL--GDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCL  404 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccchhhh--cCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhh
Confidence            578899999999999999999999999999  5899999988754433221111             1223445556666


Q ss_pred             eccC-CCC-CCH-------HHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           71 INFD-PIR-TRE-------RDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        71 ~nl~-~~~-~~~-------~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      .|+= +.. ..+       ++|+..+.+||.|..|.++           .|..||+|.+.++++.|+++|+|.+|.|++|
T Consensus       405 ~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtV  484 (500)
T KOG0120|consen  405 TNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTV  484 (500)
T ss_pred             hhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEE
Confidence            5541 111 111       4566677899999999985           3689999999999999999999999999999


Q ss_pred             EEEEee
Q 026341          131 SVEYAL  136 (240)
Q Consensus       131 ~v~~a~  136 (240)
                      .+.|--
T Consensus       485 vtsYyd  490 (500)
T KOG0120|consen  485 VASYYD  490 (500)
T ss_pred             EEEecC
Confidence            988854

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.40  E-value=1.7e-12  Score=102.71  Aligned_cols=72  Identities=22%  Similarity=0.265  Sum_probs=66.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      .+.+|||+|| ++.+++++|+++|+.||+|..|.|.     +++|||+|+++++|+.|+. |+|..|.++.|.|.....
T Consensus         4 ~g~TV~V~NL-S~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNL-SPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecC-CCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            4689999999 8899999999999999999999995     4799999999999999995 999999999999988664

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=2.2e-12  Score=80.85  Aligned_cols=53  Identities=34%  Similarity=0.644  Sum_probs=49.2

Q ss_pred             HHHhhccCCCeEEEEEeC---CeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           83 IKRHFEPYGNVLHVRIRR---NFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~k---g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      |.++|++||+|..+.+..   ++|||+|.+.++|+.|+..|||..+.|++|.|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            678999999999999964   89999999999999999999999999999999986

(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 ....

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

Probab=99.39  E-value=1.3e-12  Score=115.75  Aligned_cols=124  Identities=29%  Similarity=0.392  Sum_probs=99.9

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC--CC-------CCC--------------------CC--
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR--HR-------DGS--------------------KS--   58 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~--~~-------~~~--------------------~~--   58 (240)
                      -|.|+|.++.+|.+|+..|+...+  ...+|+++|+......  +.       ...                    ..  
T Consensus       423 ~aiv~fl~p~eAr~Afrklaysr~--k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~t  500 (725)
T KOG0110|consen  423 GAIVEFLNPLEARKAFRKLAYSRF--KSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPT  500 (725)
T ss_pred             eeeeeecCccchHHHHHHhchhhh--ccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCcc
Confidence            389999999999999999999988  5888998887632211  00       000                    00  


Q ss_pred             -------CCCCCCC-CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHh
Q 026341           59 -------MANQRPT-KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALES  119 (240)
Q Consensus        59 -------~~~~~~~-~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~  119 (240)
                             ....... +.|||.|| ++.++.++|..+|...|.|..+.|.           .|||||+|.+.++|+.|+..
T Consensus       501 e~ss~a~~a~~~~~~t~lfvkNl-nf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~  579 (725)
T KOG0110|consen  501 EESSLARVAEDEETETKLFVKNL-NFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKA  579 (725)
T ss_pred             ccccchhhhhccccchhhhhhcC-CcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHH
Confidence                   0011112 33999999 9999999999999999999999883           39999999999999999999


Q ss_pred             cCCCcccCcEEEEEEee
Q 026341          120 TDRSKLVDRVISVEYAL  136 (240)
Q Consensus       120 l~g~~~~g~~l~v~~a~  136 (240)
                      |+|+.|+|+.|.|.++.
T Consensus       580 lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  580 LQGTVLDGHKLELKISE  596 (725)
T ss_pred             hcCceecCceEEEEecc
Confidence            99999999999999998

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=2.7e-12  Score=83.59  Aligned_cols=66  Identities=44%  Similarity=0.710  Sum_probs=60.8

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      +|+|.|| |..+++++|+++|.+||.|..+.+.      +++|||+|.+.++|+.|+..|++..+.|..|.|+
T Consensus         1 ~v~i~~l-~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNL-PPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCC-CCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            4899999 8899999999999999999998874      3899999999999999999999999999998763

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

Probab=99.36  E-value=2e-12  Score=116.14  Aligned_cols=74  Identities=30%  Similarity=0.482  Sum_probs=68.2

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ....++|||+|| ++.+++++|+++|.+||.|..|.|        .+|||||+|.+.++|+.||+.|||..|.|+.|.|.
T Consensus       104 ~~~~~rLfVGnL-p~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       104 LAIMCRVYVGSI-SFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hcCCCEEEEcCC-CCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            345789999999 999999999999999999999998        37999999999999999999999999999999998


Q ss_pred             Eee
Q 026341          134 YAL  136 (240)
Q Consensus       134 ~a~  136 (240)
                      +..
T Consensus       183 rp~  185 (612)
T TIGR01645       183 RPS  185 (612)
T ss_pred             ccc
Confidence            543

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.

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

Probab=99.36  E-value=8.8e-13  Score=101.69  Aligned_cols=79  Identities=29%  Similarity=0.552  Sum_probs=72.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ....+|||++| ...+++..|...|-+||.|..|.++        +|||||+|+-.|+|.+||..||+.+|.|++|.|.+
T Consensus         8 ~~KrtlYVGGl-adeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    8 NQKRTLYVGGL-ADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             ccceeEEeccc-hHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            44689999999 8899999999999999999999985        79999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 026341          135 ALKDDSER  142 (240)
Q Consensus       135 a~~~~~~~  142 (240)
                      |++..-+.
T Consensus        87 AkP~kike   94 (298)
T KOG0111|consen   87 AKPEKIKE   94 (298)
T ss_pred             cCCccccC
Confidence            99876543

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

Probab=99.34  E-value=1.2e-11  Score=105.70  Aligned_cols=130  Identities=25%  Similarity=0.256  Sum_probs=96.6

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHH
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRER   81 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~   81 (240)
                      +.+++..|-|||||.+++++++|++ ++-+.+  +.+-|.|-.+........-....+....+..+|-+.+| |+.|+++
T Consensus        43 r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~m--g~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGL-Pfscte~  118 (510)
T KOG4211|consen   43 RRNGRPSGEAYVEFTSEEDVEKALK-KDRESM--GHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGL-PFSCTEE  118 (510)
T ss_pred             ccCCCcCcceEEEeechHHHHHHHH-hhHHHh--CCceEEEEccCCccccccccCCCCCCCCCCceEEecCC-CccCcHH
Confidence            3468999999999999999999998 666666  46767776665443221111111122245678999999 9999999


Q ss_pred             HHHHhhccCCCeEE-EEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           82 DIKRHFEPYGNVLH-VRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        82 ~l~~~f~~~G~i~~-~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ||.+||+..-.|.. +.+       +.|-|||+|++.+.|++|+.. |...|.-+-|.|-.+.
T Consensus       119 dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  119 DIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             HHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            99999997744433 222       358999999999999999985 7778888888887664

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

Probab=99.34  E-value=1.9e-12  Score=100.98  Aligned_cols=72  Identities=22%  Similarity=0.419  Sum_probs=65.0

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|||++| +|.+..++|++.|++||+|++..|        .|||+||+|.+.+.|..|++. -+-.|+|++..|++|
T Consensus        11 ~~TKifVggL-~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   11 TFTKIFVGGL-AWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             eEEEEEEcCc-ccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            4678999999 999999999999999999999887        389999999999999999985 456899999999998


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      --
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            64

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

Probab=99.33  E-value=2.2e-12  Score=96.81  Aligned_cols=73  Identities=29%  Similarity=0.396  Sum_probs=68.7

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ....+|||+|| +..++++.|+++|-+.|+|..+.++        +|||||+|.++|+|+-|++.||...+.|++|.|..
T Consensus         7 nqd~tiyvgnl-d~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    7 NQDATLYVGNL-DEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             CCCceEEEecC-CHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            45789999999 8899999999999999999999985        69999999999999999999999999999999999


Q ss_pred             ee
Q 026341          135 AL  136 (240)
Q Consensus       135 a~  136 (240)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            87

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

Probab=99.31  E-value=4.9e-12  Score=100.42  Aligned_cols=94  Identities=22%  Similarity=0.468  Sum_probs=78.5

Q ss_pred             eEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCH
Q 026341           39 RLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQ  110 (240)
Q Consensus        39 ~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~  110 (240)
                      .|+|.|+.....+      ........-.|||+.| ...++.++|++.|.+||+|..++|.        |||+||.|-+.
T Consensus        42 e~~v~wa~~p~nQ------sk~t~~~hfhvfvgdl-s~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k  114 (321)
T KOG0148|consen   42 ELKVNWATAPGNQ------SKPTSNQHFHVFVGDL-SPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNK  114 (321)
T ss_pred             hhccccccCcccC------CCCccccceeEEehhc-chhcchHHHHHHhccccccccceEeecccCCcccceeEEeccch
Confidence            5667777654222      1223334678999999 6789999999999999999999983        79999999999


Q ss_pred             HHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341          111 EEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus       111 ~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|+.||..|||+-|.++.|...||..+.
T Consensus       115 ~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  115 EDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHHHHHHHHhCCeeeccceeeccccccCc
Confidence            99999999999999999999999998765

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

Probab=99.31  E-value=3.4e-11  Score=98.73  Aligned_cols=133  Identities=20%  Similarity=0.249  Sum_probs=103.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCC--------------------------
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS--------------------------   56 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~--------------------------   56 (240)
                      +.|+.||=|.|.|...++++.|+..|++..|  .|++|.|+-|.-..+......                          
T Consensus       178 ~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~--rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd  255 (382)
T KOG1548|consen  178 NQGKLKGDALCCYIKRESVELAIKILDEDEL--RGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPD  255 (382)
T ss_pred             CCCCccCceEEEeecccHHHHHHHHhCcccc--cCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCC
Confidence            3578899999999999999999999999999  699999998873322111100                          


Q ss_pred             -CCCCCCCCCCEEEEeccCC---CCCC-------HHHHHHhhccCCCeEEEEE----eCCeEEEEecCHHHHHHHHHhcC
Q 026341           57 -KSMANQRPTKTLFVINFDP---IRTR-------ERDIKRHFEPYGNVLHVRI----RRNFAFVQFETQEEATKALESTD  121 (240)
Q Consensus        57 -~~~~~~~~~~~l~v~nl~~---~~~~-------~~~l~~~f~~~G~i~~~~~----~kg~afV~f~~~~~a~~A~~~l~  121 (240)
                       ..+......++|.|.|+-.   +..+       .++|.+-+.+||.|..|.|    +.|.+-|.|.+.++|..||+.|+
T Consensus       256 ~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~  335 (382)
T KOG1548|consen  256 RDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMD  335 (382)
T ss_pred             ccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhc
Confidence             0122334567899998721   1223       3566777899999999988    58999999999999999999999


Q ss_pred             CCcccCcEEEEEEeec
Q 026341          122 RSKLVDRVISVEYALK  137 (240)
Q Consensus       122 g~~~~g~~l~v~~a~~  137 (240)
                      |..|+|+.|..++.-.
T Consensus       336 GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  336 GRWFDGRQLTASIWDG  351 (382)
T ss_pred             CeeecceEEEEEEeCC
Confidence            9999999999887543

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

Probab=99.30  E-value=5e-13  Score=100.15  Aligned_cols=73  Identities=23%  Similarity=0.473  Sum_probs=68.2

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...-|||+|| |+..|+.||..+|++||+|+.|.+.        +||||+.|++..+..-|+..|||..|.|+.|.|...
T Consensus        34 dsA~Iyiggl-~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   34 DSAYIYIGGL-PYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             cceEEEECCC-cccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            3678999999 9999999999999999999999994        799999999999999999999999999999999886


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      ..
T Consensus       113 ~~  114 (219)
T KOG0126|consen  113 SN  114 (219)
T ss_pred             cc
Confidence            54

>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=99.30  E-value=1.9e-11  Score=79.98  Aligned_cols=67  Identities=45%  Similarity=0.718  Sum_probs=62.0

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      +|+|.|| |..+++++|.++|..+|.|..+.+.       .++|||+|.+.++|..|++.+++..+.|..|.|.+
T Consensus         1 ~i~i~~l-~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNL-PPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCC-CCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999 8899999999999999999998884       58999999999999999999999999999998864

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).

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

Probab=99.29  E-value=6e-11  Score=100.01  Aligned_cols=133  Identities=26%  Similarity=0.374  Sum_probs=105.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCC------------------------------
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH------------------------------   52 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~------------------------------   52 (240)
                      ..++.+|+|.|||+++|.+++|++.||...+  .|++|+|+-........                              
T Consensus        81 ~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~--~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~  158 (608)
T KOG4212|consen   81 ESGKARGCAVVEFKDPENVQKALEKLNKYEV--NGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGG  158 (608)
T ss_pred             cCCCcCCceEEEeeCHHHHHHHHHHhhhccc--cCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCC
Confidence            4789999999999999999999999999999  69999997544211000                              


Q ss_pred             -----------CC--------CC-------------------------CCCCCCCCCCEEEEeccCCCCCCHHHHHHhhc
Q 026341           53 -----------RD--------GS-------------------------KSMANQRPTKTLFVINFDPIRTRERDIKRHFE   88 (240)
Q Consensus        53 -----------~~--------~~-------------------------~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~   88 (240)
                                 .+        ..                         ......+....+||.|| .+.+....|++.|.
T Consensus       159 ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl-~~~vg~~kL~qvfg  237 (608)
T KOG4212|consen  159 GGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANL-DYKVGNKKLKQVFG  237 (608)
T ss_pred             CCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeecc-ccccchHHHHHHhc
Confidence                       00        00                         01124455678999999 89999999999999


Q ss_pred             cCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           89 PYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        89 ~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      -.|.|..+.+       .+|+|.|+|..+-+|-+||..|++.-+..++.++.+..-.
T Consensus       238 mAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~~~~  294 (608)
T KOG4212|consen  238 MAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLDRIP  294 (608)
T ss_pred             cceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccccceeeccccc
Confidence            9999998887       3789999999999999999999988777788777775433

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

Probab=99.28  E-value=3.7e-11  Score=100.42  Aligned_cols=131  Identities=21%  Similarity=0.254  Sum_probs=105.9

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC---------CCC------CC-------------------
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG---------RHR------DG-------------------   55 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~---------~~~------~~-------------------   55 (240)
                      .|.|+|.|.+.|..|...|+|..|+.+...|.|.|++-..-         ...      .+                   
T Consensus       190 QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~  269 (492)
T KOG1190|consen  190 QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPA  269 (492)
T ss_pred             hhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhcccccccc
Confidence            48999999999999999999999986778899988872110         000      00                   


Q ss_pred             -----C-----------CCCCCCCC--CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHH
Q 026341           56 -----S-----------KSMANQRP--TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEAT  114 (240)
Q Consensus        56 -----~-----------~~~~~~~~--~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~  114 (240)
                           .           .......+  +.+|.|.||.++.+|.+.|..+|.-||.|..|+|.   +..|+|+|.+...|+
T Consensus       270 ~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAq  349 (492)
T KOG1190|consen  270 VHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQ  349 (492)
T ss_pred             ccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHH
Confidence                 0           00011112  57899999988999999999999999999999983   679999999999999


Q ss_pred             HHHHhcCCCcccCcEEEEEEeecCCC
Q 026341          115 KALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus       115 ~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      -|++.|+|..|.|+.|.|.+++-..-
T Consensus       350 LA~~hL~g~~l~gk~lrvt~SKH~~v  375 (492)
T KOG1190|consen  350 LAMEHLEGHKLYGKKLRVTLSKHTNV  375 (492)
T ss_pred             HHHHHhhcceecCceEEEeeccCccc
Confidence            99999999999999999999986554

>smart00360 RRM RNA recognition motif

Probab=99.28  E-value=1.4e-11  Score=79.84  Aligned_cols=63  Identities=37%  Similarity=0.646  Sum_probs=57.5

Q ss_pred             EeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           70 VINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        70 v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      |+|| |..+++++|+++|.+||.|..+.+.        +++|||+|.+.++|..|+..|++..+.|+.|.|+
T Consensus         1 i~~l-~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNL-PPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCC-CcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            5788 8899999999999999999999883        4699999999999999999999999999998873

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

Probab=99.27  E-value=7.8e-11  Score=98.52  Aligned_cols=127  Identities=24%  Similarity=0.324  Sum_probs=102.3

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC-----------------------CCCCCCC-CCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR-----------------------DGSKSMA-NQR   63 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~-----------------------~~~~~~~-~~~   63 (240)
                      +--|.|+|.|...|+.|++.|+|..|+  |++|.|.+++...-+..                       .+.++.. ..+
T Consensus       335 kd~ALIQmsd~~qAqLA~~hL~g~~l~--gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~P  412 (492)
T KOG1190|consen  335 KDNALIQMSDGQQAQLAMEHLEGHKLY--GKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFP  412 (492)
T ss_pred             CcceeeeecchhHHHHHHHHhhcceec--CceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCC
Confidence            467999999999999999999999995  99999999985432211                       0111222 347


Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCe-EEEEE-e--CCeEEEEecCHHHHHHHHHhcCCCcccC-cEEEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNV-LHVRI-R--RNFAFVQFETQEEATKALESTDRSKLVD-RVISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i-~~~~~-~--kg~afV~f~~~~~a~~A~~~l~g~~~~g-~~l~v~~a~~  137 (240)
                      |+.+|++.|+ |..+++++|+++|..-|.. ....+ .  +.+|++.+++.|+|..|+..||+..+.+ ..|.|.|++.
T Consensus       413 psatlHlsni-p~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  413 PSATLHLSNI-PPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             chhheeeccC-CcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            7899999999 8899999999999988754 44443 2  4699999999999999999999999876 5899999874

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

Probab=99.26  E-value=4.3e-11  Score=98.27  Aligned_cols=72  Identities=40%  Similarity=0.650  Sum_probs=67.6

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+|||+|| +..+++++|.++|.+||.|..+.+        .+|+|||+|.+.++|..|+..|++..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL-~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNL-PYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCC-CCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            699999999 899999999999999999988877        36999999999999999999999999999999999976


Q ss_pred             c
Q 026341          137 K  137 (240)
Q Consensus       137 ~  137 (240)
                      .
T Consensus       194 ~  194 (306)
T COG0724         194 P  194 (306)
T ss_pred             c
Confidence            4

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

Probab=99.25  E-value=1e-10  Score=98.65  Aligned_cols=72  Identities=26%  Similarity=0.380  Sum_probs=65.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...|+|||.|| |+++||+.|++-|..||.|.++.|+   +..+.|.|.++++|+.|+..|+|..++|+.|.|.|.
T Consensus       534 rKa~qIiirNl-P~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNL-PFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecC-CccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            44688999999 9999999999999999999999984   446689999999999999999999999999999873

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

Probab=99.23  E-value=1.5e-10  Score=88.72  Aligned_cols=42  Identities=45%  Similarity=0.695  Sum_probs=39.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .|.+++|||||-|.+..||++|++.|+|.+|  +|+.|.|++|.
T Consensus        50 ~Tr~sRgFaFVrf~~k~daedA~damDG~~l--dgRelrVq~ar   91 (256)
T KOG4207|consen   50 YTRQSRGFAFVRFHDKRDAEDALDAMDGAVL--DGRELRVQMAR   91 (256)
T ss_pred             ccccccceeEEEeeecchHHHHHHhhcceee--ccceeeehhhh
Confidence            3778899999999999999999999999999  79999999887

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

Probab=99.20  E-value=9.3e-11  Score=97.06  Aligned_cols=130  Identities=18%  Similarity=0.203  Sum_probs=101.4

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccC-CCCCCHHHHHH
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFD-PIRTRERDIKR   85 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~-~~~~~~~~l~~   85 (240)
                      .+-.|.|+|+|.+-|+.|+.......+.+.|+...++++..+......    .....++..|.+.=|+ -+.+|.+.|..
T Consensus        66 ~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~R~g----~es~~pN~VLl~TIlNp~YpItvDVly~  141 (494)
T KOG1456|consen   66 HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIERPG----DESATPNKVLLFTILNPQYPITVDVLYT  141 (494)
T ss_pred             ccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhccCC----CCCCCCCeEEEEEeecCccccchhhhhh
Confidence            467899999999999999985545555558999999998654322211    1233455666555443 47899999999


Q ss_pred             hhccCCCeEEEEEeC---CeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCCC
Q 026341           86 HFEPYGNVLHVRIRR---NFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDDS  140 (240)
Q Consensus        86 ~f~~~G~i~~~~~~k---g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~  140 (240)
                      ++...|+|..|.|.+   -.|+|||++.+.|++|...|||..|.-  ++|+|+||++.+-
T Consensus       142 Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  142 ICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             hcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCccee
Confidence            999999999999864   279999999999999999999998863  8999999997653

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

Probab=99.18  E-value=7e-10  Score=82.95  Aligned_cols=43  Identities=47%  Similarity=0.645  Sum_probs=39.3

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +..|||||||+++.||++|+..|+|..|+  |..|.|+++.....
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~c--G~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDIC--GSRIRVELSTGRPR   87 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCcccc--CceEEEEeecCCcc
Confidence            56899999999999999999999999995  99999999996554

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

Probab=99.18  E-value=8.8e-11  Score=91.35  Aligned_cols=78  Identities=27%  Similarity=0.513  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHH----hhccCCCeEEEEE-----eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKR----HFEPYGNVLHVRI-----RRNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~----~f~~~G~i~~~~~-----~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...++.+|||.|| ...+..++|+.    +|++||+|..|..     ++|.|||.|.+.+.|..|+..|+|..+.|+++.
T Consensus         5 ~~~pn~TlYInnL-nekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    5 SVNPNGTLYINNL-NEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             ccCCCceEeehhc-cccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3455669999999 88899998887    9999999999988     479999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |+||+...
T Consensus        84 iqyA~s~s   91 (221)
T KOG4206|consen   84 IQYAKSDS   91 (221)
T ss_pred             eecccCcc
Confidence            99998654

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

Probab=99.15  E-value=1.1e-10  Score=101.07  Aligned_cols=74  Identities=27%  Similarity=0.507  Sum_probs=70.2

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ..|||+|+ |+.+++++|..+|+..|.|..+++        ++||||++|.+.++|+.|+..|||.++.|++|+|.|+..
T Consensus        19 ~~v~vgni-p~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNI-PYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCC-CCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            89999999 999999999999999999999988        489999999999999999999999999999999999986


Q ss_pred             CCC
Q 026341          138 DDS  140 (240)
Q Consensus       138 ~~~  140 (240)
                      ...
T Consensus        98 ~~~  100 (435)
T KOG0108|consen   98 RKN  100 (435)
T ss_pred             cch
Confidence            554

>smart00361 RRM_1 RNA recognition motif

Probab=99.10  E-value=2.6e-10  Score=74.72  Aligned_cols=53  Identities=25%  Similarity=0.523  Sum_probs=47.3

Q ss_pred             HHHHHHhhc----cCCCeEEEE-E----------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           80 ERDIKRHFE----PYGNVLHVR-I----------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        80 ~~~l~~~f~----~~G~i~~~~-~----------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      +++|+++|.    +||.|..+. |          ++|+|||+|.+.++|++|+..|||..+.|+.|.+
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            578888888    999999884 2          2689999999999999999999999999999976

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

Probab=99.09  E-value=1.6e-10  Score=100.79  Aligned_cols=130  Identities=22%  Similarity=0.363  Sum_probs=103.5

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC------------CCCCCCCCCCCCCEEEEeccC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR------------DGSKSMANQRPTKTLFVINFD   74 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~------------~~~~~~~~~~~~~~l~v~nl~   74 (240)
                      .++||||+|.+.++|..|+. +++..+  .|.++++--.......+.            .....+......+.|+|++| 
T Consensus       222 ~~nfa~ie~~s~~~at~~~~-~~~~~f--~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~l-  297 (500)
T KOG0120|consen  222 EKNFAFIEFRSISEATEAMA-LDGIIF--EGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGL-  297 (500)
T ss_pred             cccceeEEecCCCchhhhhc-ccchhh--CCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccC-
Confidence            48999999999999999998 888888  588887764432221111            01112234445678999999 


Q ss_pred             CCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           75 PIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        75 ~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      |..+++.++.+++..||.+....+        .+||||.+|.+......|+..|||..+.+.+|.|+.|-....
T Consensus       298 p~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~  371 (500)
T KOG0120|consen  298 PLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGAS  371 (500)
T ss_pred             cCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccch
Confidence            999999999999999999887666        479999999999999999999999999999999999875443

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

Probab=99.08  E-value=2.9e-10  Score=101.91  Aligned_cols=76  Identities=26%  Similarity=0.508  Sum_probs=70.6

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ...+||||++| +..++++||.++|+.||+|..|.+  ++++|||.+....+|++|+.+|.+..+.+..|+|.||....
T Consensus       419 V~SrTLwvG~i-~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G  496 (894)
T KOG0132|consen  419 VCSRTLWVGGI-PKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKG  496 (894)
T ss_pred             Eeeeeeeeccc-cchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCC
Confidence            34689999999 999999999999999999999998  58999999999999999999999999999999999997543

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

Probab=99.07  E-value=1.9e-10  Score=94.71  Aligned_cols=77  Identities=27%  Similarity=0.560  Sum_probs=69.9

Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC--------CeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k--------g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+|.++|||..|+| -++.++|.-+|+.||+|..|.|.+        .||||+|++.+++++|.-.|++..|+++.|.
T Consensus       234 d~~PPeNVLFVCKLNP-VTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIH  312 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNP-VTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIH  312 (479)
T ss_pred             ccCCCcceEEEEecCC-cccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEE
Confidence            3567889999999955 688899999999999999999953        5999999999999999999999999999999


Q ss_pred             EEEeec
Q 026341          132 VEYALK  137 (240)
Q Consensus       132 v~~a~~  137 (240)
                      |.|+..
T Consensus       313 VDFSQS  318 (479)
T KOG0415|consen  313 VDFSQS  318 (479)
T ss_pred             eehhhh
Confidence            999864

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

Probab=99.06  E-value=2e-10  Score=90.03  Aligned_cols=74  Identities=30%  Similarity=0.575  Sum_probs=69.6

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ..|||++| ++.+.+.+|..+|..||.|..+.+..+|+||+|++..+|..||..||+..|.|..+.|+|++....
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 PRVYIGRL-PYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             Cceeeccc-CCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            36899999 999999999999999999999999999999999999999999999999999998899999986543

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

Probab=99.03  E-value=7.9e-10  Score=90.86  Aligned_cols=76  Identities=29%  Similarity=0.482  Sum_probs=66.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc-CCCcccCcEEEEEEeec
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST-DRSKLVDRVISVEYALK  137 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l-~g~~~~g~~l~v~~a~~  137 (240)
                      ....-.+|||++| ...+++.+|.++|.+||+|..+.+.  +++|||+|.+.+.|+.|...+ +...|+|..|.|.|..+
T Consensus       224 eD~~I~tLyIg~l-~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  224 EDTSIKTLYIGGL-NDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeEEEeccc-ccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            3344689999999 5589999999999999999999884  689999999999999988754 66789999999999987

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

Probab=98.99  E-value=3.7e-10  Score=93.37  Aligned_cols=70  Identities=31%  Similarity=0.528  Sum_probs=65.7

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .-|.|||+.+ .+.+.++.|+..|..||+|+.|.+        .||||||+|+-+|.|+-|++.|||.+++|+.|+|..
T Consensus       112 iMcRvYVGSI-sfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  112 IMCRVYVGSI-SFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HhHheeeeee-EEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            3588999999 899999999999999999999998        389999999999999999999999999999999863

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.99  E-value=9.2e-11  Score=97.56  Aligned_cols=72  Identities=14%  Similarity=0.045  Sum_probs=56.9

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      .+|+|++| +..+...++.++|..+|+|.+..+.    ..+|.|+|........|+. ++|.++.-+...+.+.++..
T Consensus       152 Rt~~v~sl-~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP~k  227 (479)
T KOG4676|consen  152 RTREVQSL-ISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKPHK  227 (479)
T ss_pred             hhhhhhcc-hhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCccc
Confidence            56889999 7788889999999999999887773    4588899999999999987 58887776555555555443

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

Probab=98.96  E-value=9e-10  Score=87.60  Aligned_cols=92  Identities=27%  Similarity=0.464  Sum_probs=75.7

Q ss_pred             CceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecC
Q 026341           37 RRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFET  109 (240)
Q Consensus        37 g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~  109 (240)
                      .++|.|+.+..+...           -..++|||+-| .....|+|++.+|..||.|.+|.+       .||+|||.|.+
T Consensus         2 nrpiqvkpadsesrg-----------~~drklfvgml-~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s   69 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG-----------GDDRKLFVGML-NKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSS   69 (371)
T ss_pred             CCCccccccccccCC-----------ccchhhhhhhh-cccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEecc
Confidence            456777777654422           13678999999 788999999999999999999998       48999999999


Q ss_pred             HHHHHHHHHhcCCCc-ccC--cEEEEEEeecCCC
Q 026341          110 QEEATKALESTDRSK-LVD--RVISVEYALKDDS  140 (240)
Q Consensus       110 ~~~a~~A~~~l~g~~-~~g--~~l~v~~a~~~~~  140 (240)
                      ..+|+.||..|||.. +-|  ..|.|+|+...++
T Consensus        70 ~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkE  103 (371)
T KOG0146|consen   70 HAEAQAAINALHGSQTMPGASSSLVVKFADTDKE  103 (371)
T ss_pred             chHHHHHHHHhcccccCCCCccceEEEeccchHH
Confidence            999999999999974 444  7889999876554

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

Probab=98.92  E-value=2.7e-09  Score=79.89  Aligned_cols=46  Identities=28%  Similarity=0.408  Sum_probs=41.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .|++++|||||+|.+.++|++||+.||+..|  +|++|+|+++.....
T Consensus        71 ~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i--~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         71 ETGRSRGFGFVNFNDEGAATAAISEMDGKEL--NGRHIRVNPANDRPS  116 (144)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEeCCcCCC
Confidence            4778899999999999999999999999999  699999999986543

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

Probab=98.91  E-value=4.7e-09  Score=91.46  Aligned_cols=78  Identities=35%  Similarity=0.542  Sum_probs=69.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+..|||.+| ...+...+|+++|++||+|+..+|.        ++|+||++.+.++|.+||..||.++|.|+.|.|+
T Consensus       402 s~~gRNlWVSGL-SstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVE  480 (940)
T KOG4661|consen  402 STLGRNLWVSGL-SSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVE  480 (940)
T ss_pred             cccccceeeecc-ccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeee
Confidence            345678999999 7678889999999999999988873        5799999999999999999999999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      .++....
T Consensus       481 kaKNEp~  487 (940)
T KOG4661|consen  481 KAKNEPG  487 (940)
T ss_pred             ecccCcc
Confidence            9986543

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

Probab=98.87  E-value=1.5e-08  Score=78.75  Aligned_cols=77  Identities=19%  Similarity=0.357  Sum_probs=66.8

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCccc---CcEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLV---DRVIS  131 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~---g~~l~  131 (240)
                      ...+|||.+| |.++...+|..+|..|-..+.+.|.         +-+|||.|.+..+|++|++.|||..|+   +.+|.
T Consensus        33 ~VRTLFVSGL-P~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   33 AVRTLFVSGL-PNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             ccceeeeccC-CcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            4689999999 9999999999999998766655552         369999999999999999999999886   78999


Q ss_pred             EEEeecCCCC
Q 026341          132 VEYALKDDSE  141 (240)
Q Consensus       132 v~~a~~~~~~  141 (240)
                      |++|+...+.
T Consensus       112 iElAKSNtK~  121 (284)
T KOG1457|consen  112 IELAKSNTKR  121 (284)
T ss_pred             eeehhcCccc
Confidence            9999876543

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

Probab=98.84  E-value=4.1e-08  Score=84.83  Aligned_cols=73  Identities=23%  Similarity=0.399  Sum_probs=63.6

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+|||.|| |.++++.+|+++|.+||.|+...|.        .+||||+|.+.++++.||++ +-..|++++|.|+.-
T Consensus       287 ~~~~i~V~nl-P~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  287 DGLGIFVKNL-PPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             cccceEeecC-CCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            3456999999 9999999999999999999887762        27999999999999999996 577899999999886


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      +..
T Consensus       365 ~~~  367 (419)
T KOG0116|consen  365 RPG  367 (419)
T ss_pred             ccc
Confidence            653

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

Probab=98.82  E-value=1.6e-08  Score=77.75  Aligned_cols=77  Identities=25%  Similarity=0.427  Sum_probs=68.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccC-CCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPY-GNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~-G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .......++|..+ |..+.+.+|...|.+| |.|..+.+        .+|||||+|++++.|+-|.+.||+..|.++-|.
T Consensus        45 ~~~~~g~~~~~~~-p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   45 EQEIEGVVYVDHI-PHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             ccCCccceeeccc-ccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            4455678999999 8899999999999998 67777777        379999999999999999999999999999999


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      |.+..+.
T Consensus       124 c~vmppe  130 (214)
T KOG4208|consen  124 CHVMPPE  130 (214)
T ss_pred             eEEeCch
Confidence            9998766

>PF13893 RRM_5: RNA recognition motif

Probab=98.80  E-value=1.1e-08  Score=63.86  Aligned_cols=36  Identities=44%  Similarity=0.662  Sum_probs=34.2

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      +++|||+|.+.++|+.|++.|||..|  .|++|.|+||
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~--~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQF--NGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEE--TTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEC
Confidence            49999999999999999999999999  6999999986

(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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=98.79  E-value=8.7e-09  Score=67.44  Aligned_cols=36  Identities=36%  Similarity=0.495  Sum_probs=33.8

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEE
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSV   42 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v   42 (240)
                      +.++|||||+|.+.++|.+|+..|||..|  +|+.|.+
T Consensus        34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~~--~gr~l~~   69 (70)
T smart00361       34 NHKRGNVYITFERSEDAARAIVDLNGRYF--DGRTVKA   69 (70)
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEe
Confidence            77899999999999999999999999999  6999876

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

Probab=98.79  E-value=7e-09  Score=79.70  Aligned_cols=45  Identities=24%  Similarity=0.213  Sum_probs=41.5

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++||++||||||||++++.|+-|-+.||+.+|+  ++.|.|.+-.+.
T Consensus        86 krTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~--e~lL~c~vmppe  130 (214)
T KOG4208|consen   86 KRTGNSKGYAFVEFESEEVAKIAAETMNNYLLM--EHLLECHVMPPE  130 (214)
T ss_pred             cccCCcCceEEEEeccHHHHHHHHHHhhhhhhh--hheeeeEEeCch
Confidence            469999999999999999999999999999995  999999988765

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

Probab=98.76  E-value=4.5e-08  Score=80.18  Aligned_cols=93  Identities=25%  Similarity=0.384  Sum_probs=73.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC----CCCCCC---------CCCCCCCCCCCCCEEE
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG----ERGRHR---------DGSKSMANQRPTKTLF   69 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~----~~~~~~---------~~~~~~~~~~~~~~l~   69 (240)
                      .++.++|||||+|.++++|..|+..|++..|  .|+.|.|.++..    ......         ..............++
T Consensus       152 ~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~--~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (306)
T COG0724         152 ETGKSRGFAFVEFESEESAEKAIEELNGKEL--EGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLY  229 (306)
T ss_pred             ccCccCceEEEEecCHHHHHHHHHHcCCCeE--CCceeEeeccccccccccccccccchhhhccccccccccccccceee
Confidence            4788999999999999999999999999999  699999999642    111110         0111223445678899


Q ss_pred             EeccCCCCCCHHHHHHhhccCCCeEEEEE
Q 026341           70 VINFDPIRTRERDIKRHFEPYGNVLHVRI   98 (240)
Q Consensus        70 v~nl~~~~~~~~~l~~~f~~~G~i~~~~~   98 (240)
                      +.++ +..++..++..+|..+|.+....+
T Consensus       230 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  257 (306)
T COG0724         230 VGNL-PLKTAEEELADLFKSRGDIVRASL  257 (306)
T ss_pred             cccc-ccccchhHHHHhccccccceeeec
Confidence            9999 889999999999999999976666

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.72  E-value=4.6e-08  Score=81.10  Aligned_cols=131  Identities=21%  Similarity=0.272  Sum_probs=97.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCC-cccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEE-EeccCCCCCCH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNI-PFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLF-VINFDPIRTRE   80 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~-~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~-v~nl~~~~~~~   80 (240)
                      ..+.++|++.|.|+..+.+..|+. +.+. .+  .+..+...+............ ......+..+++ |.+| ++.++.
T Consensus       125 ~~~~sk~~~s~~f~~ks~~~~~l~-~s~~~~~--~~~~~~~dl~~~~~~~~~n~~-~~~~~~~s~~~~~~~~~-~f~~~~  199 (285)
T KOG4210|consen  125 DSLSSKGGLSVHFAGKSQFFAALE-ESGSKVL--DGNKGEKDLNTRRGLRPKNKL-SRLSSGPSDTIFFVGEL-DFSLTR  199 (285)
T ss_pred             cccccccceeeccccHHHHHHHHH-hhhcccc--ccccccCcccccccccccchh-cccccCccccceeeccc-ccccch
Confidence            356679999999999999999998 4443 44  355555444443321111111 112233445555 9999 999999


Q ss_pred             HHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           81 RDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        81 ~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|+.+|..+|.|..+.++        +++|+|.|.+...+..|+.. +...+.+.++.|....+..
T Consensus       200 d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  200 DDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             HHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            9999999999999999884        68999999999999999987 8889999999998877654

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

Probab=98.69  E-value=8.4e-08  Score=77.03  Aligned_cols=75  Identities=21%  Similarity=0.348  Sum_probs=67.4

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...|+|.|| ++.++++||+++|..||.+..+.|       ..|.|-|.|...++|..||+.+||..++|..+.++....
T Consensus        83 ~~~v~v~NL-~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNL-PYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecC-CcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            478999999 999999999999999998887777       368999999999999999999999999999999988765


Q ss_pred             CCC
Q 026341          138 DDS  140 (240)
Q Consensus       138 ~~~  140 (240)
                      ...
T Consensus       162 ~~~  164 (243)
T KOG0533|consen  162 PSQ  164 (243)
T ss_pred             ccc
Confidence            443

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

Probab=98.66  E-value=8.9e-09  Score=79.75  Aligned_cols=76  Identities=21%  Similarity=0.204  Sum_probs=67.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC------CeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR------NFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k------g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..+...+|||+|+ ...++++.|.++|-+.|+|..|.|++      .||||+|.++....-|++.|||..+.+..|.|.+
T Consensus         5 aae~drtl~v~n~-~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    5 AAEMDRTLLVQNM-YSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             CcchhhHHHHHhh-hhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3445689999999 78999999999999999999999963      3999999999999999999999999999998887


Q ss_pred             eec
Q 026341          135 ALK  137 (240)
Q Consensus       135 a~~  137 (240)
                      -..
T Consensus        84 r~G   86 (267)
T KOG4454|consen   84 RCG   86 (267)
T ss_pred             ccC
Confidence            543

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

Probab=98.58  E-value=3.9e-08  Score=82.00  Aligned_cols=128  Identities=21%  Similarity=0.232  Sum_probs=88.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC--------------CCC----CC---CCC-CCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER--------------GRH----RD---GSK-SMAN   61 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~--------------~~~----~~---~~~-~~~~   61 (240)
                      .++..|-|||.|..+++|+.|+.+ |...|   |+. +|+......              -..    ..   ... ....
T Consensus       202 dgrpTGdAFvlfa~ee~aq~aL~k-hrq~i---GqR-YIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~  276 (508)
T KOG1365|consen  202 DGRPTGDAFVLFACEEDAQFALRK-HRQNI---GQR-YIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPP  276 (508)
T ss_pred             CCCcccceEEEecCHHHHHHHHHH-HHHHH---hHH-HHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCC
Confidence            567789999999999999999974 33333   221 222211000              000    00   000 1112


Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCC-CeEE--EEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYG-NVLH--VRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~--~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .....+|-+.+| |+..+.++|.++|..|. .|..  |.+       +.|-|||+|.+++.|..|....|++.+..+.|.
T Consensus       277 ~~~kdcvRLRGL-Py~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiE  355 (508)
T KOG1365|consen  277 TRSKDCVRLRGL-PYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIE  355 (508)
T ss_pred             CCCCCeeEecCC-ChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEE
Confidence            233678999999 99999999999999886 3433  444       468999999999999999999898888888888


Q ss_pred             EEEeec
Q 026341          132 VEYALK  137 (240)
Q Consensus       132 v~~a~~  137 (240)
                      |--+..
T Consensus       356 vfp~S~  361 (508)
T KOG1365|consen  356 VFPCSV  361 (508)
T ss_pred             EeeccH
Confidence            876643

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

Probab=98.57  E-value=5.9e-08  Score=75.31  Aligned_cols=47  Identities=34%  Similarity=0.482  Sum_probs=42.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH   52 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~   52 (240)
                      +.+++|||||+|+..|||..||..||+.+|+  |+.|.|++|.+.+...
T Consensus        48 sqkHRgFgFVefe~aEDAaaAiDNMnesEL~--GrtirVN~AkP~kike   94 (298)
T KOG0111|consen   48 SQKHRGFGFVEFEEAEDAAAAIDNMNESELF--GRTIRVNLAKPEKIKE   94 (298)
T ss_pred             cccccceeEEEeeccchhHHHhhcCchhhhc--ceeEEEeecCCccccC
Confidence            5678999999999999999999999999996  9999999999876543

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

Probab=98.56  E-value=5.2e-08  Score=84.89  Aligned_cols=70  Identities=27%  Similarity=0.508  Sum_probs=64.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+..+|+|-|| |..+++++|..+|+.||+|..|..   ..+.+||+|.+..+|+.|+++|++.+|.|+.|+
T Consensus        71 ~~~~~~~L~v~nl-~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNL-PRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEec-CCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3456789999999 889999999999999999999776   479999999999999999999999999998887

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.54  E-value=5.3e-07  Score=62.29  Aligned_cols=72  Identities=18%  Similarity=0.313  Sum_probs=60.4

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccC--CCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCccc----CcEEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLV----DRVIS  131 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~--G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~----g~~l~  131 (240)
                      +||.|.|| |...+.++|.+++...  |....+.++        .|||||.|.+++.|....+.++|..+.    .+.+.
T Consensus         2 TTvMirNI-Pn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNI-PNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecC-CCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            68999999 9999999999988753  555555553        699999999999999999999999886    47888


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      |.||+-+
T Consensus        81 i~yAriQ   87 (97)
T PF04059_consen   81 ISYARIQ   87 (97)
T ss_pred             EehhHhh
Confidence            8888754

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.54  E-value=1.8e-07  Score=74.18  Aligned_cols=122  Identities=11%  Similarity=0.164  Sum_probs=90.8

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHH
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR   85 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~   85 (240)
                      ...++||+.|.....-.++-..-+++.+  +-.+|++.-.......     ...........||++.| ...++++.|-.
T Consensus       138 ~~~~~~~~~~k~s~a~~k~~~~~~~Kki--~~~~VR~a~gtswedP-----sl~ew~~~DfRIfcgdl-gNevnd~vl~r  209 (290)
T KOG0226|consen  138 PIRPEAFESFKASDALLKAETEKEKKKI--GKPPVRLAAGTSWEDP-----SLAEWDEDDFRIFCGDL-GNEVNDDVLAR  209 (290)
T ss_pred             ccCcccccCcchhhhhhhhccccccccc--cCcceeeccccccCCc-----ccccCccccceeecccc-cccccHHHHHH
Confidence            4579999999988877777777777777  3444444333222211     11123344678999999 77899999999


Q ss_pred             hhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           86 HFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        86 ~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .|.+|-.....++        .+||+||.|.+.+++..|+..|+|..++.++|++.-+
T Consensus       210 af~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  210 AFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            9999875555544        4799999999999999999999999999998877544

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

Probab=98.53  E-value=3e-07  Score=64.92  Aligned_cols=71  Identities=30%  Similarity=0.382  Sum_probs=45.8

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCC--eEEEEecCHHHHHHHHHhcC-----CCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTD-----RSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg--~afV~f~~~~~a~~A~~~l~-----g~~~~g~~l~v~~a~  136 (240)
                      ++.|+|.++ ...++.++|+++|.+||.|.+|.+.+|  .|||-|.+.+.|+.|+..+.     +..|.+..+.++...
T Consensus         1 G~il~~~g~-~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLe   78 (105)
T PF08777_consen    1 GCILKFSGL-GEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLE   78 (105)
T ss_dssp             --EEEEEE---SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---
T ss_pred             CeEEEEecC-CCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECC
Confidence            367899999 778999999999999999999999876  89999999999999998763     346778777777654

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

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

Probab=98.53  E-value=3.4e-07  Score=75.53  Aligned_cols=78  Identities=15%  Similarity=0.269  Sum_probs=67.8

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--------EEE-------eCCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--------VRI-------RRNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--------~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      ...++.|||.|| |.++|.+++.++|.++|.|..        |.|       .+|-|++.|-..+++.-|++.|++..|.
T Consensus       131 ~~~Nt~VYVsgL-P~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGL-PLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCC-CCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            344677999999 999999999999999997753        333       4799999999999999999999999999


Q ss_pred             CcEEEEEEeecCCC
Q 026341          127 DRVISVEYALKDDS  140 (240)
Q Consensus       127 g~~l~v~~a~~~~~  140 (240)
                      |+.|.|+.|+-+..
T Consensus       210 g~~~rVerAkfq~K  223 (382)
T KOG1548|consen  210 GKKLRVERAKFQMK  223 (382)
T ss_pred             CcEEEEehhhhhhc
Confidence            99999999975543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.53  E-value=8.6e-07  Score=71.26  Aligned_cols=76  Identities=24%  Similarity=0.379  Sum_probs=67.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .......+||+|+ .+.++.+++..+|+.||.|..+.|        +++|+||+|.+.+.++.|+. ||+..|.|..+.|
T Consensus        97 ~~~d~~sv~v~nv-d~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   97 KEVDAPSVWVGNV-DFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hccCCceEEEecc-ccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            3445788999999 888999999999999999987776        37899999999999999999 9999999999999


Q ss_pred             EEeecC
Q 026341          133 EYALKD  138 (240)
Q Consensus       133 ~~a~~~  138 (240)
                      .+..-.
T Consensus       175 t~~r~~  180 (231)
T KOG4209|consen  175 TLKRTN  180 (231)
T ss_pred             eeeeee
Confidence            998765

>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=98.51  E-value=4.2e-07  Score=60.06  Aligned_cols=70  Identities=26%  Similarity=0.407  Sum_probs=48.6

Q ss_pred             CEEEEeccCCCCCCHHH----HHHhhccCC-CeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           66 KTLFVINFDPIRTRERD----IKRHFEPYG-NVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~----l~~~f~~~G-~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..|+|.|| |.+.+...    |++++..+| .|..|  ..+.|+|.|.+++.|..|.+.|+|..+.|..|.|.|....
T Consensus         3 s~L~V~NL-P~~~d~~~I~~RL~qLsdNCGGkVl~v--~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNL-PTNKDPSSIKNRLRQLSDNCGGKVLSV--SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES---TTS-HHHHHHHHHHHHHTTT--EEE----TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecC-CCCCCHHHHHHHHHHHhhccCCEEEEE--eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            46999999 87777655    566666776 66665  6899999999999999999999999999999999998544

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.51  E-value=1.8e-07  Score=83.65  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      .+.++.|||+|| +..++++.|...|..||+|..+.|+           ..++||.|-+..+|++|++.|+|..+.+..+
T Consensus       171 DP~TTNlyv~Nl-npsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  171 DPQTTNLYVGNL-NPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCcccceeeecC-CccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            345688999999 6689999999999999999999984           4799999999999999999999999999999


Q ss_pred             EEEEeec
Q 026341          131 SVEYALK  137 (240)
Q Consensus       131 ~v~~a~~  137 (240)
                      ++.|++.
T Consensus       250 K~gWgk~  256 (877)
T KOG0151|consen  250 KLGWGKA  256 (877)
T ss_pred             eeccccc
Confidence            9999864

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

Probab=98.48  E-value=1.5e-07  Score=78.55  Aligned_cols=75  Identities=25%  Similarity=0.443  Sum_probs=66.4

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC--------CeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k--------g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|||++| .+.++++.|++.|.+||+|..|.+++        +|+||+|++.+...++|.. ....|+|+.|.+.-|
T Consensus         5 ~~~KlfiGgi-sw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    5 ESGKLFIGGL-SWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRA   82 (311)
T ss_pred             CCcceeecCc-CccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceec
Confidence            4688999999 99999999999999999999999964        9999999999998888863 556889999999888


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      .+...
T Consensus        83 v~r~~   87 (311)
T KOG4205|consen   83 VSRED   87 (311)
T ss_pred             cCccc
Confidence            87654

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

Probab=98.46  E-value=1.3e-07  Score=67.87  Aligned_cols=45  Identities=24%  Similarity=0.361  Sum_probs=41.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +||-.||||+|+|++.++|++||..|||..|+  |++|.|.|+..+.
T Consensus       109 RtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll--~q~v~VDw~Fv~g  153 (170)
T KOG0130|consen  109 RTGYVKGYALVEYETLKEAQAAIDALNGAELL--GQNVSVDWCFVKG  153 (170)
T ss_pred             ccccccceeeeehHhHHHHHHHHHhccchhhh--CCceeEEEEEecC
Confidence            47788999999999999999999999999995  9999999998544

>PF00076 RRM_1: RNA recognition motif

Probab=98.43  E-value=3.1e-07  Score=59.52  Aligned_cols=36  Identities=33%  Similarity=0.562  Sum_probs=32.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEE
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLS   41 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~   41 (240)
                      ++..+|||||+|.+.++|++|++.|||..|  +|++|+
T Consensus        35 ~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~--~~~~ir   70 (70)
T PF00076_consen   35 SGKSKGYAFVEFESEEDAEKALEELNGKKI--NGRKIR   70 (70)
T ss_dssp             TSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             cccccceEEEEEcCHHHHHHHHHHcCCCEE--CccCcC
Confidence            466799999999999999999999999999  688774

(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 ....

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.42  E-value=1.4e-07  Score=85.97  Aligned_cols=108  Identities=19%  Similarity=0.250  Sum_probs=91.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      ++++.+|+|+|+|..+++|.+||....++.+   |                           ...|+|.|+ |+..|.++
T Consensus       704 n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~---g---------------------------K~~v~i~g~-pf~gt~e~  752 (881)
T KOG0128|consen  704 NEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF---G---------------------------KISVAISGP-PFQGTKEE  752 (881)
T ss_pred             hccccccceeeEeecCCchhhhhhhhhhhhh---h---------------------------hhhhheeCC-CCCCchHH
Confidence            4667799999999999999999995555555   3                           235789999 99999999


Q ss_pred             HHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCC
Q 026341           83 IKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSE  141 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  141 (240)
                      |+.++..+|.++.+.+       ++|.|+|.|.++.+|..++..++...+.-..+.|+.+.+...+
T Consensus       753 ~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~~K  818 (881)
T KOG0128|consen  753 LKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPERDK  818 (881)
T ss_pred             HHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCcccc
Confidence            9999999999988866       5799999999999999999999988888888888886664433

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

Probab=98.42  E-value=7e-08  Score=83.90  Aligned_cols=45  Identities=33%  Similarity=0.571  Sum_probs=41.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .||+.+||||++|.++++|+.|++.|||.++  .|++|+|.|+....
T Consensus        55 ~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~--~gr~l~v~~~~~~~   99 (435)
T KOG0108|consen   55 ETGKPKGFGFCEFTDEETAERAIRNLNGAEF--NGRKLRVNYASNRK   99 (435)
T ss_pred             cCCCcCceeeEecCchhhHHHHHHhcCCccc--CCceEEeecccccc
Confidence            4899999999999999999999999999999  69999999998554

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.42  E-value=1.5e-08  Score=85.45  Aligned_cols=117  Identities=21%  Similarity=0.303  Sum_probs=100.3

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhh
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF   87 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f   87 (240)
                      .|||||.+.+...|.+|++.|+|+.-+ .|+.+.|+++.+++..             ...+.|.|+ |....|+.|..++
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~el-qGkr~e~~~sv~kkqr-------------srk~Qirni-ppql~wevld~Ll  101 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVEL-QGKRQEVEHSVPKKQR-------------SRKIQIRNI-PPQLQWEVLDSLL  101 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhh-cCceeeccchhhHHHH-------------hhhhhHhcC-CHHHHHHHHHHHH
Confidence            699999999999999999999998654 7999999999987654             455889999 7788899999999


Q ss_pred             ccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           88 EPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        88 ~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      .+||.+..|...     ....-|+|.+.+.+..||..|+|..+.+..++|.|--.+.
T Consensus       102 ~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  102 AQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             hccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhh
Confidence            999999888763     2344578889999999999999999999999998876543

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

Probab=98.40  E-value=2.5e-07  Score=75.88  Aligned_cols=44  Identities=27%  Similarity=0.333  Sum_probs=39.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +.--+||||||+|++++||++|-++|||..|  .|++|.|+.+...
T Consensus       131 NERGSKGFGFVTmen~~dadRARa~LHgt~V--EGRkIEVn~ATar  174 (376)
T KOG0125|consen  131 NERGSKGFGFVTMENPADADRARAELHGTVV--EGRKIEVNNATAR  174 (376)
T ss_pred             ccCCCCccceEEecChhhHHHHHHHhhccee--eceEEEEeccchh
Confidence            3344799999999999999999999999999  7999999999854

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

Probab=98.40  E-value=3.5e-06  Score=73.18  Aligned_cols=120  Identities=19%  Similarity=0.307  Sum_probs=83.8

Q ss_pred             cc---eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC-C-----------CCCCCCCCCCCCEEEEec
Q 026341            8 AG---FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR-D-----------GSKSMANQRPTKTLFVIN   72 (240)
Q Consensus         8 kG---~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~-~-----------~~~~~~~~~~~~~l~v~n   72 (240)
                      +|   |+|+.|+++..+..-|.+..-     ...++.++.+.+..+... +           -........|..|||||+
T Consensus       303 kGs~~YvflvFe~E~sV~~Ll~aC~~-----~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGg  377 (520)
T KOG0129|consen  303 KGSYGYVFLVFEDERSVQSLLSACSE-----GEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGG  377 (520)
T ss_pred             CCcccEEEEEecchHHHHHHHHHHhh-----cccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecC
Confidence            66   999999999988876654332     133444444443222210 0           011334667899999999


Q ss_pred             cCCCCCCHHHHHHhhc-cCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHh----cCCCcccCcEEEEEE
Q 026341           73 FDPIRTRERDIKRHFE-PYGNVLHVRI--------RRNFAFVQFETQEEATKALES----TDRSKLVDRVISVEY  134 (240)
Q Consensus        73 l~~~~~~~~~l~~~f~-~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~----l~g~~~~g~~l~v~~  134 (240)
                      | |..++.++|-.+|+ -||.|..+-|        ++|-|-|+|.+..+-.+||.+    |+..+|.- .|.|..
T Consensus       378 v-prpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~K-RVEIkP  450 (520)
T KOG0129|consen  378 L-PRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDK-RVEIKP  450 (520)
T ss_pred             C-CCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccce-eeeecc
Confidence            9 99999999999998 7999998877        689999999999999999874    34444432 444443

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.33  E-value=3.8e-07  Score=83.53  Aligned_cols=117  Identities=18%  Similarity=0.265  Sum_probs=97.6

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhh
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF   87 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f   87 (240)
                      --||||.|.+...|-.|...+.+..|.  .-.+.+.+...             ...+++.++|++| ..++....|...|
T Consensus       413 sa~~f~~~~n~dmtp~ak~e~s~~~I~--~g~~r~glG~~-------------kst~ttr~~sggl-g~w~p~~~l~r~f  476 (975)
T KOG0112|consen  413 SAYAFVSLLNTDMTPSAKFEESGPLIG--NGTHRIGLGQP-------------KSTPTTRLQSGGL-GPWSPVSRLNREF  476 (975)
T ss_pred             cchhhhhhhccccCcccchhhcCCccc--cCccccccccc-------------ccccceeeccCCC-CCCChHHHHHHHh
Confidence            569999999999999999999999884  22344444332             2345788999999 6678899999999


Q ss_pred             ccCCCeEEEEEeCC--eEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCCC
Q 026341           88 EPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDDS  140 (240)
Q Consensus        88 ~~~G~i~~~~~~kg--~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~  140 (240)
                      ..||.|..|.+-.|  ||+|.|++...|+.|+..|-|..|.+  +.|.|.|+.....
T Consensus       477 d~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  477 DRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             hccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            99999999999654  99999999999999999999999987  7899999876544

>smart00360 RRM RNA recognition motif

Probab=98.29  E-value=1.3e-06  Score=56.03  Aligned_cols=38  Identities=39%  Similarity=0.607  Sum_probs=33.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEE
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE   43 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~   43 (240)
                      ++.++|||||+|.+.++|..|+..|++..|  +|+.|.|+
T Consensus        34 ~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~--~~~~~~v~   71 (71)
T smart00360       34 TGKSKGFAFVEFESEEDAEKALEALNGKEL--DGRPLKVK   71 (71)
T ss_pred             CCCCCceEEEEeCCHHHHHHHHHHcCCCee--CCcEEEeC
Confidence            466789999999999999999999999888  68888773

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.19  E-value=2.5e-06  Score=55.46  Aligned_cols=35  Identities=37%  Similarity=0.537  Sum_probs=31.4

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEE
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLS   41 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~   41 (240)
                      +..+|+|||+|.++++|..|+..+++..|  +|+.|.
T Consensus        36 ~~~~~~a~v~f~~~~~a~~al~~~~~~~~--~g~~l~   70 (70)
T PF14259_consen   36 GQSRGFAFVEFSSEEDAKRALELLNGKEI--DGRKLR   70 (70)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             cccCCEEEEEeCCHHHHHHHHHHCCCcEE--CCEEcC
Confidence            56799999999999999999999998988  688774

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 ....

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

Probab=98.18  E-value=7.2e-06  Score=70.83  Aligned_cols=74  Identities=26%  Similarity=0.362  Sum_probs=61.5

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ......|.+.+| ||.+|++||.+||+.++ |..+.++      .|-|||+|++++++++|++ .|...+..+-|.|-.+
T Consensus         7 ~~~~~~vr~rGL-Pwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    7 GSTAFEVRLRGL-PWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CCcceEEEecCC-CccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            334567889999 99999999999999985 6666664      5799999999999999998 4777888888888777


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      ...
T Consensus        84 ~~~   86 (510)
T KOG4211|consen   84 GGA   86 (510)
T ss_pred             CCc
Confidence            543

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

Probab=98.16  E-value=2.9e-06  Score=68.86  Aligned_cols=43  Identities=35%  Similarity=0.630  Sum_probs=39.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|++++|||||+|+++.+...|.+..+|++|  +|+.|.|.+-..
T Consensus       138 vTgkskGYAFIeye~erdm~~AYK~adG~~I--dgrri~VDvERg  180 (335)
T KOG0113|consen  138 VTGKSKGYAFIEYEHERDMKAAYKDADGIKI--DGRRILVDVERG  180 (335)
T ss_pred             ccCCccceEEEEeccHHHHHHHHHhccCcee--cCcEEEEEeccc
Confidence            4899999999999999999999999999999  799999987664

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

Probab=98.13  E-value=6.6e-07  Score=67.62  Aligned_cols=46  Identities=26%  Similarity=0.395  Sum_probs=41.6

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++||+++||||+.|+|..+...||..|||..|  .|+.|.|.......
T Consensus        71 k~TGKSKGFaFLcYEDQRSTILAVDN~NGiki--~gRtirVDHv~~Yk  116 (219)
T KOG0126|consen   71 KKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI--LGRTIRVDHVSNYK  116 (219)
T ss_pred             CCCCcccceEEEEecCccceEEEEeccCCcee--cceeEEeeeccccc
Confidence            46999999999999999999999999999999  59999999776544

>smart00362 RRM_2 RNA recognition motif

Probab=98.09  E-value=5.5e-06  Score=53.21  Aligned_cols=37  Identities=43%  Similarity=0.611  Sum_probs=32.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEE
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE   43 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~   43 (240)
                      +.++|+|||+|.+.++|++|+..|++..|  .|+.|.|.
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~--~~~~i~v~   72 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKL--GGRPLRVE   72 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEE--CCEEEeeC
Confidence            34579999999999999999999999888  68888763

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

Probab=98.04  E-value=5.5e-06  Score=59.19  Aligned_cols=42  Identities=31%  Similarity=0.585  Sum_probs=37.6

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..=|||||+|...++|+.||..++|..|  +.++|.|.|...-.
T Consensus        76 tpCGFCFVeyy~~~dA~~AlryisgtrL--ddr~ir~D~D~GF~  117 (153)
T KOG0121|consen   76 TPCGFCFVEYYSRDDAEDALRYISGTRL--DDRPIRIDWDAGFV  117 (153)
T ss_pred             CccceEEEEEecchhHHHHHHHhccCcc--cccceeeeccccch
Confidence            3469999999999999999999999999  79999999887544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.94  E-value=1.5e-05  Score=66.37  Aligned_cols=79  Identities=24%  Similarity=0.309  Sum_probs=67.9

Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--------EEE--------eCCeEEEEecCHHHHHHHHHhcCCC
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--------VRI--------RRNFAFVQFETQEEATKALESTDRS  123 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--------~~~--------~kg~afV~f~~~~~a~~A~~~l~g~  123 (240)
                      +......+|||.+| +..+++++|.++|.++|.|..        |+|        +|+-|.|.|++...|+.||..++++
T Consensus        61 ~~~s~~~ti~v~g~-~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk  139 (351)
T KOG1995|consen   61 ADKSDNETIFVWGC-PDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK  139 (351)
T ss_pred             ccccccccceeecc-CccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc
Confidence            34556789999999 889999999999999987743        222        4789999999999999999999999


Q ss_pred             cccCcEEEEEEeecCC
Q 026341          124 KLVDRVISVEYALKDD  139 (240)
Q Consensus       124 ~~~g~~l~v~~a~~~~  139 (240)
                      .+.|.+|+|.+|....
T Consensus       140 df~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  140 DFCGNTIKVSLAERRT  155 (351)
T ss_pred             cccCCCchhhhhhhcc
Confidence            9999999999987654

>PLN03120 nucleic acid binding protein; Provisional

Probab=97.93  E-value=1.5e-05  Score=64.52  Aligned_cols=40  Identities=20%  Similarity=0.283  Sum_probs=36.2

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+|||||+|.++++|+.||. |||..|  .|+.|.|.++....
T Consensus        42 ~~GfAFVtF~d~eaAe~All-LnG~~l--~gr~V~Vt~a~~~~   81 (260)
T PLN03120         42 RSQIAYVTFKDPQGAETALL-LSGATI--VDQSVTITPAEDYQ   81 (260)
T ss_pred             CCCEEEEEeCcHHHHHHHHH-hcCCee--CCceEEEEeccCCC
Confidence            57999999999999999996 999999  69999999987543

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

Probab=97.92  E-value=0.00014  Score=61.21  Aligned_cols=119  Identities=27%  Similarity=0.296  Sum_probs=79.0

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCC--CCCCC---CCCCEEEEeccCCCCCCHH
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSK--SMANQ---RPTKTLFVINFDPIRTRER   81 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~--~~~~~---~~~~~l~v~nl~~~~~~~~   81 (240)
                      -.|.|.|.|.|+|.-+.|++ -+.+.+  +++.|.|--+.......-.+..  .....   ...-.|-+.+| |+++++.
T Consensus       101 Rnge~lvrf~d~e~Rdlalk-Rhkhh~--g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGL-Pfdat~~  176 (508)
T KOG1365|consen  101 RNGEALVRFVDPEGRDLALK-RHKHHM--GTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGL-PFDATAL  176 (508)
T ss_pred             cccceEEEecCchhhhhhhH-hhhhhc--cCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCC-CCCcchH
Confidence            46899999999999888987 444444  5788888766655432211111  11111   11334567899 9999999


Q ss_pred             HHHHhhccC-----C--CeEEEEE----eCCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           82 DIKRHFEPY-----G--NVLHVRI----RRNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        82 ~l~~~f~~~-----G--~i~~~~~----~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      ++.++|.+-     |  .|..|.-    +.|-|||.|..+++|+.|+.. |...|+-+-|
T Consensus       177 dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  177 DVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             HHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            999999632     2  2333333    368999999999999999985 4444444433

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

Probab=97.90  E-value=7.8e-06  Score=64.38  Aligned_cols=42  Identities=26%  Similarity=0.328  Sum_probs=36.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|+++||||||+|.|.++|..|++..|-++   +|++..|++|.-
T Consensus        49 ~t~rskGyGfVTf~d~~aa~rAc~dp~piI---dGR~aNcnlA~l   90 (247)
T KOG0149|consen   49 NTGRSKGYGFVTFRDAEAATRACKDPNPII---DGRKANCNLASL   90 (247)
T ss_pred             CCccccceeeEEeecHHHHHHHhcCCCCcc---cccccccchhhh
Confidence            589999999999999999999998655543   799999998874

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=97.90  E-value=2.4e-05  Score=50.40  Aligned_cols=37  Identities=43%  Similarity=0.697  Sum_probs=33.3

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEe
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEW   44 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~   44 (240)
                      ..+|+|||+|.+.++|..|+..+++..+  .|+.|.|.+
T Consensus        38 ~~~~~~~v~f~s~~~a~~a~~~~~~~~~--~~~~~~v~~   74 (74)
T cd00590          38 KSKGFAFVEFEDEEDAEKALEALNGKEL--GGRPLRVEF   74 (74)
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEeC
Confidence            4589999999999999999999999988  699998864

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).

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.90  E-value=1.6e-05  Score=70.21  Aligned_cols=78  Identities=15%  Similarity=0.235  Sum_probs=66.6

Q ss_pred             CCCCCCCCEEEEeccCCCCCCHHHHHHhhcc-CCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcc---cCcEEEE
Q 026341           59 MANQRPTKTLFVINFDPIRTRERDIKRHFEP-YGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKL---VDRVISV  132 (240)
Q Consensus        59 ~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~-~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~---~g~~l~v  132 (240)
                      +....+.+.|+|.|| -..+|..+|+.++.. .|.|...+|  +|..|||.|.+.++|.+.+.+|||..+   +++.|.|
T Consensus       438 PsR~~~SnvlhI~nL-vRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNL-VRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CCCCCccceEeeecc-cccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            345667899999999 778999999999995 557777776  689999999999999999999999876   4688999


Q ss_pred             EEeec
Q 026341          133 EYALK  137 (240)
Q Consensus       133 ~~a~~  137 (240)
                      .|+..
T Consensus       517 df~~~  521 (718)
T KOG2416|consen  517 DFVRA  521 (718)
T ss_pred             eecch
Confidence            99864

>PLN03213 repressor of silencing 3; Provisional

Probab=97.87  E-value=1.7e-05  Score=68.68  Aligned_cols=37  Identities=19%  Similarity=0.345  Sum_probs=34.7

Q ss_pred             cceEEEEeCCh--hHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            8 AGFAFVYFEDD--RDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         8 kG~aFV~F~~~--~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      +|||||+|.+.  .++.+||..|||..+  .|+.|+|+.|+
T Consensus        48 RGFAFVEMssdddaEeeKAISaLNGAEW--KGR~LKVNKAK   86 (759)
T PLN03213         48 RSFAYIDFSPSSTNSLTKLFSTYNGCVW--KGGRLRLEKAK   86 (759)
T ss_pred             CceEEEEecCCcHHHHHHHHHHhcCCee--cCceeEEeecc
Confidence            99999999988  679999999999999  59999999987

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

Probab=97.86  E-value=5.3e-05  Score=46.42  Aligned_cols=50  Identities=22%  Similarity=0.589  Sum_probs=42.0

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHH
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKAL  117 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~  117 (240)
                      +.|-|.+. +... .++|..+|..||+|..+.+.  ..+.+|+|.+..+|+.||
T Consensus         2 ~wI~V~Gf-~~~~-~~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGF-PPDL-AEEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeE-CchH-HHHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            45788888 5333 46777899999999999998  789999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.86  E-value=3.9e-05  Score=65.32  Aligned_cols=62  Identities=26%  Similarity=0.469  Sum_probs=53.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------------------CCeEEEEecCHHHHHHHHHh
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------------------RNFAFVQFETQEEATKALES  119 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------------------kg~afV~f~~~~~a~~A~~~  119 (240)
                      ...+..+|.+.|| |.+-.-+.|.++|..+|.|..|.|.                     +-+|+|+|+..+.|.+|.+.
T Consensus       227 eel~srtivaenL-P~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  227 EELPSRTIVAENL-PLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             cccccceEEEecC-CcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            3347899999999 8877779999999999999999982                     34799999999999999998


Q ss_pred             cCCC
Q 026341          120 TDRS  123 (240)
Q Consensus       120 l~g~  123 (240)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            8544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.84  E-value=5e-05  Score=62.84  Aligned_cols=74  Identities=22%  Similarity=0.455  Sum_probs=59.7

Q ss_pred             CCCCEEEEeccCCCCCCHH---HH--HHhhccCCCeEEEEEeC---------C--eEEEEecCHHHHHHHHHhcCCCccc
Q 026341           63 RPTKTLFVINFDPIRTRER---DI--KRHFEPYGNVLHVRIRR---------N--FAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~---~l--~~~f~~~G~i~~~~~~k---------g--~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      ....-+||-+|+|.-..++   .|  .++|.+||+|..|.|.+         +  -.||+|.+.++|..||..++|..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3456789999955444444   22  57899999999999853         2  2499999999999999999999999


Q ss_pred             CcEEEEEEee
Q 026341          127 DRVISVEYAL  136 (240)
Q Consensus       127 g~~l~v~~a~  136 (240)
                      |+.|++.|..
T Consensus       192 Gr~lkatYGT  201 (480)
T COG5175         192 GRVLKATYGT  201 (480)
T ss_pred             CceEeeecCc
Confidence            9999999876

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.78  E-value=5.5e-05  Score=68.04  Aligned_cols=125  Identities=17%  Similarity=0.113  Sum_probs=89.1

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC----------CCC------------------CCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG----------RHR------------------DGSKSM   59 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~----------~~~------------------~~~~~~   59 (240)
                      .|-++|+|....++.+|+. -|.+.+  -.+.|.|..+....-          .+.                  .+....
T Consensus       352 tG~~~v~f~~~~~~q~A~~-rn~~~~--~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp  428 (944)
T KOG4307|consen  352 TGRKTVMFTPQAPFQNAFT-RNPSDD--VNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVP  428 (944)
T ss_pred             CCceEEEecCcchHHHHHh-cCchhh--hhcceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCC
Confidence            6889999999999999987 444443  266676654431110          000                  011122


Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE-EEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~-~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .....+.+|||..| |..+++.++.++|...-.|+. |.|.       .+.|||+|..++++..|+..-+...+..+.|.
T Consensus       429 ~P~~ag~~lyv~~l-P~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~ir  507 (944)
T KOG4307|consen  429 FPGGAGGALYVFQL-PVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIR  507 (944)
T ss_pred             CCCCccceEEeccC-CccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEE
Confidence            34455789999999 999999999999998777766 5552       57999999999999998876666667778888


Q ss_pred             EEEee
Q 026341          132 VEYAL  136 (240)
Q Consensus       132 v~~a~  136 (240)
                      |.-..
T Consensus       508 v~si~  512 (944)
T KOG4307|consen  508 VDSIA  512 (944)
T ss_pred             eechh
Confidence            76543

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

Probab=97.76  E-value=4.3e-05  Score=52.66  Aligned_cols=44  Identities=34%  Similarity=0.354  Sum_probs=39.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +...+|-|||.|++..+|.+|+..|+|..+  .+..|.|.|..+..
T Consensus        53 ~k~TrGTAFVVYedi~dAk~A~dhlsg~n~--~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   53 TKETRGTAFVVYEDIFDAKKACDHLSGYNV--DNRYLVVLYYQPED   96 (124)
T ss_pred             ccCcCceEEEEehHhhhHHHHHHHhccccc--CCceEEEEecCHHH
Confidence            445699999999999999999999999999  59999999887654

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

Probab=97.75  E-value=2.2e-05  Score=65.36  Aligned_cols=45  Identities=24%  Similarity=0.426  Sum_probs=41.7

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++||.+..||||||++.+++++|.-+|++.+|  +.+.|.|.|+..-
T Consensus       275 ~ktgdsLqyaFiEFen~escE~AyFKMdNvLI--DDrRIHVDFSQSV  319 (479)
T KOG0415|consen  275 RKTGDSLQYAFIEFENKESCEQAYFKMDNVLI--DDRRIHVDFSQSV  319 (479)
T ss_pred             ccccchhheeeeeecchhhHHHHHhhhcceee--ccceEEeehhhhh
Confidence            47899999999999999999999999999999  8999999998753

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

Probab=97.72  E-value=2.1e-05  Score=62.62  Aligned_cols=42  Identities=21%  Similarity=0.315  Sum_probs=36.7

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ++|++++||+||.|.++.++..||.+|||+.+  +.++|++.-+
T Consensus       226 kRTgKSkgygfVSf~~pad~~rAmrem~gkyV--gsrpiklRkS  267 (290)
T KOG0226|consen  226 KRTGKSKGYGFVSFRDPADYVRAMREMNGKYV--GSRPIKLRKS  267 (290)
T ss_pred             ccccccccceeeeecCHHHHHHHHHhhccccc--ccchhHhhhh
Confidence            36999999999999999999999999999999  5777775533

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.71  E-value=0.00023  Score=52.56  Aligned_cols=76  Identities=21%  Similarity=0.316  Sum_probs=55.0

Q ss_pred             CCCCCCEEEEeccC---CC--CCCH---HHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFD---PI--RTRE---RDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~---~~--~~~~---~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .++|..+|.|.-+.   +.  ...+   .+|.+.|..||++.-+++..+.-+|+|.+-+.|.+|+. |+|.+++|+.|+|
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i  101 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGDTMWVTFRDGQSALAALS-LDGIQVNGRTLKI  101 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTCEEEEESSCHHHHHHHH-GCCSEETTEEEEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCCeEEEEECccHHHHHHHc-cCCcEECCEEEEE
Confidence            45566777776552   11  1222   36788889999999999999999999999999999998 7999999999999


Q ss_pred             EEeec
Q 026341          133 EYALK  137 (240)
Q Consensus       133 ~~a~~  137 (240)
                      ....+
T Consensus       102 ~LKtp  106 (146)
T PF08952_consen  102 RLKTP  106 (146)
T ss_dssp             EE---
T ss_pred             EeCCc
Confidence            88654

; PDB: 1UFW_A 2DNR_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.69  E-value=0.00013  Score=65.69  Aligned_cols=68  Identities=34%  Similarity=0.465  Sum_probs=58.9

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeE-EEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVL-HVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~-~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ++|-+.|+ |++++-+||.+||..|-.+- .|.+       +.|-|.|.|++.++|..|...|+++.|.+++|.|.+
T Consensus       868 ~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  868 RVLSCNNF-PFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCC-CccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            48889999 99999999999999995432 2333       578999999999999999999999999999998865

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

Probab=97.68  E-value=1.6e-05  Score=62.00  Aligned_cols=100  Identities=21%  Similarity=0.255  Sum_probs=74.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHH
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR   85 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~   85 (240)
                      +.| ||||+|+++..+..|++.|||..|.  +.+|.|.+-......                    -| ...++++.+..
T Consensus        48 ~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~--~~e~q~~~r~G~sha--------------------pl-d~r~~~ei~~~  103 (267)
T KOG4454|consen   48 EQK-FAYVFFPNENSVQLAGQLENGDDLE--EDEEQRTLRCGNSHA--------------------PL-DERVTEEILYE  103 (267)
T ss_pred             CCc-eeeeecccccchhhhhhhcccchhc--cchhhcccccCCCcc--------------------hh-hhhcchhhhee
Confidence            446 9999999999999999999999994  888887765532211                    13 45677788888


Q ss_pred             hhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcE
Q 026341           86 HFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRV  129 (240)
Q Consensus        86 ~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~  129 (240)
                      .|+.-|.+..+.+.       +.++|+.+.-....-.++...++..+--.+
T Consensus       104 v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~  154 (267)
T KOG4454|consen  104 VFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKK  154 (267)
T ss_pred             eecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCCCC
Confidence            88888888888773       468889888777777777776665544333

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.66  E-value=1.9e-05  Score=63.06  Aligned_cols=59  Identities=25%  Similarity=0.405  Sum_probs=50.5

Q ss_pred             HHHHHhhc-cCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           81 RDIKRHFE-PYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        81 ~~l~~~f~-~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|...|+ +||+|..+.|       ..|-++|.|..+++|++|++.||+..|.|++|.+++..-..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            45555555 8999999877       36899999999999999999999999999999999986544

>PLN03121 nucleic acid binding protein; Provisional

Probab=97.64  E-value=8e-05  Score=59.50  Aligned_cols=42  Identities=24%  Similarity=0.232  Sum_probs=36.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+..+|||||+|+++++|+.|+. |+|..|  .+++|.|..+...
T Consensus        40 D~et~gfAfVtF~d~~aaetAll-LnGa~l--~d~~I~It~~~~y   81 (243)
T PLN03121         40 SGEYACTAYVTFKDAYALETAVL-LSGATI--VDQRVCITRWGQY   81 (243)
T ss_pred             CCCcceEEEEEECCHHHHHHHHh-cCCCee--CCceEEEEeCccc
Confidence            34567999999999999999996 999999  5999999977643

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.50  E-value=0.00034  Score=55.98  Aligned_cols=96  Identities=23%  Similarity=0.229  Sum_probs=76.2

Q ss_pred             HHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-
Q 026341           20 DAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-   98 (240)
Q Consensus        20 ~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-   98 (240)
                      -|+.|...|++...  .++.|.|-|+..                  ..|+|.|| ...++.+.|.+.|..||+|....+ 
T Consensus         6 ~ae~ak~eLd~~~~--~~~~lr~rfa~~------------------a~l~V~nl-~~~~sndll~~~f~~fg~~e~av~~   64 (275)
T KOG0115|consen    6 LAEIAKRELDGRFP--KGRSLRVRFAMH------------------AELYVVNL-MQGASNDLLEQAFRRFGPIERAVAK   64 (275)
T ss_pred             HHHHHHHhcCCCCC--CCCceEEEeecc------------------ceEEEEec-chhhhhHHHHHhhhhcCccchheee
Confidence            47778888999988  699999999983                  56999999 667999999999999998876544 


Q ss_pred             ------eCCeEEEEecCHHHHHHHHHhcCCC----cccCcEEEEEEee
Q 026341           99 ------RRNFAFVQFETQEEATKALESTDRS----KLVDRVISVEYAL  136 (240)
Q Consensus        99 ------~kg~afV~f~~~~~a~~A~~~l~g~----~~~g~~l~v~~a~  136 (240)
                            +.+-++|+|...-.|.+|+..+.-.    .+.+.++.|....
T Consensus        65 vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~e  112 (275)
T KOG0115|consen   65 VDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPME  112 (275)
T ss_pred             ecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChhh
Confidence                  3578999999999999999877332    3445666555443

>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=97.48  E-value=0.00044  Score=48.12  Aligned_cols=70  Identities=20%  Similarity=0.391  Sum_probs=51.2

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEE-------------Ee--CCeEEEEecCHHHHHHHHHhcCCCcccCc-
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVR-------------IR--RNFAFVQFETQEEATKALESTDRSKLVDR-  128 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~-------------~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~-  128 (240)
                      ...|.|-++ |.. ....|.+.|++||.|+...             ++  ..+..|.|++..+|++||. .||..|.|. 
T Consensus         6 ~~wVtVFGf-p~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGF-PPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             CCEEEEE----GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CeEEEEEcc-CHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            456888888 544 5678899999999998875             32  4689999999999999998 499999885 


Q ss_pred             EEEEEEeec
Q 026341          129 VISVEYALK  137 (240)
Q Consensus       129 ~l~v~~a~~  137 (240)
                      -+-|.++.+
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            445777643

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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.39  E-value=0.00051  Score=60.68  Aligned_cols=71  Identities=17%  Similarity=0.330  Sum_probs=57.6

Q ss_pred             CCCEEEEeccCCCCCCH-------HHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCccc-Cc
Q 026341           64 PTKTLFVINFDPIRTRE-------RDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLV-DR  128 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~-------~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~-g~  128 (240)
                      -..+|+|.|+ |. +..       ..|..+|+++|+|..+.++       +||.|++|++..+|+.|++.|||+.|+ ++
T Consensus        57 ~D~vVvv~g~-Pv-V~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   57 FDSVVVVDGA-PV-VGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             cceEEEECCC-cc-cChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            3578899999 63 332       3467789999999999885       799999999999999999999999886 56


Q ss_pred             EEEEEEee
Q 026341          129 VISVEYAL  136 (240)
Q Consensus       129 ~l~v~~a~  136 (240)
                      ++.|..-+
T Consensus       135 tf~v~~f~  142 (698)
T KOG2314|consen  135 TFFVRLFK  142 (698)
T ss_pred             eEEeehhh
Confidence            77776544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.36  E-value=0.00012  Score=58.41  Aligned_cols=65  Identities=17%  Similarity=0.312  Sum_probs=57.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------------C--------CeEEEEecCHHHHHHHHHhcCCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------------R--------NFAFVQFETQEEATKALESTDRS  123 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------------k--------g~afV~f~~~~~a~~A~~~l~g~  123 (240)
                      ..-+||+++| |..+....|+++|..||.|-.|.|.            +        .-|.|+|.+...|..+...||+.
T Consensus        73 k~GVvylS~I-Pp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   73 KTGVVYLSNI-PPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             cceEEEeccC-CCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            4678999999 7789999999999999999999882            1        13789999999999999999999


Q ss_pred             cccCcE
Q 026341          124 KLVDRV  129 (240)
Q Consensus       124 ~~~g~~  129 (240)
                      .|.|..
T Consensus       152 ~Iggkk  157 (278)
T KOG3152|consen  152 PIGGKK  157 (278)
T ss_pred             ccCCCC
Confidence            999853

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.32  E-value=0.00017  Score=60.04  Aligned_cols=68  Identities=12%  Similarity=0.235  Sum_probs=55.6

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCC--CeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYG--NVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G--~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .++||+|| .|.+|++||.+.+...|  .+..+++        .||||+|...+....++.++.|-.++|.|+.-.|.-
T Consensus        81 ~~~YvGNL-~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   81 YCCYVGNL-LWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             EEEEecce-eEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            57999999 89999999999888776  3333333        489999999999999999999999999996555433

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.29  E-value=0.00034  Score=59.08  Aligned_cols=69  Identities=19%  Similarity=0.283  Sum_probs=55.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...|.|.|| ...++.++|+.+|...|+|..+.|.           .-.|||.|.+...+..|.. |.++.|-++.|.|-
T Consensus         7 ~~vIqvani-spsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    7 LGVIQVANI-SPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             Cceeeeccc-CchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            348999999 5589999999999999999998873           3589999999999888876 67777767666654


Q ss_pred             Ee
Q 026341          134 YA  135 (240)
Q Consensus       134 ~a  135 (240)
                      .+
T Consensus        85 p~   86 (479)
T KOG4676|consen   85 PY   86 (479)
T ss_pred             ec
Confidence            43

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.17  E-value=1.1e-05  Score=73.94  Aligned_cols=112  Identities=23%  Similarity=0.213  Sum_probs=83.9

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhcc
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEP   89 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~   89 (240)
                      ++++++....+|+.|.. ..+..+  +++.+.|..+.+........ -.+.......++||.|| +..+.+.+|...|..
T Consensus       616 ~~~~~~s~~~~~esat~-pa~~~~--a~~~~av~~ad~~~~~~~~k-vs~n~~R~~~~~fvsnl-~~~~~~~dl~~~~~~  690 (881)
T KOG0128|consen  616 QQQKVQSKHGSAESATV-PAGGAL--ANRSAAVGLADAEEKEENFK-VSPNEIRDLIKIFVSNL-SPKMSEEDLSERFSP  690 (881)
T ss_pred             hhhhhhccccchhhccc-cccccc--CCccccCCCCCchhhhhccC-cCchHHHHHHHHHHhhc-chhhcCchhhhhcCc
Confidence            78899999999988887 677777  58888888777655321110 01111233468999999 788999999999999


Q ss_pred             CCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           90 YGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        90 ~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      +|.+..+.+        .+|+|||+|...+++.+||...++..+.
T Consensus       691 ~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  691 SGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             cchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            987766655        4799999999999999999876655554

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.16  E-value=0.0011  Score=54.18  Aligned_cols=57  Identities=33%  Similarity=0.360  Sum_probs=49.4

Q ss_pred             HHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           80 ERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        80 ~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ++++++.+.+||+|..|.|.         .--.||+|+..++|.+|+-.|||..|+|+.+...|-.
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            45678889999999998873         2358999999999999999999999999999887754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.14  E-value=0.0032  Score=39.61  Aligned_cols=54  Identities=24%  Similarity=0.297  Sum_probs=43.7

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccC----CCeEEEEEeCCeEEEEecCHHHHHHHHHhc
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPY----GNVLHVRIRRNFAFVQFETQEEATKALEST  120 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~----G~i~~~~~~kg~afV~f~~~~~a~~A~~~l  120 (240)
                      ...|+|.++ . .++.++|+.+|..|    ++..--+|.-.-|-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGv-d-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-D-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-C-CCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHcC
Confidence            357999999 4 68889999999998    544434445678999999999999999865

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.08  E-value=0.0036  Score=41.59  Aligned_cols=56  Identities=21%  Similarity=0.468  Sum_probs=45.7

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR  122 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g  122 (240)
                      ....+|. + |..+...||.++|+.||.|.-..|...-|||...+.+.|..|+..+.-
T Consensus         9 dHVFhlt-F-PkeWK~~DI~qlFspfG~I~VsWi~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-F-PKEWKTSDIYQLFSPFGQIYVSWINDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE----TT--HHHHHHHCCCCCCEEEEEECTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-C-chHhhhhhHHHHhccCCcEEEEEEcCCcEEEEeecHHHHHHHHHHhcc
Confidence            3455565 7 788999999999999999999999999999999999999999988753

; 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.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=96.91  E-value=0.002  Score=42.84  Aligned_cols=42  Identities=19%  Similarity=0.253  Sum_probs=29.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +.|-|+|-|.+++.|+.|.+.|+|..++  |.+|.|.|......
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVf--G~kI~v~~~~~~r~   79 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVF--GNKISVSFSPKNRE   79 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SS--SS--EEESS--S--
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccc--cceEEEEEcCCccc
Confidence            4689999999999999999999999885  99999999875443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=96.88  E-value=0.0022  Score=44.36  Aligned_cols=44  Identities=18%  Similarity=0.341  Sum_probs=34.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccC--CCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGY--DRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~--~g~~l~v~~a~   46 (240)
                      ++..+.|||||-|.++++|....+.++|..+..  ..+...|.||.
T Consensus        40 ~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   40 KNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             cCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            466779999999999999999999999987721  24555666665

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.76  E-value=0.0017  Score=55.56  Aligned_cols=74  Identities=20%  Similarity=0.292  Sum_probs=61.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccC--CCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCC-cccCcEEEEEEeecCCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRS-KLVDRVISVEYALKDDS  140 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~--G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~~~~~  140 (240)
                      ..|||+|| ...++..+|..+|...  +.-..+-+..||+||.+.+...|.+|++.++|+ ++.|..+.|+...++..
T Consensus         2 nklyignL-~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    2 NKLYIGNL-SPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             Cccccccc-CCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            35899999 6689999999999754  333445556799999999999999999999986 68899999998876544

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

Probab=96.74  E-value=0.0061  Score=53.51  Aligned_cols=56  Identities=21%  Similarity=0.395  Sum_probs=46.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE----------eCC---eEEEEecCHHHHHHHHHhc
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI----------RRN---FAFVQFETQEEATKALEST  120 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~----------~kg---~afV~f~~~~~a~~A~~~l  120 (240)
                      -...|||++| |++++|+.|...|..||.+.--+-          ++|   |+|+.|+++...+..|.+.
T Consensus       258 ~S~KVFvGGl-p~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  258 YSRKVFVGGL-PWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccceeecCC-CccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3578999999 999999999999999997643221          467   9999999999888877654

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.72  E-value=0.0051  Score=54.46  Aligned_cols=68  Identities=15%  Similarity=0.230  Sum_probs=52.8

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhcc--CCCeEEEEE-eCCeEEEEecCHHHHHHHHHhcCC--CcccCcEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEP--YGNVLHVRI-RRNFAFVQFETQEEATKALESTDR--SKLVDRVISV  132 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~--~G~i~~~~~-~kg~afV~f~~~~~a~~A~~~l~g--~~~~g~~l~v  132 (240)
                      .-|.|+|..| +..+-.++|+.+|..  +-++..|.+ ...-=||+|++..||+.|.+.|..  ++|.|++|..
T Consensus       174 kRcIvilREI-pettp~e~Vk~lf~~encPk~iscefa~N~nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREI-PETTPIEVVKALFKGENCPKVISCEFAHNDNWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeec-CCCChHHHHHHHhccCCCCCceeeeeeecCceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4577888999 888999999999975  567888887 355678999999999999887743  3555655543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=96.64  E-value=0.0023  Score=51.60  Aligned_cols=42  Identities=26%  Similarity=0.339  Sum_probs=37.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++.+||||||+|.+.+.++.|+. ||+..|  .|..|.|.+....
T Consensus       139 ~~~~k~~~yvef~~~~~~~~ay~-l~gs~i--~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  139 RGHPKGFAYVEFSSYELVEEAYK-LDGSEI--PGPAIEVTLKRTN  180 (231)
T ss_pred             CCCcceeEEEecccHhhhHHHhh-cCCccc--ccccceeeeeeee
Confidence            44679999999999999999999 999999  6999999887744

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

Probab=96.57  E-value=0.0018  Score=57.23  Aligned_cols=129  Identities=15%  Similarity=0.106  Sum_probs=77.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC-----------CCCCCCCCCCCCEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD-----------GSKSMANQRPTKTLFVIN   72 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~-----------~~~~~~~~~~~~~l~v~n   72 (240)
                      |....|.+||+|.|..+|+.|+++|++..|  .|+.|+.............           ....+....+-..+++ .
T Consensus       108 t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~--~~~~~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~  184 (549)
T KOG4660|consen  108 TPNKRGIVFVEFYDVRDAERALKALNRREI--AGKRIKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-M  184 (549)
T ss_pred             ccccCceEEEEEeehHhHHHHHHHHHHHHh--hhhhhcCCCcccccchhcccchhhhhccchhhcCCCCCCcCCccee-e
Confidence            455689999999999999999999999999  5888872221111100000           0011122222233333 2


Q ss_pred             cCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           73 FDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        73 l~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      | ....+...+...+.-+|.+..-..  ....-|++|.+..++..+...+ |..+.+....++++.+
T Consensus       185 l-~P~~s~~~~~~~~~~~~~~~~~~~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  185 L-SPTRSSILLEHISSVDGSSPGRETPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             e-ccchhhhhhhcchhccCccccccccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            7 434555555666667776655222  2346778888888885555533 6667777766666554

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

Probab=96.55  E-value=0.0026  Score=56.48  Aligned_cols=40  Identities=28%  Similarity=0.398  Sum_probs=37.3

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++||||++.+.++|.+||+.|+.+.|  +|+.|.|+.+++..
T Consensus       447 RCYGfVTMSts~eAtkCI~hLHrTEL--HGrmISVEkaKNEp  486 (940)
T KOG4661|consen  447 RCYGFVTMSTSAEATKCIEHLHRTEL--HGRMISVEKAKNEP  486 (940)
T ss_pred             ceeEEEEecchHHHHHHHHHhhhhhh--cceeeeeeecccCc
Confidence            78999999999999999999999999  79999999998554

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.38  E-value=0.031  Score=41.06  Aligned_cols=75  Identities=17%  Similarity=0.288  Sum_probs=57.0

Q ss_pred             CCCCCCCEEEEeccCCCCCC-HHH---HHHhhccCCCeEEEEEe-CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           60 ANQRPTKTLFVINFDPIRTR-ERD---IKRHFEPYGNVLHVRIR-RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~-~~~---l~~~f~~~G~i~~~~~~-kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+|-.+|.|.=| ..++. .+|   |...++.||+|..|.+. +.-|.|.|.+..+|-+|+.+++. ..-|.-+.+.|
T Consensus        81 ~kepPMsTIVVRWl-kknm~~~edl~sV~~~Ls~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   81 TKEPPMSTIVVRWL-KKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CCCCCceeEEeehh-hhcCChHHHHHHHHHHHHhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            35667788888766 43332 344   44556789999999885 77999999999999999999876 56677777877


Q ss_pred             ee
Q 026341          135 AL  136 (240)
Q Consensus       135 a~  136 (240)
                      ..
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            54

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

Probab=96.27  E-value=0.0045  Score=51.74  Aligned_cols=40  Identities=30%  Similarity=0.385  Sum_probs=34.3

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+++|||+|.+-++|+.|.+++-..++ ++|+.|+|.|..+
T Consensus       263 ~~~CAFv~ftTR~aAE~Aae~~~n~lv-I~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  263 RKGCAFVTFTTREAAEKAAEKSFNKLV-INGFRLKIKWGRP  302 (377)
T ss_pred             ccccceeeehhhHHHHHHHHhhcceee-ecceEEEEEeCCC
Confidence            378999999999999999987655444 4899999999998

>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=96.21  E-value=0.028  Score=36.84  Aligned_cols=59  Identities=29%  Similarity=0.330  Sum_probs=38.5

Q ss_pred             CCCCHHHHHHhhccCC-----CeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           76 IRTRERDIKRHFEPYG-----NVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        76 ~~~~~~~l~~~f~~~G-----~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++..+|..++...+     .|-.+.|...|+||+-.. +.|+.++..|++..+.|+.|.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeeeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4688889988887664     566888899999999875 5788999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.89  E-value=0.019  Score=44.62  Aligned_cols=60  Identities=15%  Similarity=0.216  Sum_probs=45.1

Q ss_pred             CHHHHHHhhccCCCeEEEEEeCC--eEEEEecCHHHHHHHHHhcC--CCcccCcEEEEEEeecC
Q 026341           79 RERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTD--RSKLVDRVISVEYALKD  138 (240)
Q Consensus        79 ~~~~l~~~f~~~G~i~~~~~~kg--~afV~f~~~~~a~~A~~~l~--g~~~~g~~l~v~~a~~~  138 (240)
                      ..+.|+++|..++.+..+.+.+.  -..|.|.+.+.|..|...|+  +..+.|..|.|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999998887777664  58899999999999999999  99999999999998543

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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.83  E-value=0.011  Score=52.50  Aligned_cols=41  Identities=22%  Similarity=0.349  Sum_probs=34.6

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      +..+||.|++|++..+|+.|++.|||+.|. ....+.|...+
T Consensus       102 ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld-knHtf~v~~f~  142 (698)
T KOG2314|consen  102 GGTKGYLFVEYASMRDAKKAVKSLNGKRLD-KNHTFFVRLFK  142 (698)
T ss_pred             CCeeeEEEEEecChhhHHHHHHhcccceec-ccceEEeehhh
Confidence            447999999999999999999999999985 46667776444

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

Probab=95.69  E-value=0.021  Score=46.19  Aligned_cols=46  Identities=22%  Similarity=0.257  Sum_probs=40.4

Q ss_pred             cccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            2 CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         2 ~~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ...+.+.|.|=|.|...+||+.||+.+||+.|  +|++|+++......
T Consensus       118 ~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~l--dG~~mk~~~i~~~~  163 (243)
T KOG0533|consen  118 DRAGRSLGTADVSFNRRDDAERAVKKYNGVAL--DGRPMKIEIISSPS  163 (243)
T ss_pred             CCCCCCCccceeeecchHhHHHHHHHhcCccc--CCceeeeEEecCcc
Confidence            45788899999999999999999999999777  89999998777544

>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=95.65  E-value=0.035  Score=42.97  Aligned_cols=73  Identities=16%  Similarity=0.219  Sum_probs=50.2

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhcc-CCCe---EEEEE--e--------CCeEEEEecCHHHHHHHHHhcCCCcccC--
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEP-YGNV---LHVRI--R--------RNFAFVQFETQEEATKALESTDRSKLVD--  127 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~-~G~i---~~~~~--~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--  127 (240)
                      ....|.|.+| |..+|++++.+.+.. ++..   .++..  .        -.-|||.|.+.+++...+..++|..|.+  
T Consensus         6 ~~~KvVIR~L-PP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    6 EGTKVVIRRL-PPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ---EEEEEEE--TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             cCceEEEeCC-CCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            4568999999 789999999998877 6654   33331  1        2469999999999999999999976643  


Q ss_pred             ---cEEEEEEeec
Q 026341          128 ---RVISVEYALK  137 (240)
Q Consensus       128 ---~~l~v~~a~~  137 (240)
                         ....|++|--
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               4556777754

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=95.65  E-value=0.017  Score=39.10  Aligned_cols=74  Identities=16%  Similarity=0.240  Sum_probs=46.7

Q ss_pred             EEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhc
Q 026341           11 AFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFE   88 (240)
Q Consensus        11 aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~   88 (240)
                      |.|+|.++.-|+..+. +....+.+++..+.|....-.....  ............+|.|.|| |....+++|++.++
T Consensus         1 AlITF~e~~VA~~i~~-~~~~~v~l~~~~~~V~v~P~~~~~~--~k~qv~~~vs~rtVlvsgi-p~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILK-KKKHPVPLEDCCVRVKVSPVTLGHL--QKFQVFSGVSKRTVLVSGI-PDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHh-CCEEEEEECCEEEEEEEEeEecCCc--eEEEEEEcccCCEEEEeCC-CCCCChhhheeeEE
Confidence            7899999999998887 4444444456666555332111110  0011123445788999999 77899999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.61  E-value=0.043  Score=45.23  Aligned_cols=69  Identities=20%  Similarity=0.307  Sum_probs=51.9

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcE-EEEEEeecC
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRV-ISVEYALKD  138 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~-l~v~~a~~~  138 (240)
                      =|.|.+++|  -...-|..+|++||+|+.....  -.+-+|.|.+..+|++||.. ||+.|+|.. |-|.-+..+
T Consensus       199 WVTVfGFpp--g~~s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  199 WVTVFGFPP--GQVSIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             eEEEeccCc--cchhHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCCH
Confidence            356667733  3346789999999999887764  35899999999999999984 999998854 445554443

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=95.60  E-value=0.085  Score=33.70  Aligned_cols=56  Identities=16%  Similarity=0.272  Sum_probs=45.8

Q ss_pred             CCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           76 IRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        76 ~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..++-++|+..+..|+ ...|..-+.-=||.|.+..+|++|....+|..+.+..|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~-~~~I~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYR-WDRIRDDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCC-cceEEecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3678899999999996 4445555555689999999999999999999988877655

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=95.58  E-value=0.018  Score=53.07  Aligned_cols=45  Identities=24%  Similarity=0.514  Sum_probs=39.9

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +.++|+|||.+..-++|++|+.+|+...|  .++.|+|.|+..+...
T Consensus       454 i~~R~cAfI~M~~RqdA~kalqkl~n~kv--~~k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  454 IPPRGCAFIKMVRRQDAEKALQKLSNVKV--ADKTIKIAWAVGKGPK  498 (894)
T ss_pred             ccCCceeEEEEeehhHHHHHHHHHhcccc--cceeeEEeeeccCCcc
Confidence            34599999999999999999999999888  6999999999976543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.53  E-value=0.0076  Score=52.38  Aligned_cols=72  Identities=21%  Similarity=0.281  Sum_probs=57.2

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      .+.|-+.-.+...-+-++|..+|.+||+|..|.+-  --.|.|+|.+..+|-+|.. .++..|+|+.|+|.|-.+
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 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            34455555522234568999999999999998873  4689999999999977765 699999999999999886

>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=95.45  E-value=0.52  Score=33.43  Aligned_cols=70  Identities=19%  Similarity=0.250  Sum_probs=48.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEEeC------CeEEEEecCHHHHHHHHHhcCCCcccC---cEEEEEE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRR------NFAFVQFETQEEATKALESTDRSKLVD---RVISVEY  134 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~~k------g~afV~f~~~~~a~~A~~~l~g~~~~g---~~l~v~~  134 (240)
                      ...+.+... |+.++.++|..+.+.+- .|..+.|.+      -.++|.|.+.++|.+-...+||+.+.-   ..+.|-|
T Consensus        13 ~~~~~l~vp-~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvvf   91 (110)
T PF07576_consen   13 STLCCLAVP-PYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVVF   91 (110)
T ss_pred             ceEEEEEeC-cccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEEE
Confidence            334444444 77777777877766664 566777742      378999999999999999999997653   4444444


Q ss_pred             e
Q 026341          135 A  135 (240)
Q Consensus       135 a  135 (240)
                      .
T Consensus        92 V   92 (110)
T PF07576_consen   92 V   92 (110)
T ss_pred             E
Confidence            3

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.44  E-value=0.01  Score=47.71  Aligned_cols=39  Identities=26%  Similarity=0.418  Sum_probs=35.5

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +.|=++|.|..+++|++|+..||+..|  .|++|..++...
T Consensus       109 l~GNVYV~f~~Ee~ae~a~~~lnnRw~--~G~pi~ae~~pv  147 (260)
T KOG2202|consen  109 LVGNVYVKFRSEEDAEAALEDLNNRWY--NGRPIHAELSPV  147 (260)
T ss_pred             hhhhhhhhcccHHHHHHHHHHHcCccc--cCCcceeeecCc
Confidence            478899999999999999999999999  699999887764

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.95  E-value=0.0085  Score=50.02  Aligned_cols=72  Identities=14%  Similarity=0.375  Sum_probs=54.7

Q ss_pred             CEEEEeccCCCCCCHH-HH--HHhhccCCCeEEEEEeC-----------CeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           66 KTLFVINFDPIRTRER-DI--KRHFEPYGNVLHVRIRR-----------NFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~-~l--~~~f~~~G~i~~~~~~k-----------g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .-+||-+| +..+..+ .|  .+.|.+||.|..|.+.+           .-++|+|+..++|..||...+|..++|+.|+
T Consensus        78 nlvyvvgl-~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGL-PLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCC-CccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            45677777 4444333 34  34678889999988843           2489999999999999999999999999988


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      +.+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7776543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.88  E-value=0.018  Score=52.13  Aligned_cols=72  Identities=18%  Similarity=0.170  Sum_probs=63.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..++..++||+|+ .+.+..+-++.++..+|-|..+...+ |+|.+|..+..+..|+..++-..++|..+.+..
T Consensus        36 ~~~~~~~vfv~~~-~~~~s~~~~~~il~~~g~v~s~kr~~-fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   36 PLPPRDTVFVGNI-SYLVSQEFWKSILAKSGFVPSWKRDK-FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCCceeEecch-hhhhhHHHHHHHHhhCCcchhhhhhh-hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            4567789999999 78899999999999999887776655 999999999999999999999999998887765

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=94.20  E-value=0.032  Score=46.99  Aligned_cols=45  Identities=24%  Similarity=0.163  Sum_probs=40.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +|+..||-|.|.|+|+..|+.||.-+++..|+  +..|+|.+|....
T Consensus       111 eT~~~KGeatvS~~D~~~akaai~~~agkdf~--gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  111 ETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC--GNTIKVSLAERRT  155 (351)
T ss_pred             cccCcCCceeeeecChhhhhhhhhhhcccccc--CCCchhhhhhhcc
Confidence            58889999999999999999999999999995  7899998887544

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

Probab=94.18  E-value=0.044  Score=50.16  Aligned_cols=37  Identities=24%  Similarity=0.465  Sum_probs=34.5

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      ..+|||-|-+-.||+.|++.|+|+.++  +.+|++.|++
T Consensus       219 r~cgfvafmnR~D~era~k~lqg~iv~--~~e~K~gWgk  255 (877)
T KOG0151|consen  219 RNCGFVAFMNRADAERALKELQGIIVM--EYEMKLGWGK  255 (877)
T ss_pred             cccceeeehhhhhHHHHHHHhcceeee--eeeeeecccc
Confidence            679999999999999999999999995  8999999996

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.08  E-value=0.0085  Score=55.92  Aligned_cols=72  Identities=24%  Similarity=0.355  Sum_probs=60.3

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..+.+||++|| +..+++.+|...|..+|.|..|.|.       ..|+||.|.+...+-.|...+.+..|..-.+.+-+.
T Consensus       370 ~atrTLf~Gnl-~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNL-DSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCc-ccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            34689999999 8899999999999999999999983       259999999999999999988888776545444444

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=93.90  E-value=1.6  Score=40.80  Aligned_cols=61  Identities=8%  Similarity=0.196  Sum_probs=49.2

Q ss_pred             CCCCHHHHHHhhccCCCe-----EEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           76 IRTRERDIKRHFEPYGNV-----LHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        76 ~~~~~~~l~~~f~~~G~i-----~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ..++..+|..++..-+.|     -.|.|...|.||+... ..|...+..|++..+.|+.|.|+.+..
T Consensus       497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        497 DGVEVRHIVGAIANEGDISSRYIGNIKLFASHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             cCCCHHHHHHHHHhhcCCChhhCCcEEEeCCceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            468888888888766544     4567788999999764 568889999999999999999998853

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.24  E-value=0.34  Score=43.55  Aligned_cols=75  Identities=24%  Similarity=0.417  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEeccCCCC-CCHHHHHHhhccC----CCeEEEEE-----------------e------------------
Q 026341           60 ANQRPTKTLFVINFDPIR-TRERDIKRHFEPY----GNVLHVRI-----------------R------------------   99 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~-~~~~~l~~~f~~~----G~i~~~~~-----------------~------------------   99 (240)
                      ....++..|-|.|| .|. +...+|.-+|..|    |.|..|.|                 +                  
T Consensus       169 ~~~~~T~RLAVvNM-DWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  169 VLGEETKRLAVVNM-DWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             ccccccceeeEecc-ccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            34677899999999 664 7789999998876    58888887                 1                  


Q ss_pred             -----------C---------CeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEe
Q 026341          100 -----------R---------NFAFVQFETQEEATKALESTDRSKLVD--RVISVEYA  135 (240)
Q Consensus       100 -----------k---------g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a  135 (240)
                                 +         -||.|+|.+.+.|.+....++|.+|..  ..|.+.|.
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                       0         279999999999999999999999875  45555554

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

Probab=93.14  E-value=0.093  Score=46.01  Aligned_cols=39  Identities=33%  Similarity=0.460  Sum_probs=30.4

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      +++.+||||+|++.+++..||.+-   .+.+++++|.|+--.
T Consensus       327 ~~~~~fgFV~f~~~~~~~~~i~As---p~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  327 GKNPCFGFVEFENAAAVQNAIEAS---PLEIGGRKLNVEEKR  365 (419)
T ss_pred             CCcCceEEEEEeecchhhhhhhcC---ccccCCeeEEEEecc
Confidence            344599999999999999999844   444489999988544

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=92.72  E-value=0.076  Score=49.61  Aligned_cols=77  Identities=25%  Similarity=0.325  Sum_probs=60.8

Q ss_pred             CCCCEEEEeccCC-----------CCCCHHHHHHhhccCCCeEEEEEeC--CeEEEEecCHHHHHHHHHhcCCCcc--cC
Q 026341           63 RPTKTLFVINFDP-----------IRTRERDIKRHFEPYGNVLHVRIRR--NFAFVQFETQEEATKALESTDRSKL--VD  127 (240)
Q Consensus        63 ~~~~~l~v~nl~~-----------~~~~~~~l~~~f~~~G~i~~~~~~k--g~afV~f~~~~~a~~A~~~l~g~~~--~g  127 (240)
                      .++.+|-|.|+.|           ...+-.-|-.+|.+||.|...+..+  ..|.|+|.+.+.|..|+++|+|+++  .|
T Consensus       284 ~ptn~isisnv~plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g  363 (1007)
T KOG4574|consen  284 LPTNTISISNVFPLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTG  363 (1007)
T ss_pred             cccCcceecccccCcchhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccC
Confidence            3455666666533           3455567889999999999999865  5799999999999999999999864  58


Q ss_pred             cEEEEEEeecCC
Q 026341          128 RVISVEYALKDD  139 (240)
Q Consensus       128 ~~l~v~~a~~~~  139 (240)
                      -+.+|.+|+.-.
T Consensus       364 ~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  364 APSRVSFAKTLP  375 (1007)
T ss_pred             CceeEEeccccc
Confidence            889999987543

>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=92.12  E-value=0.24  Score=32.34  Aligned_cols=35  Identities=23%  Similarity=0.419  Sum_probs=22.0

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ..|+||+-... .|+.++..|++..+  .|++|.|+.|
T Consensus        40 ~~~S~vev~~~-~a~~v~~~l~~~~~--~gk~v~ve~A   74 (74)
T PF03880_consen   40 DNFSFVEVPEE-VAEKVLEALNGKKI--KGKKVRVERA   74 (74)
T ss_dssp             SS-EEEEE-TT--HHHHHHHHTT--S--SS----EEE-
T ss_pred             eeEEEEEECHH-HHHHHHHHhcCCCC--CCeeEEEEEC
Confidence            57899999877 69999999999999  6999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.76  E-value=0.71  Score=40.39  Aligned_cols=63  Identities=17%  Similarity=0.354  Sum_probs=53.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEEeC------CeEEEEecCHHHHHHHHHhcCCCcccC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRR------NFAFVQFETQEEATKALESTDRSKLVD  127 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~~k------g~afV~f~~~~~a~~A~~~l~g~~~~g  127 (240)
                      ++..|+|-.+ |..++.-||..|+..+- .|..+.+.+      -.++|.|.+.++|....+.+||..|..
T Consensus        73 ~~~mLcilaV-P~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAV-PAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEec-cccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            3889999999 88899999999998764 677777743      368899999999999999999998764

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=91.00  E-value=0.43  Score=35.46  Aligned_cols=36  Identities=28%  Similarity=0.425  Sum_probs=29.9

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +.-+|+|.+-++|-+|+. |+|..+  .|+.|+|..-.+
T Consensus        71 ~~mwVTF~dg~sALaals-~dg~~v--~g~~l~i~LKtp  106 (146)
T PF08952_consen   71 DTMWVTFRDGQSALAALS-LDGIQV--NGRTLKIRLKTP  106 (146)
T ss_dssp             TCEEEEESSCHHHHHHHH-GCCSEE--TTEEEEEEE---
T ss_pred             CeEEEEECccHHHHHHHc-cCCcEE--CCEEEEEEeCCc
Confidence            457899999999999998 999999  599999987664

; PDB: 1UFW_A 2DNR_A.

>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=90.21  E-value=0.41  Score=30.58  Aligned_cols=29  Identities=24%  Similarity=0.494  Sum_probs=24.4

Q ss_pred             EEEeCChhHHHHHHHhhCCCcccCCCceEEE
Q 026341           12 FVYFEDDRDAADAIRGLDNIPFGYDRRRLSV   42 (240)
Q Consensus        12 FV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v   42 (240)
                      ||.|.+.++|++|....+|..++  +-.|.+
T Consensus        37 YIvF~~~~Ea~rC~~~~~~~~~f--~y~m~M   65 (66)
T PF11767_consen   37 YIVFNDSKEAERCFRAEDGTLFF--TYRMQM   65 (66)
T ss_pred             EEEECChHHHHHHHHhcCCCEEE--EEEEEe
Confidence            89999999999999999999884  555544

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=87.38  E-value=0.74  Score=32.37  Aligned_cols=35  Identities=17%  Similarity=0.311  Sum_probs=21.1

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCC---cccCCCceEEEE
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNI---PFGYDRRRLSVE   43 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~---~~~~~g~~l~v~   43 (240)
                      ..|||-|.++++|+.|+..+...   .+.+.+..+.+.
T Consensus        38 ~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen   38 TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            47999999999999999877555   332245544444

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

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=87.23  E-value=0.81  Score=38.73  Aligned_cols=39  Identities=13%  Similarity=0.187  Sum_probs=33.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEE
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE   43 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~   43 (240)
                      .+|++||||+|...++...++.|+.|-.+.|  +|+.-.|-
T Consensus       119 ~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~i--HGQ~P~V~  157 (498)
T KOG4849|consen  119 TNGQSKGYALLVLNSDAAVKQTMEILPTKTI--HGQSPTVL  157 (498)
T ss_pred             cCCcccceEEEEecchHHHHHHHHhccccee--cCCCCeee
Confidence            4889999999999999999999999999998  57665554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=86.39  E-value=0.93  Score=38.21  Aligned_cols=34  Identities=24%  Similarity=0.427  Sum_probs=31.4

Q ss_pred             EEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341           12 FVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus        12 FV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ||+|.+.+||..||.+.+|..+  +|+.|+..|...
T Consensus       169 YITy~~kedAarcIa~vDgs~~--DGr~lkatYGTT  202 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLL--DGRVLKATYGTT  202 (480)
T ss_pred             EEEecchHHHHHHHHHhccccc--cCceEeeecCch
Confidence            9999999999999999999998  899999887763

>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=85.88  E-value=1.3  Score=34.49  Aligned_cols=39  Identities=26%  Similarity=0.276  Sum_probs=28.3

Q ss_pred             ceEEEEeCChhHHHHHHHhhC--CCcccCCCceEEEEeccCCC
Q 026341            9 GFAFVYFEDDRDAADAIRGLD--NIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~--g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +=..|.|.+.++|..|...|+  +..|  .|..|.|.|+....
T Consensus        32 rRi~v~f~~~~~A~~~r~~l~~~~~~~--~g~~l~~yf~~~~~   72 (184)
T PF04847_consen   32 RRIRVVFESPESAQRARQLLHWDGTSF--NGKRLRVYFGQPTP   72 (184)
T ss_dssp             TEEEEE-SSTTHHHHHHHTST--TSEE--TTEE-EEE----SS
T ss_pred             CEEEEEeCCHHHHHHHHHHhccccccc--CCCceEEEEccccc
Confidence            446899999999999999999  8888  59999999996443

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.

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=85.43  E-value=0.53  Score=39.48  Aligned_cols=18  Identities=39%  Similarity=0.431  Sum_probs=7.6

Q ss_pred             CCCCCCCCCCCCCCCCCc
Q 026341          218 YGRNRSPNFGRYRSRSPV  235 (240)
Q Consensus       218 ~~rs~s~~~~r~rsrs~~  235 (240)
                      ++|++|+++++++.+||.
T Consensus       383 RSR~~sRSrsrsre~s~k  400 (453)
T KOG2888|consen  383 RSRSRSRSRSRSREPSPK  400 (453)
T ss_pred             hhcccccccccccCCCcc
Confidence            333334444444444544

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=85.38  E-value=2.6  Score=29.90  Aligned_cols=28  Identities=18%  Similarity=0.376  Sum_probs=24.8

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCccc
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFG   34 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~   34 (240)
                      ++=.+.|.|.+.++|......+||+.|.
T Consensus        53 nrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   53 NRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3557899999999999999999999983

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=85.35  E-value=0.43  Score=39.90  Aligned_cols=72  Identities=17%  Similarity=0.119  Sum_probs=55.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..+++|++++ .+.+.+.++..++..+|.+..+.+        .++++.|.|...+.+..|+.......+.+..+...+.
T Consensus        87 ~~~~~f~g~~-s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGEL-SENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccc-ccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            3678899999 788888878888888887666554        4799999999999999999864445666666555444


Q ss_pred             e
Q 026341          136 L  136 (240)
Q Consensus       136 ~  136 (240)
                      .
T Consensus       166 ~  166 (285)
T KOG4210|consen  166 T  166 (285)
T ss_pred             c
Confidence            4

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=84.23  E-value=2  Score=29.94  Aligned_cols=37  Identities=11%  Similarity=0.215  Sum_probs=28.9

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++--|+|.++.+|.+||. .||.+|. +.-.+-|.+++
T Consensus        54 ~NWi~I~Y~~~~~A~rAL~-~NG~i~~-g~~mvGV~~~~   90 (100)
T PF05172_consen   54 GNWIHITYDNPLSAQRALQ-KNGTIFS-GSLMVGVKPCD   90 (100)
T ss_dssp             TTEEEEEESSHHHHHHHHT-TTTEEET-TCEEEEEEE-H
T ss_pred             CCEEEEECCCHHHHHHHHH-hCCeEEc-CcEEEEEEEcH
Confidence            5678899999999999998 8999994 23455577764

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.

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=83.25  E-value=0.63  Score=38.17  Aligned_cols=36  Identities=22%  Similarity=0.502  Sum_probs=26.9

Q ss_pred             CCCCEEEEeccCCC------------CCCHHHHHHhhccCCCeEEEEEe
Q 026341           63 RPTKTLFVINFDPI------------RTRERDIKRHFEPYGNVLHVRIR   99 (240)
Q Consensus        63 ~~~~~l~v~nl~~~------------~~~~~~l~~~f~~~G~i~~~~~~   99 (240)
                      .-..+|++.+| |-            -.++..|...|..||.|..|.|+
T Consensus       147 erpdti~la~i-p~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdip  194 (445)
T KOG2891|consen  147 ERPDTIHLAGI-PCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIP  194 (445)
T ss_pred             CCCCceeecCC-cceeeeecccccccCChHHHHHHHHHHhccceecCCc
Confidence            33467888777 52            13467799999999999999884

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=81.17  E-value=2.1  Score=36.06  Aligned_cols=7  Identities=43%  Similarity=0.734  Sum_probs=2.6

Q ss_pred             CCHHHHH
Q 026341           78 TRERDIK   84 (240)
Q Consensus        78 ~~~~~l~   84 (240)
                      +++++|.
T Consensus       213 ~~k~eid  219 (367)
T KOG0835|consen  213 TTKREID  219 (367)
T ss_pred             CcHHHHH
Confidence            3333333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	240
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		8e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-05
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		2e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-05
2kvi_A	96	Structure Of Nab3 Rrm Length = 96		1e-04
1wf2_A	98	Solution Structure Of Rrm Domain In Hnrpc Protein L		1e-04
2l41_A	77	Nab3 Rrm - Ucuu Complex Length = 77		3e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		6e-04
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		6e-04

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 46  RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFV 105
           RG    HR   + ++N R    LFV  F P+  +E ++   F P+G +  V+I   FAFV
Sbjct: 17  RGSHMHHRQEGE-LSNTR----LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFV 70
Query: 106 QFETQEEATKALESTDRSKLVDRVISVEYA 135
           +FE  E A KA+E        ++ + V Y+
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVYS 100

>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 = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKT 67
           G+A+V F+     ADA R LD + F   + + + + W++ +    + G            
Sbjct: 58  GYAYVNFQQ---PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGN 105
Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 121
           +F+ N D      + +   F  +GN+L  ++       + + FV FETQE A +A+E  +
Sbjct: 106 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 122 RSKLVDRVISV 132
              L DR + V
Sbjct: 165 GMLLNDRKVFV 175

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           LFV  F P+  +E ++   F P+G +  V+I   FAFV+FE  E A KA+E        +
Sbjct: 7   LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 65
Query: 128 RVISVEYA 135
           + + V Y+
Sbjct: 66  QPLEVVYS 73

>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 = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKT 67
           G+A+V F+     ADA R LD + F   + + + + W++ +    + G            
Sbjct: 53  GYAYVNFQQ---PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGN 100
Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 121
           +F+ N D      + +   F  +GN+L  ++       + + FV FETQE A +A+E  +
Sbjct: 101 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 122 RSKLVDRVISV 132
              L DR + V
Sbjct: 160 GMLLNDRKVFV 170

>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/77 (25%), Positives = 37/77 (48%)
Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
           M N  P   LF+ N       + D+ R F PYG+++ + I+  F F+QF+  +    A+E
Sbjct: 4   MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
Query: 119 STDRSKLVDRVISVEYA 135
              +     + + +E +
Sbjct: 64  CESQEMNFGKKLILEVS 80

>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein Length = 98

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 127
           +F+ N + +  ++ D++  F  YG ++   + + FAFVQ+  +  A  A+   D   +  
Sbjct: 18  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 128 RVISVEYA 135
           +V+ +  A
Sbjct: 78  QVLDINLA 85

>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex Length = 77

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
           P   LF+ N       + D+ R F PYG+++ + I+  F F+QF+  +    A+E
Sbjct: 1   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 55

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
           GS   +    TK +  +        ++ +   F P+G++  ++I         R FAFV+
Sbjct: 1   GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 107 FETQEEATKALESTDRSKLVDRVISVEYA 135
           FE  E+A  A+++ + S+L  R I V  A
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRVNLA 89

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHV-RIRRN--------FAFVQFETQEEATKALE 118
           +F+ N DP    E+ +   F  +G +L   +I R+        +AF+ F + + +  A+E
Sbjct: 8   IFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 119 STDRSKLVDRVISVEYALKDDSE 141
           + +   L +R I+V YA K DS+
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSK 89

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	240
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-22
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-21
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-05
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-20
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-19
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-17
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-17
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-17
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-15
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-14
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-14
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-05
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	9e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-12
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-12
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-12
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-12
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-05
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	7e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-05
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-06
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-10
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	5e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-08
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	8e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	6e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-06
2div_A	99	TRNA selenocysteine associated protein; structural	2e-06
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-06
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-05
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	7e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	9e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	3e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-04

>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 = 99.7 bits (249), Expect = 2e-25
 Identities = 28/138 (20%), Positives = 55/138 (39%), Gaps = 16/138 (11%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
            FA++      DA   +  L+ +    +   L  + +           ++ +     + +
Sbjct: 160 RFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSN----PLEKSKRTDSATLEGREI 213

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEEATKALES 119
            + N       E  ++  FE +G++  + I             AF+ FE ++ A +AL+ 
Sbjct: 214 MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ- 272

Query: 120 TDRSKLVDRVISVEYALK 137
            +RS L +R ISV  A K
Sbjct: 273 MNRSLLGNREISVSLADK 290

>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 = 77.3 bits (191), Expect = 4e-17
 Identities = 29/153 (18%), Positives = 53/153 (34%), Gaps = 32/153 (20%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
            FA + F     A  AI     +        + V                        TL
Sbjct: 82  RFARIEFARYDGALAAITKTHKVVGQ---NEIIVSHLTE------------------CTL 120

Query: 69  FVINFDPIRTRERDIKRHFEPYGNV-LHVRIR-------RNFAFVQFETQEEATKALEST 120
           ++ NF P  T+  +I+   +    V L +R+        R FA++   ++E+A   +E  
Sbjct: 121 WMTNFPPSYTQR-NIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 121 DRSKLVDRVISVEYALKDDSERDDRYDSPRRGG 153
           +  K+    +  + +  +  E+  R DS    G
Sbjct: 180 NGLKIEGYTLVTKVS--NPLEKSKRTDSATLEG 210

>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 = 60.4 bits (147), Expect = 5e-11
 Identities = 15/88 (17%), Positives = 35/88 (39%), Gaps = 8/88 (9%)

Query: 52  HRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------FAFV 105
            +  ++++   R   T+ V N       +  + ++F+  G ++HV +  +      FA +
Sbjct: 28  SKKANEALTRNRELTTVLVKNLPK-SYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARI 86

Query: 106 QFETQEEATKALESTDRSKLVDRVISVE 133
           +F   + A  A+       +    I V 
Sbjct: 87  EFARYDGALAAIT-KTHKVVGQNEIIVS 113

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 86.1 bits (214), Expect = 4e-22
 Identities = 22/99 (22%), Positives = 42/99 (42%), Gaps = 6/99 (6%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 118
           M N  P   LF+ N       + D+ R F PYG+++ + I+  F F+QF+  +    A+E
Sbjct: 4   MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63

Query: 119 STDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRH 157
              +     + + +E +        +       G +G +
Sbjct: 64  CESQEMNFGKKLILEVS------SSNARPQFDHGDHGTN 96

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 2/53 (3%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMAN 61
           F F+ F++ +   DAI            ++L +E +        D      N
Sbjct: 46 AFGFIQFDNPQSVRDAIECESQEMN--FGKKLILEVSSSNARPQFDHGDHGTN 96

>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 = 89.7 bits (223), Expect = 1e-21
 Identities = 26/134 (19%), Positives = 42/134 (31%), Gaps = 17/134 (12%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G+ F  +     AA A   L   P G   R L V W    +               ++ L
Sbjct: 138 GYGFAEYMKKDSAARAKSDLLGKPLG--PRTLYVHWTDAGQLT--------PALLHSRCL 187

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALESTD 121
            V    P       + R      +    ++          FA +++ET E A +A +  D
Sbjct: 188 CVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQAD 247

Query: 122 RSKLVDRVISVEYA 135
              L    + V + 
Sbjct: 248 GLSLGGSHLRVSFC 261

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 76.6 bits (189), Expect = 9e-17
 Identities = 24/135 (17%), Positives = 42/135 (31%), Gaps = 28/135 (20%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G AFV   +   A  AI            R LSV+                        L
Sbjct: 58  GTAFVTLLNGEQAEAAINAFHQSRLR--ERELSVQLQP-----------------TDALL 98

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALEST 120
            V N  P  T++   +    P+G++    +  +        + F ++  ++ A +A    
Sbjct: 99  CVANLPPSLTQQ-QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 121 DRSKLVDRVISVEYA 135
               L  R + V + 
Sbjct: 158 LGKPLGPRTLYVHWT 172

>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 = 55.0 bits (133), Expect = 3e-09
 Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRS 123
           + + +          +++      Y  + +  + +    AFV     E+A  A+ +  +S
Sbjct: 23  RKILIRGLPG-DVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQS 80

Query: 124 KLVDRVISVEYALKD 138
           +L +R +SV+    D
Sbjct: 81  RLRERELSVQLQPTD 95

>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 = 86.7 bits (214), Expect = 5e-21
 Identities = 24/161 (14%), Positives = 47/161 (29%), Gaps = 33/161 (20%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSV------------------------EW 44
           G A V   D      AI  L+N      +  + V                          
Sbjct: 43  GAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSE 102

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------ 98
           +R  R    + +     Q P+  L   N     T E +     +  G      +      
Sbjct: 103 SRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVT-EENFFEICDELGVKRPTSVKVFSGK 161

Query: 99  --RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK 137
             R +   ++++++ +A + L   +  ++ +      Y LK
Sbjct: 162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202

>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 = 69.7 bits (170), Expect = 9e-15
 Identities = 17/127 (13%), Positives = 40/127 (31%), Gaps = 5/127 (3%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALEST 120
            +  L V   D  +     +   F  YGNV  V+    +   A V+        +A+   
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 121 DRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGR 180
           + + +  + ++V  + +        Y         +   +  S +  +         R +
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKD--FSESRNNRFSTPEQAAKNRIQ 120

Query: 181 SPAYDRY 187
            P+   +
Sbjct: 121 HPSNVLH 127

>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 = 83.1 bits (206), Expect = 7e-21
 Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 4/99 (4%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEAT 114
           GS  MA     K LFV N       E  +++ F  +G +  V+  +++AF+ F+ ++ A 
Sbjct: 4   GSSGMAK---VKVLFVRNLAN-TVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAV 59

Query: 115 KALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGG 153
           KA+E  +   L    I + +A   D +R +R    +   
Sbjct: 60  KAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAS 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 = 41.9 bits (99), Expect = 1e-05
 Identities = 8/59 (13%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR--GERGRHRDGSKSMANQRPT 65
            +AF++F++   A  A+  ++      +   + + +A+   ++ + R   +  A+   +
Sbjct: 46  DYAFIHFDERDGAVKAMEEMNGKDL--EGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 84.7 bits (210), Expect = 2e-20
 Identities = 25/137 (18%), Positives = 53/137 (38%), Gaps = 11/137 (8%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GFAFV +E    A  A+  ++++      R + V              +     R    +
Sbjct: 71  GFAFVEYEVPEAAQLALEQMNSVML--GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRI 128

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
           +V +     + + DIK  FE +G +    +         + + F+++E  + +  A+ S 
Sbjct: 129 YVASVHQDLS-DDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 121 DRSKLVDRVISVEYALK 137
           +   L  + + V  A+ 
Sbjct: 188 NLFDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 61.6 bits (150), Expect = 8e-12
 Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 11/123 (8%)

Query: 38  RRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVR 97
             ++      + GR     +          ++V +       E  I++ F P+G +  + 
Sbjct: 2   SHMASMTGGQQMGRGSAAQRQ-GALAIMSRVYVGSIYY-ELGEDTIRQAFAPFGPIKSID 59

Query: 98  I--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSP 149
           +         + FAFV++E  E A  ALE  +   L  R I V        +     D  
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN-IGQAQPIIDQL 118

Query: 150 RRG 152
              
Sbjct: 119 AEE 121

>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 = 82.3 bits (204), Expect = 1e-19
 Identities = 27/132 (20%), Positives = 52/132 (39%), Gaps = 16/132 (12%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
            F +V FE   D   A+  L  +        + +E  +G   +           R  +TL
Sbjct: 55  KFGYVDFESAEDLEKAL-ELTGLKV--FGNEIKLEKPKGRDSK---------KVRAARTL 102

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVR---IRRNFAFVQFETQEEATKALESTDRSKL 125
              N       E ++K  FE    +  V      +  A+++F+++ +A K LE    +++
Sbjct: 103 LAKNLSF-NITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161

Query: 126 VDRVISVEYALK 137
             R +S+ Y  +
Sbjct: 162 DGRSVSLYYTGE 173

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 12/102 (11%)

Query: 50  GRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNF 102
           G H       +       LF+ N +P      ++K           + +        R F
Sbjct: 1   GSHMVEG---SESTTPFNLFIGNLNP-NKSVAELKVAISELFAKNDLAVVDVRTGTNRKF 56

Query: 103 AFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDD 144
            +V FE+ E+  KALE     K+    I +E     DS++  
Sbjct: 57  GYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVR 97

>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 = 78.8 bits (195), Expect = 2e-18
 Identities = 31/138 (22%), Positives = 55/138 (39%), Gaps = 22/138 (15%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKT 67
           G  FV F   + A +A   L N+         + ++ A  E+    +  K          
Sbjct: 48  GCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK---------- 97

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
           LF+       T E DI+  F  +G +   RI R         AFV F T+  A  A+++ 
Sbjct: 98  LFIGMISKKCT-ENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 121 DRSKLVD---RVISVEYA 135
            +++ ++     + V++A
Sbjct: 157 HQAQTMEGCSSPMVVKFA 174

>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 = 61.1 bits (149), Expect = 6e-12
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN----------FAFVQFETQEEATKA 116
            +FV         E+D++  FE YG V  + + R+            FV F T++ A +A
Sbjct: 5   KMFVGQVPR-TWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 117 LESTDRSKLVDRVISVEYALKDDSERDDRYD 147
             +    K++  +         DSE+++  +
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>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 = 77.2 bits (190), Expect = 1e-17
 Identities = 31/156 (19%), Positives = 51/156 (32%), Gaps = 32/156 (20%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR--------------------GE 48
             A V   D   A  A+  L+        + + +  ++                    G 
Sbjct: 42  ENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 99

Query: 49  RGRHRDGSKSMANQR----PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----R 100
              HR       N +    P+ TL + N  P  + E D+K  F   G V+         R
Sbjct: 100 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEE-DLKVLFSSNGGVVKGFKFFQKDR 158

Query: 101 NFAFVQFETQEEATKALESTDRSKLVD-RVISVEYA 135
             A +Q  + EEA +AL       L +   + V ++
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>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 = 67.6 bits (165), Expect = 4e-14
 Identities = 26/121 (21%), Positives = 48/121 (39%), Gaps = 7/121 (5%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTD 121
              L V N +P R   + +   F  YG+V  V+I   ++  A VQ     +A  A+   +
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 122 RSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRGRS 181
             KL  + I +  +      ++ +     +   G    YG SP   +++  S ++     
Sbjct: 63  GHKLHGKPIRITLS----KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

Query: 182 P 182
           P
Sbjct: 119 P 119

>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 = 75.7 bits (187), Expect = 2e-17
 Identities = 35/137 (25%), Positives = 58/137 (42%), Gaps = 24/137 (17%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G+AFV F  + D+  AI+ L+ I      +RL V +AR   G     +           L
Sbjct: 46  GYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYARP-GGESIKDTN----------L 92

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
           +V N     T +  +   F  YG+++   I         R  AFV++  +EEA +A+ + 
Sbjct: 93  YVTNLPRTIT-DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 121 DRSKL--VDRVISVEYA 135
           +        + +SV  A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168

>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 = 55.3 bits (134), Expect = 7e-10
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
            L V         +R++   F   G +   RI R+        +AFV F ++ ++ +A++
Sbjct: 5   NLIVNYLPQ-DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 119 STDRSKLVDRVISVEYALKDDSERDD 144
             +   + ++ + V YA        D
Sbjct: 64  VLNGITVRNKRLKVSYARPGGESIKD 89

>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 = 73.5 bits (181), Expect = 3e-17
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 52  HRDGSKSMANQRPTKT-LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQ 110
           H   S  +      K+ LF+ N       + D+ R F PYG+++ + I+  F F+QF+  
Sbjct: 8   HHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNP 67

Query: 111 EEATKALESTDRSKLVDRVISVEYA 135
           +    A+E   +     + + +E +
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVS 92

>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 = 48.9 bits (117), Expect = 4e-08
 Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
           F F+ F++ +   DAI            ++L +E +    
Sbjct: 58 AFGFIQFDNPQSVRDAIEXESQEMN--FGKKLILEVSSSNA 96

>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 = 73.2 bits (180), Expect = 6e-17
 Identities = 16/98 (16%), Positives = 40/98 (40%)

Query: 49  RGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFE 108
           + +  + +     +     +F+ N +    ++ D++  F  YG V    + + +AFVQ+ 
Sbjct: 11  KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYS 70

Query: 109 TQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
            +  A  A+   +   L  + + +  A +   +R    
Sbjct: 71  NERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPS 108

>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 = 52.0 bits (125), Expect = 3e-09
 Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           G+AFV + ++R A  A+ G +        + L +  A   +      S
Sbjct: 63  GYAFVQYSNERHARAAVLGENGRVL--AGQTLDINMAGEPKPDRSGPS 108

>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 = 75.9 bits (187), Expect = 1e-16
 Identities = 35/195 (17%), Positives = 59/195 (30%), Gaps = 29/195 (14%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GF F+  E    A  A   LD        R L + +A                      L
Sbjct: 59  GFGFIRLESRTLAEIAKAELDGTIL--KSRPLRIRFAT-----------------HGAAL 99

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALES-T 120
            V N  P+ +    +++ F  +G V    +            FV+F  +  A KALE   
Sbjct: 100 TVKNLSPVVS-NELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158

Query: 121 DRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDYGRG- 179
           D + L+            +   D+     +     +     R   P + +  + ++    
Sbjct: 159 DGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYAS 218

Query: 180 RSPAYDRYNGPVYDQ 194
           R  A D       +Q
Sbjct: 219 RWKALDEMEKQQREQ 233

>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 = 59.3 bits (144), Expect = 1e-10
 Identities = 27/95 (28%), Positives = 36/95 (37%), Gaps = 7/95 (7%)

Query: 50  GRHRDGSKSMANQRPTK----TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFA 103
           G   D    +     T      LFV N       E D KR FE YG    V I   R F 
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPT-DITEEDFKRLFERYGEPSEVFINRDRGFG 61

Query: 104 FVQFETQEEATKALESTDRSKLVDRVISVEYALKD 138
           F++ E++  A  A    D + L  R + + +A   
Sbjct: 62  FIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG 96

>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 = 71.9 bits (177), Expect = 1e-16
 Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 7/91 (7%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTD 121
             K L+V N     T E  I++ F         R++  R++AFV F  +E+A +A+++ +
Sbjct: 14  SVKILYVRNLML-STSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 72

Query: 122 RSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
              L    I V  A       D     P  G
Sbjct: 73  GKVLDGSPIEVTLA----KPVDKDSSGPSSG 99

>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 = 45.7 bits (109), Expect = 6e-07
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           +AFV+F +  DA +A++ L+      D   + V  A+         S
Sbjct: 52 DYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAKPVDKDSSGPS 97

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 31/137 (22%), Positives = 61/137 (44%), Gaps = 24/137 (17%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G+ FV + D +DA  AI  L+ +      + + V +AR      RD +           L
Sbjct: 45  GYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYARPSSASIRDAN-----------L 91

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALEST 120
           +V       T ++++++ F  YG ++  RI  +          F++F+ + EA +A++  
Sbjct: 92  YVSGLPKTMT-QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 121 DRSKL--VDRVISVEYA 135
           +  K       I+V++A
Sbjct: 151 NGQKPSGATEPITVKFA 167

>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 = 53.3 bits (129), Expect = 4e-09
 Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 9/87 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
            L V         + + +  F   G +   ++ R+        + FV +   ++A KA+ 
Sbjct: 4   NLIVNYLPQ-NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 119 STDRSKLVDRVISVEYALKDDSERDDR 145
           + +  +L  + I V YA    +   D 
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSASIRDA 89

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 73.3 bits (181), Expect = 2e-16
 Identities = 28/137 (20%), Positives = 55/137 (40%), Gaps = 20/137 (14%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
            +AFV +    DA  A++ L+      +   + + WA   +    D          T  L
Sbjct: 42  NYAFVEYHQSHDANIALQTLNGKQI--ENNIVKINWAFQSQQSSSD---------DTFNL 90

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
           FV + +     +  ++  F+ + + L   +         R + FV F +Q++A  A++S 
Sbjct: 91  FVGDLNV-NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

Query: 121 DRSKLVDRVISVEYALK 137
               L  R + + +A K
Sbjct: 150 QGQDLNGRPLRINWAAK 166

>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 = 55.2 bits (134), Expect = 8e-10
 Identities = 17/86 (19%), Positives = 43/86 (50%), Gaps = 8/86 (9%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALE 118
           + L+V N D     E  +K++F+  G + +++I  +       +AFV++    +A  AL+
Sbjct: 1   RVLYVGNLDK-AITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 119 STDRSKLVDRVISVEYALKDDSERDD 144
           + +  ++ + ++ + +A +      D
Sbjct: 60  TLNGKQIENNIVKINWAFQSQQSSSD 85

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 75.3 bits (184), Expect = 2e-16
 Identities = 28/160 (17%), Positives = 55/160 (34%), Gaps = 10/160 (6%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRN-----FAFVQFE 108
           ++   RP  T+++ N +  + ++ ++K+     F  +G +L + + R+      AFV F+
Sbjct: 2   AVPETRPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60

Query: 109 TQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAY 168
               AT AL S       D+ + ++YA  D         +       R     +S     
Sbjct: 61  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120

Query: 169 RRRPSPDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRSPVP 208
            ++     G        +   P            H  P  
Sbjct: 121 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQ 160

>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 = 51.0 bits (121), Expect = 7e-08
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 52  HRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFE 108
               ++ ++   P   LF+ N  P  T E  +   F  +     VR+   R + AFV+F+
Sbjct: 194 QMPPAQPLSENPPNHILFLTNL-PEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFD 252

Query: 109 TQEEATKALESTDRSKLV-DRVISVEYA 135
            + +A  A ++    K+  +  + + +A
Sbjct: 253 NEVQAGAARDALQGFKITQNNAMKISFA 280

>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 = 73.9 bits (181), Expect = 3e-16
 Identities = 31/156 (19%), Positives = 54/156 (34%), Gaps = 32/156 (20%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH---------------- 52
             A V   D   A  A+  L+        + + +  ++ +  +                 
Sbjct: 73  ENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 130

Query: 53  -------RDGSKSMAN-QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----R 100
                  + GSK+  N   P+ TL + N  P  + E D+K  F   G V+         R
Sbjct: 131 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS-EEDLKVLFSSNGGVVKGFKFFQKDR 189

Query: 101 NFAFVQFETQEEATKALESTDRSKLVD-RVISVEYA 135
             A +Q  + EEA +AL       L +   + V ++
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>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 = 65.0 bits (158), Expect = 5e-13
 Identities = 26/126 (20%), Positives = 47/126 (37%), Gaps = 7/126 (5%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKA 116
                   L V N +P R   + +   F  YG+V  V+I   ++  A VQ     +A  A
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLA 88

Query: 117 LESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPDY 176
           +   +  KL  + I +  +       + +     +   G    YG SP   +++  S ++
Sbjct: 89  MSHLNGHKLHGKPIRITLSKHQ----NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144

Query: 177 GRGRSP 182
                P
Sbjct: 145 QNIFPP 150

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 31/149 (20%), Positives = 60/149 (40%), Gaps = 18/149 (12%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G+A+V F+   DA  A+  ++        + + + W++ +    + G     N      +
Sbjct: 58  GYAYVNFQQPADAERALDTMNFDVI--KGKPVRIMWSQRDPSLRKSGV---GN------I 106

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDR 122
           F+ N D      + +   F  +GN+L  ++       + + FV FETQE A +A+E  + 
Sbjct: 107 FIKNLDKSID-NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165

Query: 123 SKLVDRVISVEYALKDDSERDDRYDSPRR 151
             L DR + V           +     + 
Sbjct: 166 MLLNDRKVFVGRFKSRKEREAELGARAKE 194

>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 = 50.0 bits (120), Expect = 1e-07
 Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 9/93 (9%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQE 111
           A   P  +L+V +  P    E  +   F P G +L +R+ R+        +A+V F+   
Sbjct: 10  APSYPMASLYVGDLHP-DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDD 144
           +A +AL++ +   +  + + + ++ +D S R  
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKS 101

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 70.2 bits (172), Expect = 6e-16
 Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 11/101 (10%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQF 107
           G   + N    +++++  F    T + DIK   E  G VL++++RR          FV F
Sbjct: 1   GRWILKNDVKNRSVYIKGFPTDATLD-DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 59

Query: 108 ETQEEATKALESTD---RSKLVDRVISVEYALKDDSERDDR 145
           ++ E A K +E+     +   +  +   +Y  K + ER   
Sbjct: 60  DSIESAKKFVETPGQKYKETDLLILFKDDYFAKKNEERKQN 100

>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 = 72.4 bits (178), Expect = 7e-16
 Identities = 22/144 (15%), Positives = 47/144 (32%), Gaps = 21/144 (14%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR---------HRDGSKSM 59
            FAF+ F    +   A+   D I F    + L +      +           +  G  S 
Sbjct: 52  NFAFLEFRSVDETTQAM-AFDGIIF--QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVST 108

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQE 111
                   LF+         +  +K     +G +    + ++        +AF ++    
Sbjct: 109 VVPDSAHKLFIGGLPNYLN-DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN 167

Query: 112 EATKALESTDRSKLVDRVISVEYA 135
              +A+   +  +L D+ + V+ A
Sbjct: 168 VTDQAIAGLNGMQLGDKKLLVQRA 191

>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 = 56.6 bits (137), Expect = 4e-10
 Identities = 18/109 (16%), Positives = 35/109 (32%), Gaps = 16/109 (14%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------------RNFAFVQFETQ 110
             + L+V N       E  +   F     +  +                +NFAF++F + 
Sbjct: 3   MARRLYVGNIPF-GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 111 EEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSP 159
           +E T+A+   D      + + +     D        ++P     G  S 
Sbjct: 62  DETTQAMA-FDGIIFQGQSLKIRRP-HDYQPLPGMSENPSVYVPGVVST 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 70.0 bits (172), Expect = 9e-16
 Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 47  GERGRHRDGSKSMANQRPTKT-LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFV 105
                             + T LFV  F     +E ++   F P+G +  V+I   FAFV
Sbjct: 12  SGLVPRGSHMHHRQEGELSNTRLFVRPFPL-DVQESELNEIFGPFGPMKEVKILNGFAFV 70

Query: 106 QFETQEEATKALESTDRSKLVDRVISVEYA 135
           +FE  E A KA+E        ++ + V Y+
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVYS 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR 53
           GFAFV FE+   AA AI  +    F    + L V +++    R+R
Sbjct: 66  GFAFVEFEEAESAAKAIEEVHGKSFA--NQPLEVVYSKLPAKRYR 108

>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 = 70.0 bits (172), Expect = 3e-15
 Identities = 20/135 (14%), Positives = 42/135 (31%), Gaps = 23/135 (17%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
            FAF+ F    +   A+   D I F    + L +                         L
Sbjct: 52  NFAFLEFRSVDETTQAM-AFDGIIF--QGQSLKIRR-----------PHDYQPLPGAHKL 97

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
           F+         +  +K     +G +    +         + +AF ++       +A+   
Sbjct: 98  FIGGLPN-YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 121 DRSKLVDRVISVEYA 135
           +  +L D+ + V+ A
Sbjct: 157 NGMQLGDKKLLVQRA 171

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 15/92 (16%), Positives = 30/92 (32%), Gaps = 16/92 (17%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------------RNFAFVQFETQEE 112
           + L+V N       E  +   F     +  +                +NFAF++F + +E
Sbjct: 5   RRLYVGNIPF-GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSERDD 144
            T+A+   D      + + +     D      
Sbjct: 64  TTQAMAF-DGIIFQGQSLKIRRP-HDYQPLPG 93

>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 = 68.5 bits (168), Expect = 3e-15
 Identities = 29/114 (25%), Positives = 43/114 (37%), Gaps = 13/114 (11%)

Query: 47  GERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------- 98
           GE  R      S     P K L++ N  P R  ERD+   F  +       I        
Sbjct: 7   GEEIRKIPMFSSYNPGEPNKVLYLKNLSP-RVTERDLVSLFARFQEKKGPPIQFRMMTGR 65

Query: 99  RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            R  AF+ F  +E A +AL   +  KL  +++ +E+       +  R   P  G
Sbjct: 66  MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG----KNKKQRSSGPSSG 115

>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 = 43.4 bits (103), Expect = 5e-06
 Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
           G AF+ F +   A  A+  ++        + L +E+ + ++ R
Sbjct: 68  GQAFITFPNKEIAWQALHLVNGYKL--YGKILVIEFGKNKKQR 108

>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 = 68.0 bits (167), Expect = 4e-15
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTD 121
           PT  L+V    P  T    + R F+ +G++  +      +FA++Q+E+ + A  A     
Sbjct: 16  PTTRLWVGGLGP-NTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMR 74

Query: 122 RSKL--VDRVISVEYA 135
              L   DR + V++A
Sbjct: 75  GFPLGGPDRRLRVDFA 90

>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 = 53.4 bits (129), Expect = 8e-10
 Identities = 12/43 (27%), Positives = 19/43 (44%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
           FA++ +E    A  A   +   P G   RRL V++A+     
Sbjct: 54 SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 68.8 bits (168), Expect = 4e-15
 Identities = 16/118 (13%), Positives = 41/118 (34%), Gaps = 13/118 (11%)

Query: 45  ARGERGRHRDGSKSMA--NQRPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRI 98
           A+ ER             +  P++ + + N +P    +  ++          G++L + +
Sbjct: 7   AKFERQHMDSPDLGSTPPHTEPSQVVLITNINP-EVPKEKLQALLYALASSQGDILDIVV 65

Query: 99  RRN-----FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRR 151
             +      A++ F TQE A   +E+          + + ++ +    +     S   
Sbjct: 66  DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS-ETPQSQVAEDGSLEH 122

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 2/40 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
           G A++ F     A   +      PF      L + ++   
Sbjct: 73  GKAYIVFATQESAQAFVEAFQGYPF--QGNPLVITFSETP 110

>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 = 67.3 bits (165), Expect = 5e-15
 Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 5/95 (5%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKAL 117
           S ++ + +  L V N        ++++  FE YG V+   I +++AFV  E  E+A +A+
Sbjct: 3   SGSSGKASTKLHVGNI-SPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAI 61

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
              D ++   + + V+ +    + R      P  G
Sbjct: 62  RGLDNTEFQGKRMHVQLS----TSRLRTASGPSSG 92

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           +AFV+ E   DA +AIRGLDN  F    +R+ V+ +          S
Sbjct: 45 DYAFVHMERAEDAVEAIRGLDNTEF--QGKRMHVQLSTSRLRTASGPS 90

>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 = 67.6 bits (166), Expect = 5e-15
 Identities = 24/94 (25%), Positives = 47/94 (50%), Gaps = 11/94 (11%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRN-----FAFVQFE 108
           ++   RP  T+++ N +  + ++ ++K+     F  +G +L + + R+      AFV F+
Sbjct: 1   AVPETRPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 59

Query: 109 TQEEATKALESTDRSKLVDRVISVEYALKDDSER 142
               AT AL S       D+ + ++YA K DS+ 
Sbjct: 60  EVSSATNALRSMQGFPFYDKPMRIQYA-KTDSDI 92

>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 = 42.6 bits (101), Expect = 7e-06
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
          G AFV F++   A +A+R +   PF    + + +++A+ +
Sbjct: 52 GQAFVIFKEVSSATNALRSMQGFPFY--DKPMRIQYAKTD 89

>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 = 67.5 bits (165), Expect = 6e-15
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATK 115
           S ++ R    +   N  P  T   +I+  F  +G++  V +      A V+F    EA K
Sbjct: 3   SGSSGRSKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPR 150
           A      SK     + +E+A         +    +
Sbjct: 62  AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96

>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 = 40.2 bits (94), Expect = 7e-05
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTK 66
             A V F +  +A  A R L      +    L +EWA           K   +++P +
Sbjct: 47  ITAIVEFLEPLEARKAFRHLAY--SKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 67.8 bits (166), Expect = 6e-15
 Identities = 19/99 (19%), Positives = 35/99 (35%), Gaps = 10/99 (10%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           P K +     +    RE  +K     YG V  V I  +         A V F +   A +
Sbjct: 5   PLKEVTFARLND-NVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGY 154
            +++   + ++  +I  +       +R   Y+    G Y
Sbjct: 64  TVKNLHLTSVMGNIIHAQLD-IKGQQRMKYYELIVNGSY 101

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 2/45 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR 53
          G A V F   R A + ++ L           +  +     + R +
Sbjct: 49 GLARVLFTSTRGAKETVKNLHLTSV--MGNIIHAQLDIKGQQRMK 91

>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 = 66.2 bits (162), Expect = 1e-14
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 10/101 (9%)

Query: 55  GSKSMANQRPTK-TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQE 111
           GS           TL+V   D        ++  F P+GN++ + +   RN AFV +E  E
Sbjct: 4   GSSGERRAPRKGNTLYVYGED---MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKME 60

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            A +A+   + +++    + V  A     ++      P  G
Sbjct: 61  SADQAVAELNGTQVESVQLKVNIA----RKQPMLDSGPSSG 97

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
            AFV +E    A  A+  L+         +L V  AR
Sbjct: 50 NCAFVTYEKMESADQAVAELNGTQVE--SVQLKVNIAR 85

>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 = 65.7 bits (161), Expect = 2e-14
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKAL 117
           S  +   T  +FV N        ++++  FE  G V+   + +++AFV  E + +A  A+
Sbjct: 2   SSGSSGNTWKIFVGNV-SAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAI 60

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
              +  ++  + I+VE +      +  +   P  G
Sbjct: 61  AQLNGKEVKGKRINVELS-----TKGQKKSGPSSG 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 = 54.5 bits (132), Expect = 3e-10
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           +AFV+ E + DA  AI  L+        +R++VE +   + +    S
Sbjct: 44 DYAFVHMEKEADAKAAIAQLNGKEV--KGKRINVELSTKGQKKSGPSS 89

>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 = 64.9 bits (159), Expect = 4e-14
 Identities = 26/93 (27%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALES 119
           +       LF+ N  P    E++I+  FE YG VL   I +N+ FV  E +  A  A+ +
Sbjct: 3   SGSSGMVKLFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRN 61

Query: 120 TDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
               KL    I+VE +      +      P  G
Sbjct: 62  LHHYKLHGVNINVEAS----KNKSKASSGPSSG 90

>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 = 55.7 bits (135), Expect = 1e-10
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           + FV+ ED   A DAIR L +         ++VE ++ +       S
Sbjct: 43 NYGFVHIEDKTAAEDAIRNLHHYKL--HGVNINVEASKNKSKASSGPS 88

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 65.2 bits (159), Expect = 9e-14
 Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 15/108 (13%)

Query: 36  DRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH 95
           +     V+   G  G          +    + L+V         ++ +   F P+G++  
Sbjct: 40  NCTERHVDGGSGGSGGSG------GSATTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITD 92

Query: 96  VRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           ++I         R FAFV+FE  E+A  A+++ + S+L  R I V  A
Sbjct: 93  IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
           GFAFV FE   DAA AI  ++        R + V  A
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLA 140

>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 = 64.2 bits (157), Expect = 9e-14
 Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 15/107 (14%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQ 106
           S  +  ++ T  + V N  P +  +R+I+  F  +G +  VR+          R F FV 
Sbjct: 6   SGQVPKKQTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 107 FETQEEATKALESTDRSKLVD-RVISVEYALKDDSERDDRYDSPRRG 152
           F T+++A KA  +   S  +  R + +E+A             P  G
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWA----DSEVTVQSGPSSG 107

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 17/49 (34%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSK 57
           GF FV F   +DA  A   L +       RRL +EWA  E       S 
Sbjct: 59  GFGFVDFITKQDAKKAFNALCH-STHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 63.8 bits (156), Expect = 1e-13
 Identities = 25/100 (25%), Positives = 36/100 (36%), Gaps = 7/100 (7%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEE 112
            S           LFV N  P    E ++++ FE YG    V I   + F F++ ET+  
Sbjct: 5   SSGGEKTFTQRSRLFVGNLPP-DITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTL 63

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           A  A    D   L  + + V +A             P  G
Sbjct: 64  AEIAKVELDNMPLRGKQLRVRFA----CHSASLTSGPSSG 99

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
          GF F+  E    A  A   LDN+P     ++L V +A          S
Sbjct: 52 GFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFACHSASLTSGPS 97

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 63.9 bits (156), Expect = 1e-13
 Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSK 124
           T ++ N       E D+   F+ +G +L  +    +   F++++T E+A   + +     
Sbjct: 29  TAYIGNIPH-FATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87

Query: 125 LVDRVISVEYA 135
              R +   + 
Sbjct: 88  FQGRNLRTGWG 98

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          G  F+ ++    AA  I  L N PF    R L   W +
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPFQ--GRNLRTGWGK 99

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 63.0 bits (154), Expect = 2e-13
 Identities = 29/93 (31%), Positives = 39/93 (41%), Gaps = 13/93 (13%)

Query: 55  GSKSMANQR----PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNF 102
           GS   +  R    P   L V     + T ERD++  F  YG +  V I         R F
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59

Query: 103 AFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           AFV FE  ++A +A E  +  +L  R I V   
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>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 = 41.8 bits (99), Expect = 1e-05
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          GFAFVYFE+  DA +A    + +    D RR+ V    
Sbjct: 58 GFAFVYFENVDDAKEAKERANGMEL--DGRRIRVSGPS 93

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 63.1 bits (154), Expect = 3e-13
 Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 11/103 (10%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFET 109
           S +  ++   K L V N  P R R+ D+++ F  +G +L V I       + F FV FE 
Sbjct: 6   SGNSESKSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFEN 64

Query: 110 QEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
             +A +A E    + +  R I V  A    + R      P  G
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNA----TARVMTNSGPSSG 103

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
           GF FV FE+  DA  A   L       + R++ V  A   R     G  S
Sbjct: 56  GFGFVTFENSADADRAREKLHGTVV--EGRKIEVNNAT-ARVMTNSGPSS 102

>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 = 62.8 bits (153), Expect = 4e-13
 Identities = 18/109 (16%), Positives = 39/109 (35%), Gaps = 6/109 (5%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-----FAFVQFETQEEATKAL 117
              + L++ N  P +    ++   F  YG +  +R+         A+V +E   +A  A+
Sbjct: 6   EVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAV 64

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSP 166
           +      + +R + V Y   + + +                 YG +  P
Sbjct: 65  DHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 113

>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 = 47.4 bits (113), Expect = 2e-07
 Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG-RHRDGSKSMANQRPTKT 67
           G A+V +ED  DA +A+  L         R L V +    R  +  D  K     +  K 
Sbjct: 48  GTAYVVYEDIFDAKNAVDHLSGFNV--SNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE 105

Query: 68  LFVINFDP 75
            + IN DP
Sbjct: 106 KYGINTDP 113

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 62.3 bits (152), Expect = 5e-13
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 15/88 (17%)

Query: 62  QRPTKTLFVINFDPIRTRERDIKRHFEPYGN--VLHVRIRRN--------FAFVQFETQE 111
                T+ + N  P  T    I     PY +  V ++R+ ++        FAFVQ  +  
Sbjct: 6   HHHMDTIILRNIAP-HTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 112 EATKALES---TDRSKLVD-RVISVEYA 135
           +A++ L+          +D + I V++A
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDN--IPFGYDRRRLSVEWARG 47
          GFAFV      DA+  ++ L +   P   D + + V++A+ 
Sbjct: 54 GFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 62.2 bits (152), Expect = 5e-13
 Identities = 26/100 (26%), Positives = 37/100 (37%), Gaps = 16/100 (16%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------FAFVQFETQEEA 113
           +       +FV N  P     + +K  F   G+VL+  I+           V+FE+ E A
Sbjct: 3   SGSSGACQIFVRNL-PFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61

Query: 114 TKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGG 153
            +A    +  KL  R I V         R DR  S    G
Sbjct: 62  ERACRMMNGMKLSGREIDV---------RIDRNASGPSSG 92

>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 = 62.9 bits (153), Expect = 7e-13
 Identities = 25/129 (19%), Positives = 48/129 (37%), Gaps = 15/129 (11%)

Query: 36  DRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV-- 93
            RR L       E        +S     P   ++V N      +E+D+K  F  Y +   
Sbjct: 16  SRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAK-HVQEKDLKYIFGRYVDFSS 74

Query: 94  ------LHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSER 142
                   +R+      +  AF+    ++ A KAL+  +   L  + + V++A +    +
Sbjct: 75  ETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA-RSARPK 133

Query: 143 DDRYDSPRR 151
            D  +  R+
Sbjct: 134 QDPKEGKRK 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 = 63.0 bits (153), Expect = 8e-13
 Identities = 27/133 (20%), Positives = 43/133 (32%), Gaps = 7/133 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE---WARGERGRHRDGSKSMANQRPT 65
           G       D   A    +   N                +   E   H        +    
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLD 73

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDR 122
             ++V N       + +++R F  YG +  V + RN   FAFV+FE   +A  A+   D 
Sbjct: 74  CKVYVGNLGN-NGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132

Query: 123 SKLVDRVISVEYA 135
             L    + VE +
Sbjct: 133 RTLCGCRVRVELS 145

>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 = 49.1 bits (117), Expect = 1e-07
 Identities = 22/41 (53%), Positives = 26/41 (63%), Gaps = 2/41 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
           GFAFV FED RDAADA+R LD         R+ VE + GE+
Sbjct: 111 GFAFVEFEDPRDAADAVRELDGRTL--CGCRVRVELSNGEK 149

>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 = 61.9 bits (151), Expect = 8e-13
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 13/106 (12%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
            S S       + L+V         ++ +   F P+G++  ++I         R FAFV+
Sbjct: 2   SSGSSGMATTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           FE  E+A  A+++ + S+L  R I V  A         +   P  G
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRVNLA----KPMRIKESGPSSG 102

>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 = 40.7 bits (96), Expect = 3e-05
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           GFAFV FE   DAA AI  ++        R + V  A+  R +    S
Sbjct: 55  GFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAKPMRIKESGPS 100

>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 = 61.5 bits (150), Expect = 9e-13
 Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTD-R 122
             L++ N  P      D+++ F      L  ++  +  +AFV +  Q  A +A+E+   +
Sbjct: 9   NKLYIGNLSP-AVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67

Query: 123 SKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            +L  +++ V+Y+      +  R   P  G
Sbjct: 68  VELHGKIMEVDYS----VSKKLRSSGPSSG 93

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
          G+AFV + D   A  AI  L +       + + V+++  ++ R    S
Sbjct: 45 GYAFVDYPDQNWAIRAIETL-SGKVELHGKIMEVDYSVSKKLRSSGPS 91

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 16/84 (19%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSK 124
           T++          ++ +++ F P+G ++ +R+   + ++FV+F T E A  A+ S + + 
Sbjct: 27  TVYCGGIAS-GLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTT 85

Query: 125 LVDRVISVEYALKDDSERDDRYDS 148
           +   V+   +  K+  +      S
Sbjct: 86  IEGHVVKCYWG-KESPDMTSGPSS 108

>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 = 61.0 bits (149), Expect = 1e-12
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 11/86 (12%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFET 109
           SMA  +  + L+V         ++ +   F P+G++  ++I         R FAFV+FE 
Sbjct: 2   SMATTK--RVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58

Query: 110 QEEATKALESTDRSKLVDRVISVEYA 135
            E+A  A+++ + S+L  R I V  A
Sbjct: 59  AEDAAAAIDNMNESELFGRTIRVNLA 84

>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 = 42.1 bits (100), Expect = 8e-06
 Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          GFAFV FE   DAA AI  ++        R + V  A+
Sbjct: 50 GFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAK 85

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.3 bits (149), Expect = 1e-12
 Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-----RRNFAFVQFET 109
            S S+  ++  + L + N  P   +   +      YG V                V + +
Sbjct: 5   SSGSVPKRQRIRKLQIRNI-PPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSS 63

Query: 110 QEEATKALESTDRSKLVDRVISVEYA 135
           +++A +AL+  +  +L +  + V Y 
Sbjct: 64  KDQARQALDKLNGFQLENFTLKVAYI 89

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 8/40 (20%), Positives = 13/40 (32%), Gaps = 2/40 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
              V +     A  A+  L+   F  +   L V +   E
Sbjct: 55 AVVNVTYSSKDQARQALDKLNG--FQLENFTLKVAYIPDE 92

>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 = 61.1 bits (149), Expect = 1e-12
 Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 9/104 (8%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFE 108
              S +      +KTL + N       E  ++  FE    +   + +    + +AF++F 
Sbjct: 3   SGSSGNSTWSGESKTLVLSNL-SYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFA 61

Query: 109 TQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           + E+A +AL S ++ ++  R I +E        R      P  G
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQ----GPRGSPNSGPSSG 101

>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 = 40.0 bits (94), Expect = 6e-05
 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
          G+AF+ F    DA +A+   +      + R + +E        +   S
Sbjct: 54 GYAFIEFASFEDAKEALNSCNKREI--EGRAIRLELQGPRGSPNSGPS 99

>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 = 60.7 bits (148), Expect = 2e-12
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 4/85 (4%)

Query: 54  DGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQ 110
           +   +    R  +TL   N       E ++K  FE    +  V      +  A+++F+++
Sbjct: 5   EDPCTSKKVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSE 63

Query: 111 EEATKALESTDRSKLVDRVISVEYA 135
            +A K LE    +++  R +S+ Y 
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYT 88

>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 = 60.8 bits (148), Expect = 2e-12
 Identities = 30/125 (24%), Positives = 46/125 (36%), Gaps = 17/125 (13%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQE 111
           M        LF+   +   T E+ +K  F  +G +  V +        R FAF+ FE   
Sbjct: 1   MVEADHPGKLFIGGLNR-ETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPA 59

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRR 171
           +A  A +  +   L  + I VE A K          S + GG  R     R+ SP+    
Sbjct: 60  DAKNAAKDMNGKSLHGKAIKVEQAKK---------PSFQSGGRRRPPASSRNRSPSGSLE 110

Query: 172 PSPDY 176
               +
Sbjct: 111 HHHHH 115

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRP 64
           GFAF+ FE+  DA +A + ++        + + VE A+    +     +  A+ R 
Sbjct: 49  GFAFITFENPADAKNAAKDMNGKSL--HGKAIKVEQAKKPSFQSGGRRRPPASSRN 102

>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 = 62.2 bits (151), Expect = 2e-12
 Identities = 32/154 (20%), Positives = 59/154 (38%), Gaps = 18/154 (11%)

Query: 15  FEDDRDAADAIRGLDNI-------PFGYDRRRLSVEWARGERGRHRDGSKSMANQR--PT 65
           FE D D    I  L           FG D        +        D       QR    
Sbjct: 13  FEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEG 72

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
             LFV +      +E +I+  F  YG + ++ +         + +A V++ET ++A  A 
Sbjct: 73  WILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRR 151
           E+ + ++++ + I V++      +R  + +  RR
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165

>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 = 39.8 bits (93), Expect = 2e-04
 Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
           G+A V +E  + A  A   L+        + + V+W   +  +    S+ 
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEI--MGQTIQVDWCFVKGPKRVKKSEK 162

>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 = 60.3 bits (147), Expect = 2e-12
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
            +  LFV N     + E D+++ F  YG +  +           + FAFV F   E A K
Sbjct: 7   GSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGG 153
           A    D      R++ V  +    + + +   S    G
Sbjct: 66  AYAEVDGQVFQGRMLHVLPS----TIKKEASQSGPSSG 99

>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 = 41.8 bits (99), Expect = 1e-05
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
          GFAFV F     A  A   +D   F    R L V  +  ++   + G  S
Sbjct: 51 GFAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHVLPSTIKKEASQSGPSS 98

>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 = 60.3 bits (147), Expect = 3e-12
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEE 112
           A +   +T+FV N +  R RE  +   F   G +  V I        ++F FV F+  E 
Sbjct: 11  AQEEADRTVFVGNLEA-RVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES 69

Query: 113 ATKALESTDRSKLVDRVISVEYA 135
            + A+   +  +L  R I+V   
Sbjct: 70  VSYAIALLNGIRLYGRPINVSGP 92

>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 = 60.8 bits (148), Expect = 3e-12
 Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 17/118 (14%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQF 107
            S ++   R   T+FV N D  +   + +K  F   G V+   I  +          V F
Sbjct: 5   SSGALQAGRLGSTVFVANLDY-KVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTF 63

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPS 165
           E   EA +A+   +   L DR + V+               P+   +    P    PS
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMD---------ERALPKGDFFPPERPQQSGPS 112

>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 = 60.3 bits (147), Expect = 3e-12
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFET 109
           S  M +    +TL+V N       E  I + F   G     ++         + FV+F  
Sbjct: 6   SGMMEDDGQPRTLYVGNLSR-DVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYE 64

Query: 110 QEEATKALESTDRSKLVDRVISVEYALKDDSER 142
             +A  AL + +  K++ + + V +A    S +
Sbjct: 65  HRDAAAALAAMNGRKILGKEVKVNWA-TTPSSQ 96

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 5/85 (5%)

Query: 55  GSKSMANQRPT-KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQE 111
           GS   + +  T  TL+V       T E D++ HF  +G +  + +  R+  AF+QF T++
Sbjct: 1   GSSGSSGEDKTITTLYVGGLGDTIT-ETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ 59

Query: 112 EATKALEST-DRSKLVDRVISVEYA 135
            A  A E + ++  +  R ++V++ 
Sbjct: 60  AAEVAAEKSFNKLIVNGRRLNVKWG 84

>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 = 59.9 bits (146), Expect = 3e-12
 Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 13/106 (12%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
              S  +     TL V N    RT    ++R FE YG V  V I         R FAFV+
Sbjct: 3   SGSSGPDVDGMITLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           F  + +A  A  + D ++L  R + V+ A             P  G
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVA----RYGRRDLSGPSSG 103

>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 = 44.1 bits (105), Expect = 2e-06
 Identities = 21/48 (43%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           GFAFV F D RDA DA   +D      D R L V+ AR  R      S
Sbjct: 56  GFAFVRFHDRRDAQDAEAAMDGAEL--DGRELRVQVARYGRRDLSGPS 101

>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 = 59.9 bits (146), Expect = 3e-12
 Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 13/105 (12%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------R-RNFAFVQF 107
           S S         LFV       T E+ +++ F  YG +  V +       R R F FV F
Sbjct: 3   SGSSGMASDEGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           E  ++A  A+ + +   +  R I V+ A     +  D    P  G
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQA----GKSSDNRSGPSSG 102

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
           GF FV FE+  DA DA+  ++      D R++ V+ A  +   +R G  S
Sbjct: 55  GFGFVTFENIDDAKDAMMAMNGKSV--DGRQIRVDQAG-KSSDNRSGPSS 101

>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 = 59.9 bits (146), Expect = 3e-12
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 10/101 (9%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAF 104
              S          T+ V N     TRE D++  F P+G++  + + ++        FAF
Sbjct: 3   SGSSGPNRRADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDR 145
           + F  +E+A +A+           +++VE+A K  +     
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWA-KPSTNSGPS 101

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 20/38 (52%), Positives = 24/38 (63%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          GFAF+ F    DAA AI G+    FGYD   L+VEWA+
Sbjct: 58 GFAFISFHRREDAARAIAGVSG--FGYDHLILNVEWAK 93

>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 = 59.9 bits (146), Expect = 4e-12
 Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 13/97 (13%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
            +  L+V +       E  ++  FEP+G + ++ +         + + F+ F   E A +
Sbjct: 4   GSSGLYVGSL-HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           ALE  +  +L  R + V +     +ER D    P  G
Sbjct: 63  ALEQLNGFELAGRPMRVGHV----TERLDGGSGPSSG 95

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 37.1 bits (87), Expect = 5e-04
 Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 3/50 (6%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
          G+ F+ F D   A  A+  L+        R + V     ER     G  S
Sbjct: 48 GYGFITFSDSECARRALEQLNGFEL--AGRPMRVGHVT-ERLDGGSGPSS 94

>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 = 60.1 bits (146), Expect = 4e-12
 Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 19/111 (17%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 107
           S   ++    KT+F+ N     + E  +    + +G++ +VR+         +  AF QF
Sbjct: 6   SGLPSDVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 108 ETQEEATKALESTDRSKLVD------RVISVEYALKDDSERDDRYDSPRRG 152
            TQE A K L +              R + V+ A+     RD+    P  G
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV----TRDEAASGPSSG 111

>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 = 59.5 bits (145), Expect = 4e-12
 Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 9/90 (10%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
              S        T++V N  P      D+ R F  YG V+ V I         +  AF+ 
Sbjct: 6   SGMSGGLAPSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYAL 136
           F  ++ A     + +  +L  RVI    A+
Sbjct: 65  FLDKDSAQNCTRAINNKQLFGRVIKASIAI 94

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
          G AF+ F D   A +  R ++N       R +    A
Sbjct: 59 GVAFILFLDKDSAQNCTRAINNKQL--FGRVIKASIA 93

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 61.4 bits (149), Expect = 4e-12
 Identities = 30/135 (22%), Positives = 44/135 (32%), Gaps = 9/135 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           G       D   A    +   N                              +     +L
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSL 73

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
            V N    RT    ++R FE YG V  V I         R FAFV+F  + +A  A+++ 
Sbjct: 74  KVDNL-TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132

Query: 121 DRSKLVDRVISVEYA 135
           D + L  R + V+ A
Sbjct: 133 DGAVLDGRELRVQMA 147

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 21/48 (43%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           GFAFV F D RDA DA+  +D      D R L V+ AR  R      S
Sbjct: 113 GFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMARYGRPPDSHHS 158

>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 = 60.0 bits (146), Expect = 5e-12
 Identities = 24/116 (20%), Positives = 42/116 (36%), Gaps = 14/116 (12%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----- 99
           + G+             +R  +T+F +     R R RD++  F   G V  VRI      
Sbjct: 5   SSGKSPVREPVDNLSPEERDARTVFCMQLAA-RIRPRDLEDFFSAVGKVRDVRIISDRNS 63

Query: 100 ---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
              +  A+V+F   +    A+      +L+   I V+ +        +R   P  G
Sbjct: 64  RRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS----QAEKNRLSGPSSG 114

>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 = 58.8 bits (143), Expect = 8e-12
 Identities = 20/100 (20%), Positives = 35/100 (35%), Gaps = 16/100 (16%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-----------FAFVQFETQEE 112
            +  LF+ N +   T E  +K  F   G +    I +            F FV+++  E+
Sbjct: 4   GSSGLFIKNLNF-STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           A KAL+      +    + V  + +           P  G
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISER----ATKPASGPSSG 98

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.3 bits (144), Expect = 9e-12
 Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQ 106
           R    +  N+   K L V N  P R R+ D+++ F  +G +L V I       + F FV 
Sbjct: 17  RGSHMNTENKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 75

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYA 135
           FE   +A +A E    + +  R I V  A
Sbjct: 76  FENSADADRAREKLHGTVVEGRKIEVNNA 104

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 11/87 (12%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALE 118
           +  +F+ N D      + +   F  +GN+L  ++       + + FV FETQE A +A+E
Sbjct: 5   SGNIFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 63

Query: 119 STDRSKLVDRVISVEYALKDDSERDDR 145
             +   L DR + V         R +R
Sbjct: 64  KMNGMLLNDRKVFVGRFKS----RKER 86

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA--RGERGRHRDGSKSMANQRPTK 66
           G+ FV+FE    A  AI  ++ +    + R++ V     R ER             +   
Sbjct: 46  GYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSRKEREAELGA-----RAKEFT 98

Query: 67  TLFVINFDPIRTRE 80
            +++ NF P  TR 
Sbjct: 99  NVYIKNFGPGSTRA 112

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 14/83 (16%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEE 112
           +       LF+    P    + +++   + +G V  +R+        +  A+V++E + +
Sbjct: 12  STSLEKHKLFISGL-PFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQ 70

Query: 113 ATKALESTDRSKLVDRVISVEYA 135
           A++A+   D   + + +I V  +
Sbjct: 71  ASQAVMKMDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 8/38 (21%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          G A+V +E++  A+ A+  +D +        + V  + 
Sbjct: 59 GLAYVEYENESQASQAVMKMDGMTI--KENIIKVAISN 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.2 bits (141), Expect = 1e-11
 Identities = 14/94 (14%), Positives = 33/94 (35%), Gaps = 6/94 (6%)

Query: 47  GERGRHR-DGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFA 103
           G    H  +          +  + +         E D+    + +G + +V +  ++  A
Sbjct: 2   GHHHHHHMENYDDPHKTPASPVVHIRGL-IDGVVEADLVEALQEFGPISYVVVMPKKRQA 60

Query: 104 FVQFETQEEATKALE--STDRSKLVDRVISVEYA 135
            V+FE    A  A+   + ++  +      V Y+
Sbjct: 61  LVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS 94

>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 = 57.8 bits (140), Expect = 2e-11
 Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRNFAFVQFETQEEATKALESTDRS 123
           +  + V N  P  +  +++    + Y     +V   +  AFV     E+A  A++   + 
Sbjct: 5   SSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 124 KLVDRVISVEYA 135
               + + V+  
Sbjct: 64  SFRGKDLIVQLQ 75

>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 = 39.3 bits (92), Expect = 9e-05
 Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 2/47 (4%)

Query: 2  CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
          C        AFV   +   A +AI+      F    + L V+    +
Sbjct: 34 CYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF--RGKDLIVQLQPTD 78

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 30/107 (28%), Positives = 46/107 (42%), Gaps = 9/107 (8%)

Query: 37  RRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV 96
              ++      + GR      + AN  P   L V     + T ERD++  F  YG +  V
Sbjct: 18  GSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADV 76

Query: 97  RI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
            I         R FAFV FE  ++A +A E  +  +L  R I V+++
Sbjct: 77  SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER 49
           GFAFVYFE+  DA +A    + +    D RR+ V+++  +R
Sbjct: 89  GFAFVYFENVDDAKEAKERANGMEL--DGRRIRVDFSITKR 127

>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 = 58.0 bits (141), Expect = 2e-11
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 16/108 (14%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 111
           A  R  +++FV N  P    E  +K  F   G V+  R+         + + F +++ QE
Sbjct: 3   AVDRSLRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSP 159
            A  A+ + +  +   R + V+ A           +       G  +P
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNA-------ASEKNKEELKSLGTGAP 102

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ 62
           G+ F  ++D   A  A+R L+   F    R L V+ A  E+ +    S      
Sbjct: 51  GYGFCEYQDQETALSAMRNLNGREF--SGRALRVDNAASEKNKEELKSLGTGAP 102

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 9/96 (9%)

Query: 48  ERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------R 99
           +                   LFV         E DI   F  YG + ++ +         
Sbjct: 6   DSVEQDGDEPGPQRSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64

Query: 100 RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           + +  V++ET +EA  A+E  +   L+ + ISV++ 
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100

>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 = 1e-04
 Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
           G+  V +E  ++A  A+ GL+        + +SV+W  
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDL--MGQPISVDWCF 101

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 13/105 (12%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 107
           S  ++ +    T++V   D  +  E  +   F   G V++  +         + + FV+F
Sbjct: 6   SGPISERNQDATVYVGGLDE-KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            ++E+A  A++  D  KL  + I V  A    S  +     P  G
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKA----SAHNKNLSGPSSG 105

>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 = 37.6 bits (88), Expect = 5e-04
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR 53
           G+ FV F  + DA  AI+ +D I      + + V  A        
Sbjct: 58  GYGFVEFLSEEDADYAIKIMDMIKL--YGKPIRVNKASAHNKNLS 100

>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 = 57.6 bits (140), Expect = 3e-11
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 9/95 (9%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
           P++ +++ +  P    E  I       G V+++++         + +AF++F   E +  
Sbjct: 1   PSRVVYLGSI-PYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPR 150
           A+ + +  +L  R +   Y+   D           
Sbjct: 60  AVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ 62
          G+AF+ F D   +A A+R L+    G   R L   ++               + 
Sbjct: 45 GYAFIEFRDLESSASAVRNLNGYQLG--SRFLKCGYSSNSDISGVSLEHHHHHH 96

>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 = 58.0 bits (140), Expect = 3e-11
 Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 5/108 (4%)

Query: 47  GERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAF 104
           G   R      S +   P++ + +    PI   E ++     P+G V ++ +   +N AF
Sbjct: 13  GLVPRGSHMGDSRSAGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAF 71

Query: 105 VQFETQEEATKALE--STDRSKLVDRVISVEYALKDDSERDDRYDSPR 150
           ++  T+E A   +   ++    L  + I ++++   + + D   +  R
Sbjct: 72  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119

>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 = 58.2 bits (141), Expect = 3e-11
 Identities = 30/132 (22%), Positives = 47/132 (35%), Gaps = 20/132 (15%)

Query: 48  ERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------R 99
           +                   LFV         E DI   F  YG + ++ +         
Sbjct: 5   DSVEQDGDEPGPQRSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63

Query: 100 RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSP 159
           + +  V++ET +EA  A+E  +   L+ + ISV++              P +G   R   
Sbjct: 64  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC---------FVRGPPKG--KRRGG 112

Query: 160 YGRSPSPAYRRR 171
             RS SP  RRR
Sbjct: 113 RRRSRSPDRRRR 124

>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 = 38.5 bits (90), Expect = 3e-04
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 8/61 (13%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR------GERGRHRDGSKSMANQ 62
           G+  V +E  ++A  A+ GL+        + +SV+W        G+R   R  S+S   +
Sbjct: 65  GYTLVEYETYKEAQAAMEGLNGQDL--MGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRR 122

Query: 63  R 63
           R
Sbjct: 123 R 123

>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 = 4e-11
 Identities = 24/115 (20%), Positives = 45/115 (39%), Gaps = 21/115 (18%)

Query: 44  WARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-- 101
            + G+R                  L+V N D     +  +++ F P+G +   ++     
Sbjct: 4   GSSGDRITRYQVVN----------LYVKNLDD-GIDDERLRKAFSPFGTITSAKVMMEGG 52

Query: 102 ----FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
               F FV F + EEATKA+   +   +  + + V  A +    +++R   P  G
Sbjct: 53  RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQR----KEERQSGPSSG 103

>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 = 57.3 bits (139), Expect = 5e-11
 Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 9/98 (9%)

Query: 46  RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------- 98
           R       +             LFV +      +E +I+  F  YG + ++ +       
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTG 65

Query: 99  -RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
             + +A V++ET ++A  A E+ + ++++ + I V++ 
Sbjct: 66  FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103

>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 = 38.8 bits (91), Expect = 2e-04
 Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
           G+A V +E  + A  A   L+        + + V+W  
Sbjct: 69  GYALVEYETHKQALAAKEALNGAEI--MGQTIQVDWCF 104

>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 = 59.7 bits (144), Expect = 5e-11
 Identities = 26/174 (14%), Positives = 46/174 (26%), Gaps = 14/174 (8%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----- 99
              + G+    +           L++ N     T + D+       G    + I+     
Sbjct: 48  VGDDVGKGAAPNVVYTYTGKRIALYIGNLTW-WTTDEDLTEAVHSLGVNDILEIKFFENR 106

Query: 100 -----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGY 154
                + FA V   ++  + K ++   + +L  +   V    K    + +          
Sbjct: 107 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSG 166

Query: 155 GRHSPYGRSPSPAYRRRPSPDYGRGRSPAYDRYNGPVYDQRRSPDHGRHRSPVP 208
                    P     R   P  GRGR        G     R     G    P P
Sbjct: 167 QMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGG---DRFPGPAGPGGPPPP 217

>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 = 56.9 bits (138), Expect = 5e-11
 Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 10/105 (9%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQF 107
              S   A  +P+KTLFV       T E  +K  F+       V  R     + F FV F
Sbjct: 3   SGSSGPNARSQPSKTLFVKGL-SEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDF 61

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            ++E+A  A E+ +  ++    +++++A      + +    P  G
Sbjct: 62  NSEEDAKAAKEAMEDGEIDGNKVTLDWA----KPKGEGGSGPSSG 102

>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 = 40.7 bits (96), Expect = 3e-05
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
           GF FV F  + DA  A   +++     D  +++++WA+  +G    G  S
Sbjct: 55  GFGFVDFNSEEDAKAAKEAMEDGEI--DGNKVTLDWAK-PKGEGGSGPSS 101

>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 = 56.8 bits (137), Expect = 7e-11
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 55  GSKSMANQR----PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFE 108
           GS   +  +    P++ L +    P    E ++     P+G V ++ +   +N AF++  
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELA 59

Query: 109 TQEEATKALE--STDRSKLVDRVISVEYA 135
           T+E A   +   S     L ++ I ++Y+
Sbjct: 60  TEEAAITMVNYYSAVTPHLRNQPIYIQYS 88

>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 = 56.5 bits (137), Expect = 7e-11
 Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 21/112 (18%)

Query: 55  GSKSMANQRPTKT----LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FA 103
           GS   +           LFV   +  ++ E D+ R F+P+G +    + R         A
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQS-EEDVLRLFQPFGVIDECTVLRGPDGSSKGCA 59

Query: 104 FVQFETQEEATKALESTDRSKLVD---RVISVEYALKDDSERDDRYDSPRRG 152
           FV+F +  EA  A+ +   S+ +      + V++A   D E       P  G
Sbjct: 60  FVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFA-DTDKESG-----PSSG 105

>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 = 56.6 bits (137), Expect = 8e-11
 Identities = 25/113 (22%), Positives = 39/113 (34%), Gaps = 10/113 (8%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----- 99
           + G  G    G            ++V N  P   R +DI+  F  YG +  + ++     
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGG 60

Query: 100 RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
             FAFV+FE   +A  A+   D        + VE+              P  G
Sbjct: 61  PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP----RSGRGTGSGPSSG 109

>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 = 52.7 bits (127), Expect = 2e-09
 Identities = 23/48 (47%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
            FAFV FED RDA DA+ G D   +  D  RL VE+ R  RG     S
Sbjct: 62  PFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEFPRSGRGTGSGPS 107

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.4 bits (136), Expect = 9e-11
 Identities = 17/94 (18%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALE 118
           +  P++ + +    PI   E ++     P+G V ++ +   +N AF++  T+E A   + 
Sbjct: 12  SGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVN 70

Query: 119 STDRSKLV--DRVISVEYALKDDSERDDRYDSPR 150
                  V   + I ++++   + + D   +  R
Sbjct: 71  YYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 104

>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 = 57.5 bits (140), Expect = 1e-10
 Identities = 23/137 (16%), Positives = 48/137 (35%), Gaps = 25/137 (18%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GF F+ FE      + ++    +    D + +  + A                Q  T  +
Sbjct: 46  GFGFLSFEKPSSVDEVVKTQHIL----DGKVIDPKRA-----------IPRDEQDKTGKI 90

Query: 69  FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 120
           FV    P   R ++ +  F  +G ++  ++         R F FV +++ +   +  +  
Sbjct: 91  FVGGIGP-DVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-N 148

Query: 121 DRSKLVDRVISVEYALK 137
                 DR I ++ A  
Sbjct: 149 KFIDFKDRKIEIKRAEP 165

>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 = 46.0 bits (110), Expect = 2e-06
 Identities = 19/91 (20%), Positives = 45/91 (49%), Gaps = 16/91 (17%)

Query: 63  RPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEE 112
           + +  +F+  +N+D   T E +++ +F  YG V  ++I ++        F F+ FE    
Sbjct: 1   KESCKMFIGGLNWD---TTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS 57

Query: 113 ATKALESTDRSKLVDRVISVEYAL-KDDSER 142
             + ++   +  L  +VI  + A+ +D+ ++
Sbjct: 58  VDEVVK--TQHILDGKVIDPKRAIPRDEQDK 86

>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 = 57.2 bits (137), Expect = 2e-10
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 11/86 (12%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-------NFAFVQFETQEEA 113
           N    +++++  F    T + DIK   E  G VL++++RR          FV F++ E A
Sbjct: 105 NDVKNRSVYIKGFPTDATLD-DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 163

Query: 114 TKALESTDRSKLVDRVISVEYALKDD 139
            K +E T   K  +  + +    KDD
Sbjct: 164 KKFVE-TPGQKYKETDLLIL--FKDD 186

>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 = 54.9 bits (133), Expect = 3e-10
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 11/93 (11%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKAL 117
             T+FV   D  R  E +I+  F  YG+V  V+I        + + FV F    +  K +
Sbjct: 9   PNTVFVGGIDV-RMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPR 150
           E   +     + + +  A++        +  PR
Sbjct: 68  E--SQINFHGKKLKLGPAIRKQ-NLSTYHVQPR 97

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 21/83 (25%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 75  PIRTRERDIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVIS 131
                + +++R F  YG +  V I RN   FAFV+FE   +A  A+   D   +    + 
Sbjct: 9   GTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR 68

Query: 132 VEYALKDDSERDDRYDSPRRGGY 154
           VE +              RR   
Sbjct: 69  VELSTGMPRRSRFDRPPARRKLL 91

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 23/48 (47%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
          GFAFV FED RDA DA+RGLD         R+ VE + G   R R   
Sbjct: 38 GFAFVEFEDPRDAEDAVRGLDGKVI--CGSRVRVELSTGMPRRSRFDR 83

>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 = 54.5 bits (132), Expect = 3e-10
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 11/84 (13%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEEA 113
           +PTK + +         +  I   F  YG +  + +          + +A+V+FE  +EA
Sbjct: 3   KPTK-VHIGRL-TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 114 TKALESTDRSKLVDRVISVEYALK 137
            KAL+  D  ++  + I+    L 
Sbjct: 61  EKALKHMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
          G+A+V FE+  +A  A++ +D      D + ++         R
Sbjct: 48 GYAYVEFENPDEAEKALKHMDGGQI--DGQEITATAVLAPWPR 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 54.5 bits (131), Expect = 3e-10
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 4/92 (4%)

Query: 47  GERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---FA 103
           G  G    GS           ++V N  P   R  D+KR     G+V      +     A
Sbjct: 1   GSSGSSGPGSPPGEGAPLAADVYVGNL-PRDARVSDLKRALRELGSVPLRLTWQGPRRRA 59

Query: 104 FVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           F+ +     A +A+      +L    + V  A
Sbjct: 60  FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
            AF+++ D   A  A+  L  +  G     L V  AR +R +
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLG--TDTLRVALARQQRDK 97

>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 = 55.6 bits (134), Expect = 5e-10
 Identities = 31/148 (20%), Positives = 55/148 (37%), Gaps = 22/148 (14%)

Query: 49  RGRHRDGSKSMANQR--PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------- 98
           R +H  G      +    + TL+V N     T E  I   F   G++  + +        
Sbjct: 21  RDQHFRGDNEEQEKLLKKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT 79

Query: 99  RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHS 158
              F FV++ ++ +A  A+   + ++L DR+I  ++       R  +Y   R GG  R  
Sbjct: 80  ACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR--QYGRGRSGGQVRDE 137

Query: 159 PYGRSPSPAYRRRPSPDYGRGRSPAYDR 186
                    YR+      G     A ++
Sbjct: 138 ---------YRQDYDAGRGGYGKLAQNQ 156

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQR 63
           GF FV +    DA +A+R ++      D R +  +W  G +   + G      Q 
Sbjct: 82  GFCFVEYYSRADAENAMRYINGTRL--DDRIIRTDWDAGFKEGRQYGRGRSGGQV 134

>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 = 54.2 bits (131), Expect = 5e-10
 Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 8/92 (8%)

Query: 51  RHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFA 103
               G    A       L V N D     + DI+  F  +G +    +           A
Sbjct: 15  LFDSGFGGGAGVETGGKLLVSNLDF-GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTA 73

Query: 104 FVQFETQEEATKALESTDRSKLVDRVISVEYA 135
            V FE + +A KA++  +   L  R ++++  
Sbjct: 74  DVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105

>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 = 54.3 bits (131), Expect = 5e-10
 Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 13/92 (14%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQ 106
           GS  M +    K LF+    P    E+D+K  FE +G +  + + ++         AF+ 
Sbjct: 4   GSSGMKDHDAIK-LFIGQI-PRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 107 FETQEEATKALESTDRSKLVD---RVISVEYA 135
           +  +E A KA  +    K +    R I V+ A
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPA 93

>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 = 37.3 bits (87), Expect = 6e-04
 Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 2/51 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNI-PFGYDRRRLSVEWARGERGRHRDGSKS 58
           G AF+ + +   A  A   L          R + V+ A     R   G  S
Sbjct: 56  GCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPAD-SESRGGSGPSS 105

>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 = 54.2 bits (131), Expect = 6e-10
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 13/93 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           LF+ +       ++D+ + F P+GNV+  ++  +        F FV ++    A  A++S
Sbjct: 28  LFIYHLPQ-EFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 120 TDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            +  ++  + + V+        ++D    P  G
Sbjct: 87  MNGFQIGMKRLKVQLKRS----KNDSKSGPSSG 115

>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 = 38.1 bits (89), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH 52
            F FV +++   A  AI+ ++    G   +RL V+  R +    
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGFQIG--MKRLKVQLKRSKNDSK 109

>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 = 53.7 bits (130), Expect = 6e-10
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 10/81 (12%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEAT 114
              ++++V N D       +++ HF   G+V  V I         + FA+++F  +E   
Sbjct: 4   ADARSIYVGNVDY-GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 115 KALESTDRSKLVDRVISVEYA 135
            +L   D S    R I V   
Sbjct: 63  TSLA-LDESLFRGRQIKVIPK 82

>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 = 54.0 bits (130), Expect = 7e-10
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 5/94 (5%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALE 118
               +  + V         E D+    E +G + +V +   +  A V+FE  + A + + 
Sbjct: 11  KVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVT 69

Query: 119 STDRSKLV--DRVISVEYALKDDSERDDRYDSPR 150
                 +    +     Y+      R        
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 26/99 (26%), Positives = 41/99 (41%), Gaps = 9/99 (9%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------ 98
            +          +   +     +L V N    RT    ++R FE YG V  V I      
Sbjct: 27  GQQMGRGSMSYGRPPPDVEGMTSLKVDNL-TYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 85

Query: 99  --RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
              R FAFV+F  + +A  A+++ D + L  R + V+ A
Sbjct: 86  KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 21/48 (43%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           GFAFV F D RDA DA+  +D      D R L V+ AR  R      S
Sbjct: 90  GFAFVRFHDKRDAEDAMDAMDG--AVLDGRELRVQMARYGRPPDSHHS 135

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 54.3 bits (131), Expect = 8e-10
 Identities = 15/76 (19%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           LF+ +       + D+   F P+GNV+  ++  +        F FV F+  + A  A+++
Sbjct: 43  LFIYHLPQ-EFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 120 TDRSKLVDRVISVEYA 135
            +  ++  + + V+  
Sbjct: 102 MNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
            F FV F++   A  AI+ ++    G   +RL V+  +
Sbjct: 83  CFGFVSFDNPDSAQVAIKAMNGFQVG--TKRLKVQLKK 118

>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 = 54.1 bits (130), Expect = 8e-10
 Identities = 17/96 (17%), Positives = 33/96 (34%), Gaps = 15/96 (15%)

Query: 55  GSKSMANQR--PTKTLFVINFDPIRTRERDIKRH--FEPYGNVLHVRIRRN--------- 101
              S A+ R      +FV+           +KR   F  +G +  V I  +         
Sbjct: 3   SGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP 62

Query: 102 --FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
              A+V +   E+A +A++  +   +  R +     
Sbjct: 63  SASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>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 = 53.8 bits (130), Expect = 8e-10
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 106
            +           L+V +       E  ++  FEP+G +  +++         + + F+ 
Sbjct: 16  ANNLQKGSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYA 135
           F   E A KALE  +  +L  R + V + 
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHV 103

>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 = 53.8 bits (129), Expect = 1e-09
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 62  QRPTKTLFVINFD-PIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALE 118
              T++L V N           +    E  G V  + +   + ++F ++ T EE+ +A  
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81

Query: 119 STDRSKLVD 127
           + +  ++VD
Sbjct: 82  TLNGKEVVD 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 = 55.0 bits (133), Expect = 1e-09
 Identities = 30/120 (25%), Positives = 48/120 (40%), Gaps = 21/120 (17%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTL 68
           GF FV +    +   A   ++  P   D R +  + A       R+ S+        K +
Sbjct: 56  GFGFVTYATVEEVDAA---MNARPHKVDGRVVEPKRAVS-----REDSQRPGAHLTVKKI 107

Query: 69  FV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
           FV  I  D   T E  ++ +FE YG +  + I        +R FAFV F+  +   K + 
Sbjct: 108 FVGGIKED---TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164

>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 = 48.8 bits (117), Expect = 2e-07
 Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 17/108 (15%)

Query: 56  SKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFV 105
           S+S       + LF+  ++F+   T +  ++ HFE +G +    + R+        F FV
Sbjct: 4   SESPKEPEQLRKLFIGGLSFE---TTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 106 QFETQEEATKALESTDRSKLVD-RVISVEYAL-KDDSERDDRYDSPRR 151
            + T EE   A+ +  R   VD RV+  + A+ ++DS+R   + + ++
Sbjct: 61  TYATVEEVDAAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 106

>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 = 53.1 bits (128), Expect = 2e-09
 Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 9/102 (8%)

Query: 51  RHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFA 103
               G            L V N D     + DI+  F  +G +    +           A
Sbjct: 21  LFDSGCGGGEGVETGAKLLVSNLDF-GVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 79

Query: 104 FVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDR 145
            V FE + +A KA++      L  R + ++       + +  
Sbjct: 80  DVHFERRADALKAMKQYKGVPLDGRPMDIQLV-ASQIDLEHH 120

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 9/86 (10%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKA 116
               LF+ N +P      ++K           + +        R F +V FE+ E+  KA
Sbjct: 16  TPFNLFIGNLNP-NKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 74

Query: 117 LESTDRSKLVDRVISVEYALKDDSER 142
           LE     K+    I +E     D  R
Sbjct: 75  LE-LTGLKVFGNEIKLEKPKGRDGTR 99

>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 = 52.2 bits (126), Expect = 2e-09
 Identities = 24/98 (24%), Positives = 45/98 (45%), Gaps = 14/98 (14%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVR--IR-------RNFAFVQFETQEEAT 114
            +  +F+ N DP    E+ +   F  +G +L     +R       + +AF+ F + + + 
Sbjct: 4   GSSGIFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 115 KALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
            A+E+ +   L +R I+V YA K    +D +   P  G
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFK----KDSKGSGPSSG 96

>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 = 52.3 bits (126), Expect = 2e-09
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 10/95 (10%)

Query: 55  GSKSMANQRPTKT-LFVINFDPIRTRERDIKRHFEPYGNVLH-VRIRRN-------FAFV 105
           GS   ++ +P  T + V N  P      +I   F  Y  +   V ++ N        A V
Sbjct: 4   GSSGASSGKPGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 106 QFETQEEATKALESTDRSKLVDRVISVEYALKDDS 140
            FE+++EAT A+   +   +  R + +       S
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSS 97

>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 = 52.8 bits (127), Expect = 3e-09
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 10/96 (10%)

Query: 48  ERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------R 99
             G  +  S     +   ++++V N D   +  +D++ HF   G++  + I         
Sbjct: 19  TEGPPQPLSAEEKKEIDKRSVYVGNVDY-GSTAQDLEAHFSSCGSINRITILCDKFSGHP 77

Query: 100 RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
           + +A+++F  +     A+   D +    R I V   
Sbjct: 78  KGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPK 112

>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 = 52.1 bits (125), Expect = 3e-09
 Identities = 19/112 (16%), Positives = 37/112 (33%), Gaps = 11/112 (9%)

Query: 50  GRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------F 102
           G      K +        + V    P    E D++  F     V  V + ++        
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGM-PFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGN 58

Query: 103 AFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD-SERDDRYDSPRRGG 153
             V+F + ++  +AL+  +R  ++ R + V  A +           S    G
Sbjct: 59  GLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>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 = 52.3 bits (126), Expect = 4e-09
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 8/75 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
           L++ N       E++++   +P+G V+  RI R+         F + E+ E+    +   
Sbjct: 28  LYISNLPL-SMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 121 DRSKLVDRVISVEYA 135
           +   +          
Sbjct: 87  NGKFIKTPPGVSAPT 101

>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 = 52.8 bits (127), Expect = 4e-09
 Identities = 21/130 (16%), Positives = 50/130 (38%), Gaps = 13/130 (10%)

Query: 32  PFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYG 91
            +    +   ++  + ++ +H   ++        + L V    P    E  +++ FE YG
Sbjct: 9   QYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYI-PTTVDEVQLRQLFERYG 67

Query: 92  NVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERD 143
            +  V+I         R + FV+F++   A +A+   +   ++++ + V  A    +   
Sbjct: 68  PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA----ASGH 123

Query: 144 DRYDSPRRGG 153
            R       G
Sbjct: 124 QRPGIAGAVG 133

>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 = 38.2 bits (89), Expect = 5e-04
 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR-GERGRHRDGSKSMAN 61
           G+ FV F+    A  AI GL+        +RL V  A  G +     G+    N
Sbjct: 85  GYGFVKFQSGSSAQQAIAGLNGFNI--LNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 51.7 bits (124), Expect = 5e-09
 Identities = 25/109 (22%), Positives = 40/109 (36%), Gaps = 18/109 (16%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIR---------RNFAFV 105
           S S  N      LF+    P   +  +I          VL V +          R FAFV
Sbjct: 3   SGSSGN----CRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFV 57

Query: 106 QFETQEEATKALE--STDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           ++E+   A  A       R +L    I+V++A + + + D+       G
Sbjct: 58  EYESHRAAAMARRKLMPGRIQLWGHQIAVDWA-EPEIDVDEDVMETVSG 105

>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 = 6e-07
 Identities = 17/51 (33%), Positives = 25/51 (49%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSM 59
           GFAFV +E  R AA A R L          +++V+WA  E     D  +++
Sbjct: 53  GFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103

>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 = 50.8 bits (122), Expect = 7e-09
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRIRRN-------FAFVQFET 109
           S + +     + V N  P      +I   F  Y  +   V ++ N        A V FE+
Sbjct: 8   SSSGKPGPTVIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 110 QEEATKALESTDRSKLVDRVISVEYA 135
           ++EAT A+   +   +  R + +   
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 50.7 bits (122), Expect = 9e-09
 Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 16/100 (16%)

Query: 62  QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---------FAFVQFETQEE 112
           + P  T F+ N  P    E  IK  F     +  VR+ R          F + +FE  + 
Sbjct: 12  KSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
              AL   +   L ++ I V+ A     +  D+   P  G
Sbjct: 70  LLSALS-LNEESLGNKRIRVDVA----DQAQDKDSGPSSG 104

>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 = 51.0 bits (122), Expect = 1e-08
 Identities = 20/124 (16%), Positives = 37/124 (29%), Gaps = 14/124 (11%)

Query: 44  WARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL-HVRIRRN- 101
             +   G+ R  S+S         +++    P     + +   F+    V   + I    
Sbjct: 6   SGKSPSGQKRSRSRS--PHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGP 62

Query: 102 ------FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYG 155
                   FV+F  + +   AL    +  + +R I V    K         D  R+    
Sbjct: 63  NGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEK--IDMIRKRLQS 119

Query: 156 RHSP 159
             S 
Sbjct: 120 GPSS 123

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 50.3 bits (120), Expect = 1e-08
 Identities = 16/95 (16%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNF 102
           + G++   +   K    Q   + + + N       +  + +  EPYG + +  +   ++ 
Sbjct: 5   SSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ 64

Query: 103 AFVQFETQEEATKALE--STDRSKLVDRVISVEYA 135
           AF++ ET+E+A   ++           R + V+ +
Sbjct: 65  AFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 4/59 (6%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALE 118
              +++FV  F         +  +F  +G V  V + ++   FA V+          L 
Sbjct: 6   SGLRSVFVSGFPR-GVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS 63

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 20/98 (20%), Positives = 35/98 (35%), Gaps = 15/98 (15%)

Query: 60  ANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEAT 114
            +   +  +FV     D     E +++  F  YG+V+ V I    R FAFV F   + A 
Sbjct: 1   GSSGSSG-VFVGRCTGD---MTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQ 56

Query: 115 KALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
                 +   +    + +  A      + +    P  G
Sbjct: 57  SLCG--EDLIIKGISVHISNAEP----KHNSNSGPSSG 88

>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 = 49.0 bits (118), Expect = 3e-08
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------R-RNFAFVQFETQEEATKA 116
           T  LFV + +     +  ++  F+ + + L   +         R + FV F +Q++A  A
Sbjct: 1   TFNLFVGDLNV-NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59

Query: 117 LESTDRSKLVDRVISVEYA 135
           ++S     L  R + + +A
Sbjct: 60  MDSMQGQDLNGRPLRINWA 78

>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 = 37.1 bits (87), Expect = 5e-04
 Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          G+ FV F    DA +A+  +       + R L + WA 
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWAA 79

>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 = 49.7 bits (119), Expect = 3e-08
 Identities = 21/113 (18%), Positives = 35/113 (30%), Gaps = 14/113 (12%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRIRRN-------FAFVQF 107
           S             + N  P    + D+ +  E      + V +  +        A VQF
Sbjct: 6   SGEGDVNSAKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64

Query: 108 ETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPY 160
           + +++A K+     R KL  R   V       +  D R         G+  P 
Sbjct: 65  KNEDDARKSER-LHRKKLNGREAFVHVV----TLEDMREIEKNPPAQGKSGPS 112

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 52.1 bits (124), Expect = 3e-08
 Identities = 25/128 (19%), Positives = 49/128 (38%), Gaps = 17/128 (13%)

Query: 31  IPFGYDRRRLSV------EWARGERGRHRDGSKSMAN-QRPTKTLFVINFDPIRTR---- 79
           IP   D  +L++       + R +   +R+    + + ++  KTL+V   D         
Sbjct: 93  IPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLK 152

Query: 80  ----ERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE 133
               E  I+  F   G++  +R    +N  FV+F+ Q  A  A E+     L+       
Sbjct: 153 PAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEW 212

Query: 134 YALKDDSE 141
              ++ + 
Sbjct: 213 DDRREGTG 220

>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 = 49.1 bits (118), Expect = 3e-08
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKA 116
           +  L++       T ++D+ +  +PYG ++  +          + + FV F++   A KA
Sbjct: 5   SSGLYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 117 LESTDRSKLVDRVISVE 133
           + +   S +  ++    
Sbjct: 64  VTALKASGVQAQMAKQS 80

>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 = 37.5 bits (88), Expect = 4e-04
 Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 2/38 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          G+ FV F+    A  A+  L     G   +        
Sbjct: 48 GYGFVDFDSPSAAQKAVTALKA--SGVQAQMAKQSGPS 83

>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 = 49.3 bits (118), Expect = 3e-08
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 10/85 (11%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQF 107
            S S         + +    P R  E DI   F P  N + V I           A V+F
Sbjct: 5   SSGSSFQSTTGHCVHMRGL-PYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEF 62

Query: 108 ETQEEATKALESTDRSKLVDRVISV 132
            T E+A  A+   D++ +  R + +
Sbjct: 63  ATHEDAVAAMAK-DKANMQHRYVEL 86

>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 = 49.4 bits (118), Expect = 3e-08
 Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 14/100 (14%)

Query: 55  GSKSMANQRP----TKTLFVINFDPIRTRERDIKRHFEPYGNVL-HVRIRRN-------F 102
           GS   +   P       + +    P    + +I + F     V   + +  +        
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGE 59

Query: 103 AFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSER 142
           AFVQF +QE A KAL+   + ++  R I +  + + +   
Sbjct: 60  AFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRT 98

>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 = 49.4 bits (118), Expect = 3e-08
 Identities = 26/112 (23%), Positives = 41/112 (36%), Gaps = 9/112 (8%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-FAFVQFETQE 111
              S    ++R    + V    P     +D+K H    G+V +  + R+    V+F  +E
Sbjct: 3   SGSSGGPPSRRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKE 61

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRS 163
           + T A+   D +K         Y          + D PR   YGR    G S
Sbjct: 62  DMTYAVRKLDNTKFRSHEGETAYI-------RVKVDGPRSPSYGRSRSSGPS 106

>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 = 48.8 bits (117), Expect = 4e-08
 Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 14/99 (14%)

Query: 46  RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------- 98
           RG    H   S+    + P  T F+ N  P    E  IK  F     +  VR+       
Sbjct: 2   RGSHHHHHHRSRLP--KSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNP 57

Query: 99  --RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
              + F + +FE  +    AL   +   L +R I V+ A
Sbjct: 58  ERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVA 95

>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 = 48.4 bits (116), Expect = 4e-08
 Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 11/85 (12%)

Query: 56  SKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQ 110
                +   +K +FV     D       ++++ F  YG V+ V I    R FAFV F   
Sbjct: 3   GSHHHHHHGSK-VFVGRCTED---MTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADD 58

Query: 111 EEATKALESTDRSKLVDRVISVEYA 135
           + A       +   +    + +  A
Sbjct: 59  KVAQSLCG--EDLIIKGISVHISNA 81

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 50.6 bits (121), Expect = 5e-08
 Identities = 25/134 (18%), Positives = 44/134 (32%), Gaps = 11/134 (8%)

Query: 19  RDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRT 78
           R+     RG  N P  Y R +      + +      G            L V N D    
Sbjct: 44  RNRPAIARGGRNRPAPYSRPK--PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDF-GV 100

Query: 79  RERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVDRVIS 131
            + DI+  F  +G +    +  +        A V FE + +A KA++      L  R + 
Sbjct: 101 SDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160

Query: 132 VEYALKDDSERDDR 145
           ++       + +  
Sbjct: 161 IQLV-ASQIDLEHH 173

>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 = 48.7 bits (117), Expect = 5e-08
 Identities = 23/108 (21%), Positives = 45/108 (41%), Gaps = 19/108 (17%)

Query: 55  GSKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAF 104
           GS   +  +  K +FV  I  +     E +++ +F+ +G V  V +         R F F
Sbjct: 1   GSSGSSGSKSNK-IFVGGIPHN---CGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGF 56

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           + FE ++   +A+       ++ + + V+ A      RD +   P  G
Sbjct: 57  ITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE----PRDSKSSGPSSG 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 48.9 bits (117), Expect = 5e-08
 Identities = 20/111 (18%), Positives = 32/111 (28%), Gaps = 19/111 (17%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH------VRIR----------RNFAFVQ 106
               T+FV            +  +F+  G +          I           +  A V 
Sbjct: 5   SDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRH 157
           F+    A  A++  D  +     I V +A        +R     RGG   H
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFA--TRRADFNRGGGNGRGGLEHH 112

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 2/56 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRP 64
           G A V F+D   A  AI   D   F      + V +A      +R G         
Sbjct: 58  GEATVSFDDPPSAKAAIDWFDGKEF--SGNPIKVSFATRRADFNRGGGNGRGGLEH 111

>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 = 49.0 bits (117), Expect = 6e-08
 Identities = 27/116 (23%), Positives = 42/116 (36%), Gaps = 3/116 (2%)

Query: 50  GRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-FAFVQFE 108
           G    G     ++R    + V    P     +D+K H    G+V +  + R+    V+F 
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFV 59

Query: 109 TQEEATKALESTDRSKLVDRVISVEYA-LKDDSERDDRYDSPRRGGYGRHSPYGRS 163
            +E+ T A+   D +K         Y  +K D  R   Y   R     R     RS
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSRS 115

>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 = 49.5 bits (118), Expect = 6e-08
 Identities = 27/115 (23%), Positives = 39/115 (33%), Gaps = 11/115 (9%)

Query: 48  ERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------ 101
           + GR    S+          + +    P +  E DI   F P    + V I         
Sbjct: 29  QMGRGSGDSEFTVQSTTGHCVHMRGL-PYKATENDIYNFFSPLN-PVRVHIEIGPDGRVT 86

Query: 102 -FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYG 155
             A V+F T EEA  A+   DR+ +  R I +       +     Y S    G G
Sbjct: 87  GEADVEFATHEEAVAAMSK-DRANMQHRYIELFLNSTTGASN-GAYSSQVMQGMG 139

>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 = 47.7 bits (114), Expect = 8e-08
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQ 110
           S ++     T+ +    P    E+++     P    + +RI RN       + FV F  +
Sbjct: 3   SGSSGTTCHTVKLRGA-PFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNE 60

Query: 111 EEATKALESTDRSKLVDRVISV 132
           EE  +AL+  +R  +  R I V
Sbjct: 61  EEVKQALKC-NREYMGGRYIEV 81

>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 = 47.5 bits (114), Expect = 9e-08
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 14/94 (14%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
           + ++V N          +K  F  +G V +V++         + F FV+ +  E  ++A+
Sbjct: 2   RNIYVGNL-VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRR 151
              D +  + R I V  A    + +         
Sbjct: 60  AKLDNTDFMGRTIRVTEA----NPKKSLEHHHHH 89

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIR-----RNFAFVQFE 108
           S  +      + V N D  R   +++++     F  +G V  V +      +  A VQ E
Sbjct: 2   SSGSSGNGADVQVSNIDY-RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQME 60

Query: 109 TQEEATKALESTDRSKLVDRVISVEYA 135
             ++A  A+ S  R K+  + I V  A
Sbjct: 61  NLQDAIGAVNSLHRYKIGSKKILVSLA 87

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 9/98 (9%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATK 115
               +FV +  P      DIK  F P+G +   R+         + + FV F  + +A  
Sbjct: 14  NHFHVFVGDLSP-EITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGG 153
           A++      L  R I   +A +        Y+S  +  
Sbjct: 73  AIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>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 = 38.1 bits (89), Expect = 4e-04
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ 62
           G+ FV F +  DA +AI+ +         R++   WA  +    +   +S   Q
Sbjct: 58  GYGFVSFFNKWDAENAIQQMGGQWL--GGRQIRTNWATRKPPAPKSTYESNTKQ 109

>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 = 46.5 bits (111), Expect = 3e-07
 Identities = 25/111 (22%), Positives = 42/111 (37%), Gaps = 22/111 (19%)

Query: 55  GSKSMANQRPTKT--LFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------F 102
           GS  M N    +   LFV  +++    T +  ++ +F  YG V+   I ++        F
Sbjct: 4   GSSGMNNSGADEIGKLFVGGLDWS---TTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 103 AFVQFETQEEATKALESTDRSKLVD-RVISVEYALKDDSERDDRYDSPRRG 152
            FV+F+        L    R   +D R I  +      + R  +   P  G
Sbjct: 61  GFVKFKDPNCVGTVLA--SRPHTLDGRNIDPKPC----TPRGMQPSGPSSG 105

>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 = 46.1 bits (110), Expect = 3e-07
 Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 17/89 (19%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH------VRIR----------RNFAFVQ 106
               T+FV            +  +F+  G +          I           +  A V 
Sbjct: 11  SDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 69

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYA 135
           F+    A  A++  D  +     I V +A
Sbjct: 70  FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 37.7 bits (88), Expect = 4e-04
 Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
          G A V F+D   A  AI   D   F      + V +A
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEF--SGNPIKVSFA 98

>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 = 46.8 bits (111), Expect = 3e-07
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 10/97 (10%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV-LHVRIRRN-- 101
           A    G+      + A+      + +    P    + +I + F     V   + +  +  
Sbjct: 22  ASMTGGQQMGRGSNSADSANDGFVRLRGL-PFGCTKEEIVQFFSGLEIVPNGITLPVDPE 80

Query: 102 -----FAFVQFETQEEATKALESTDRSKLVDRVISVE 133
                 AFVQF +QE A KAL    + ++  R I V 
Sbjct: 81  GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF 116

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 25/98 (25%), Positives = 39/98 (39%), Gaps = 15/98 (15%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEAT 114
            P  T +V N  P  T + DI   F+    +  VR+         + F +V+F+  +   
Sbjct: 13  EPPYTAYVGNL-PFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70

Query: 115 KALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           +AL   D + L DR + V+ A      R      P  G
Sbjct: 71  EALT-YDGALLGDRSLRVDIA----EGRKQDKSGPSSG 103

>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 = 44.8 bits (107), Expect = 6e-07
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 13/61 (21%)

Query: 68  LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
           +FV  ++ D   T E  I+ +F  +G V  + +        RR F F+ F+ +E   K +
Sbjct: 2   IFVGGLSPD---TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

Query: 118 E 118
           E
Sbjct: 59  E 59

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 17/123 (13%), Positives = 37/123 (30%), Gaps = 14/123 (11%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH----VRIRR 100
           +    G   +      ++     + +    P      ++   F  +  +      +    
Sbjct: 3   SGSSGGGTSNEVAQFLSKENQVIVRMRGL-PFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 101 N-------FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERD-DRYDSPRRG 152
                    AFV F  +E A  AL    +  L  R I +  +   + ++  +R+ S    
Sbjct: 62  YPDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGP 120

Query: 153 GYG 155
             G
Sbjct: 121 SSG 123

>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 = 45.7 bits (109), Expect = 6e-07
 Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 20/113 (17%)

Query: 50  GRHRDGSKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN------ 101
           G         A Q+ +  L V  + +    T E+D+K +F  +G VL V+++++      
Sbjct: 1   GSSGSSGVKRAVQKTSD-LIVLGLPWK---TTEQDLKEYFSTFGEVLMVQVKKDLKTGHS 56

Query: 102 --FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
             F FV+F   E   K +    R  +  R    +        +  +   P  G
Sbjct: 57  KGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPN----SKQSQDSGPSSG 103

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.8 bits (111), Expect = 6e-07
 Identities = 15/135 (11%), Positives = 33/135 (24%), Gaps = 23/135 (17%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----- 99
            +               +     ++V +F    T ++ + +     G    V ++     
Sbjct: 35  PKPNNKTPAILYTYSGLRNRRAAVYVGSF-SWWTTDQQLIQVIRSIGVYDVVELKFAENR 93

Query: 100 -----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGY 154
                + +A V   ++    K LE      L    + V  A            + +    
Sbjct: 94  ANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA------------TRQNLSQ 141

Query: 155 GRHSPYGRSPSPAYR 169
                  R      R
Sbjct: 142 FEAQARKRECVRVPR 156

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 44.8 bits (107), Expect = 8e-07
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 16/80 (20%)

Query: 68  LFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKAL 117
           +F+  +++    T +  ++ +F  +G V    + R+        F FV F  Q    K L
Sbjct: 3   MFIGGLSWQ---TTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59

Query: 118 ESTDRSKLVD-RVISVEYAL 136
                   +D + I  + A 
Sbjct: 60  A--QSRHELDSKTIDPKVAF 77

>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 = 44.9 bits (107), Expect = 9e-07
 Identities = 12/89 (13%), Positives = 29/89 (32%), Gaps = 12/89 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKAL 117
           L++ N     T + D+       G    + I+          + FA V   ++  + K +
Sbjct: 4   LYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRY 146
           +   + +L  +   V  +          +
Sbjct: 63  DLLPKRELHGQNPVVTPS-NKLEHHHHHH 90

>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 = 37.6 bits (88), Expect = 4e-04
 Identities = 7/45 (15%), Positives = 12/45 (26%), Gaps = 2/45 (4%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR 53
          GFA V    +  +   +  L         +   V  +      H 
Sbjct: 46 GFALVGVGSEASSKKLMDLLPKREL--HGQNPVVTPSNKLEHHHH 88

>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 = 44.5 bits (106), Expect = 1e-06
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 16/92 (17%)

Query: 55  GSKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAF 104
           G  +  N+     +FV  +++D   T ++D+K +F  +G V+   I+ +        F F
Sbjct: 1   GINASKNEEDAGKMFVGGLSWD---TSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGF 57

Query: 105 VQFETQEEATKALESTDRSKLVD-RVISVEYA 135
           + F+      K L+   +   +D RVI  + A
Sbjct: 58  ILFKDAASVEKVLD--QKEHRLDGRVIDPKKA 87

>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 = 44.9 bits (107), Expect = 1e-06
 Identities = 21/114 (18%), Positives = 38/114 (33%), Gaps = 24/114 (21%)

Query: 47  GERGRHRDGSK------SMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI 98
           G    H   S       S       K +F+  +++    T +  ++ +F  +G V    +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGSSGCK-MFIGGLSWQ---TTQEGLREYFGQFGEVKECLV 57

Query: 99  RRN--------FAFVQFETQEEATKALESTDRSKLVD-RVISVEYAL-KDDSER 142
            R+        F FV F  Q    K L        +D + I  + A  +    +
Sbjct: 58  MRDPLTKRSRGFGFVTFMDQAGVDKVLA--QSRHELDSKTIDPKVAFPRRAQPK 109

>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 = 44.6 bits (106), Expect = 2e-06
 Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 10/71 (14%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRN--------FAFVQFE 108
           S  +     +L++ + +P    E  I R F   G  V+ V+I RN        + FV+F 
Sbjct: 2   SSGSSGMAASLWMGDLEP-YMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 109 TQEEATKALES 119
               A K L  
Sbjct: 61  DLATAEKCLHK 71

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 17/89 (19%), Positives = 42/89 (47%), Gaps = 8/89 (8%)

Query: 55  GSKSMANQR----PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFE 108
           GS   + Q+      + + +++F   +     + +  EP+G + +  I  + N AF++  
Sbjct: 1   GSSGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMA 60

Query: 109 TQEEATKALE--STDRSKLVDRVISVEYA 135
           T E+A  A++  +T  + +  + + V  +
Sbjct: 61  TTEDAQAAVDYYTTTPALVFGKPVRVHLS 89

>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 = 44.5 bits (105), Expect = 2e-06
 Identities = 17/98 (17%), Positives = 30/98 (30%), Gaps = 12/98 (12%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPY---GNVLHVRIRRN-------FAF 104
           GSK          +      P      D+   F           +    N        A 
Sbjct: 1   GSKLEEEVDDVFLIRAQGL-PWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDAL 59

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYALKDDSER 142
           ++ E++++  KALE   R  +  R + V     +D + 
Sbjct: 60  IEMESEQDVQKALEK-HRMYMGQRYVEVYEINNEDVDA 96

>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 = 43.7 bits (104), Expect = 2e-06
 Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 115
               +FV +  P       I   F P+G +   R+         + + FV F  + +A  
Sbjct: 5   SHFHVFVGDLSP-EITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

Query: 116 ALESTDRSKLVDRVISVEYA 135
           A++      L  R I   +A
Sbjct: 64  AIQQMGGQWLGGRQIRTNWA 83

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 22/113 (19%), Positives = 44/113 (38%), Gaps = 22/113 (19%)

Query: 53  RDGSKSMANQRPTKT--LFV--INFDPIRTRERDIKRHFEPYGNVLHVRIRRN------- 101
                    +   +   LF+  ++F+   T E  ++ ++E +G +    + R+       
Sbjct: 13  ETVPLERKKREKEQFRKLFIGGLSFE---TTEESLRNYYEQWGKLTDCVVMRDPASKRSR 69

Query: 102 -FAFVQFETQEEATKALESTDRSKLVD-RVISVEYALKDDSERDDRYDSPRRG 152
            F FV F +  E   A+    R   +D RV+  + A+     R++    P  G
Sbjct: 70  GFGFVTFSSMAEVDAAMA--ARPHSIDGRVVEPKRAV----AREESGSGPSSG 116

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 43.2 bits (103), Expect = 2e-06
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 13/61 (21%)

Query: 68  LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 117
           +FV  ++ +   T   D+K +FE +G V    +         R F FV FE+++   K  
Sbjct: 2   IFVGGLSVN---TTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

Query: 118 E 118
           E
Sbjct: 59  E 59

>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 = 45.1 bits (106), Expect = 3e-06
 Identities = 30/168 (17%), Positives = 56/168 (33%), Gaps = 23/168 (13%)

Query: 14  YFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINF 73
           +      A  A++ ++++  G      S            D   +MA Q P   + V N 
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAAS--------AAAVDAGMAMAGQSPVLRIIVENL 54

Query: 74  DPIRTRERDIKRHFEPYGNVLHVRI----RRNFAFVQFETQEEATKALESTDRSKLVDR- 128
               T +  + + F  +G VL +       +  A +Q+     A  A  S D   + +  
Sbjct: 55  FYPVTLD-VLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC 113

Query: 129 -VISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSPAYRRRPSPD 175
             + ++++           D  R         Y R   P+   +PS D
Sbjct: 114 CTLRIDFSKLTSLNVKYNNDKSR--------DYTRPDLPSGDSQPSLD 153

>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 = 42.7 bits (100), Expect = 1e-05
 Identities = 17/127 (13%), Positives = 35/127 (27%), Gaps = 12/127 (9%)

Query: 26  RGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR 85
               +   G   R   +    G +   R              + +    P      D++ 
Sbjct: 5   HHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGL-PWSCSVEDVQN 63

Query: 86  HFEPY---GNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 135
                        V             AFV+  ++++   AL+  DR  +  R I V  +
Sbjct: 64  FLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK-DRESMGHRYIEVFKS 122

Query: 136 LKDDSER 142
            + + + 
Sbjct: 123 HRTEMDW 129

>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 = 42.3 bits (100), Expect = 1e-05
 Identities = 22/116 (18%), Positives = 46/116 (39%), Gaps = 19/116 (16%)

Query: 55  GSKSMANQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI-------R-RNFAF 104
              S  +   TK +FV  + +    T +  ++++FE +G++    +       + R + F
Sbjct: 8   MHGSQKDTTFTK-IFVGGLPYH---TTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 105 VQFETQEEATKALESTDRSKLVD-RVISVEYALKDDSERDDRYDSPRRGGYGRHSP 159
           V    +  A +A +  D + ++D R  +V  A      R  +  +    G    S 
Sbjct: 64  VTMADRAAAERACK--DPNPIIDGRKANVNLAYLGAKPRSLQ--TGFAIGVSGPSS 115

>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 = 42.0 bits (99), Expect = 1e-05
 Identities = 21/122 (17%), Positives = 32/122 (26%), Gaps = 25/122 (20%)

Query: 47  GERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV------LHVRIR- 99
           G  G   D  +   N      ++V           D+   F+  G V          I  
Sbjct: 1   GSSGSSGDPDEDSDN----SAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHI 55

Query: 100 ---------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPR 150
                    +  A V +E    A  A+E  D        + V  A     ++      P 
Sbjct: 56  YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA----RKKPPMNSGPS 111

Query: 151 RG 152
            G
Sbjct: 112 SG 113

>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 = 37.0 bits (86), Expect = 9e-04
 Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 2/38 (5%)

Query: 9   GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
           G A V +ED   A  A+   D   F     +L V  AR
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDF--QGSKLKVSLAR 101

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 9/52 (17%), Positives = 22/52 (42%), Gaps = 6/52 (11%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRN------FAFVQFETQEEATKALESTDRSKL 125
           +  I + F  +G + +            + F+++ +   A  A+++ D  KL
Sbjct: 21  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 1/34 (2%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSV 42
          G+ F+ +     A DA++  D       +    V
Sbjct: 48 GYIFLEYASPAHAVDAVKNADGYKLD-KQHTFRV 80

>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 = 41.8 bits (98), Expect = 2e-05
 Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 11/78 (14%)

Query: 75  PIRTRERDIKRHFEPY---GNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSK 124
           P      D++           V  V             AFV+ E++++   AL+  DR  
Sbjct: 26  PWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKK-DRES 84

Query: 125 LVDRVISVEYALKDDSER 142
           +  R I V  + + + + 
Sbjct: 85  MGHRYIEVFKSHRTEMDW 102

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 17/93 (18%), Positives = 31/93 (33%), Gaps = 6/93 (6%)

Query: 46  RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV-----LHVRIRR 100
               G    GS           + + N  P     +D+K              ++ R   
Sbjct: 9   HHSSGLVPRGSHMSKLPAKRYRITMKNL-PEGCSWQDLKDLARENSLETTFSSVNTRDFD 67

Query: 101 NFAFVQFETQEEATKALESTDRSKLVDRVISVE 133
               ++F ++E   +ALE  +  +    VI+VE
Sbjct: 68  GTGALEFPSEEILVEALERLNNIEFRGSVITVE 100

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 7/88 (7%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERD-IKRHFEPYGNVLHVRI----RRNFAFVQFET 109
               MA    +  L +I  +       D + + F  +G VL +       +  A +Q+  
Sbjct: 16  VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYAD 75

Query: 110 QEEATKALESTDRSKLVDR--VISVEYA 135
              A  A  S D   + +    + ++++
Sbjct: 76  PVSAQHAKLSLDGQNIYNACCTLRIDFS 103

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 13/84 (15%)

Query: 64  PTKTLFVIN-FDPIRTRER--------DIKRHFEPYGNVLHVRIRRN----FAFVQFETQ 110
            T+   + N F+P    E         D+      +G V+H+ + +N      +V+  + 
Sbjct: 6   ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSI 65

Query: 111 EEATKALESTDRSKLVDRVISVEY 134
             A  A+ +        ++I+  Y
Sbjct: 66  AAAIAAVNALHGRWFAGKMITAAY 89

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 19/93 (20%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 49  RGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD-IKRHFEPYGNVLHVRI---RRNFAF 104
             R      +       K L +   +P+     D +     P G V  + I       A 
Sbjct: 7   GKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAM 66

Query: 105 VQFETQEEATKALESTDRSKLVDR--VISVEYA 135
           V+FE+   A KA  + + + +      + +EYA
Sbjct: 67  VEFESVLCAQKAKAALNGADIYAGCCTLKIEYA 99

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVL--HVRIRRNFAFVQFETQEEATKALESTDR 122
           +  L + N    +     ++     +G ++  H  + +  A  ++ T+EEA KA  + + 
Sbjct: 7   SSWLLLKNLTA-QIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNN 65

Query: 123 SKLVDRVISVEYALKDDSER 142
             L +  I  E   +++ + 
Sbjct: 66  CVLANTTIFAESPSENEVQS 85

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 14/86 (16%)

Query: 63  RPTKTLFVIN-FDP---------IRTRERDIKRHFEPYGNVLHVRIRRN----FAFVQFE 108
           R  + + + N F P         +     D++     +G +  + +        A V F 
Sbjct: 13  RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFR 72

Query: 109 TQEEATKALESTDRSKLVDRVISVEY 134
             EEA   +++ D      R I+ + 
Sbjct: 73  DPEEADYCIQTLDGRWFGGRQITAQA 98

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 22/96 (22%), Positives = 32/96 (33%), Gaps = 13/96 (13%)

Query: 62  QRPTKTLFVIN-FDPIRTR---ERDIKRHFEPYGNVLHVRIRRN---------FAFVQFE 108
           + PTK + + N           E + K   E YG V    I              F++FE
Sbjct: 5   KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFE 64

Query: 109 TQEEATKALESTDRSKLVDRVISVEYALKDDSERDD 144
             E A KA+   +      RV+   +   D     D
Sbjct: 65  RVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLD 100

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.8 bits (93), Expect = 9e-05
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 19/102 (18%)

Query: 64  PTKTLFVIN-FDP--------IRTRERDIKRHFEPYGNVLHVRIRRN----------FAF 104
           PT+ L ++N   P              D++     YG V  + I R             F
Sbjct: 4   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 63

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
           V+F +  +  KA++     K  +RV+  +Y   D   R D +
Sbjct: 64  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW 105

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 16/94 (17%)

Query: 57  KSMANQRPTKTLFVIN-FDPIRTR---ERDIKRHFEPYGNVLHVRIRRNFA--------- 103
           + +  ++ +  + + N  DP       E ++      +G V  V I +            
Sbjct: 12  QKLLRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEII 71

Query: 104 ---FVQFETQEEATKALESTDRSKLVDRVISVEY 134
              FV+F    E  KA+++ +      R +  E 
Sbjct: 72  VKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 70  VINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTD 121
           VI    +   ++ +   F   G V+++    +        F FV+  +  +A K ++S  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 122 RSKL 125
             +L
Sbjct: 76  GKRL 79

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 13/72 (18%)

Query: 66  KTLFVINFDPIRTRER------DIKRHFEPYGNVLHVRIRRN------FAFVQFETQEEA 113
             + V N  P    +R       I + F  +G + +            + F+++ +   A
Sbjct: 16  SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74

Query: 114 TKALESTDRSKL 125
             A+++ D  KL
Sbjct: 75  VDAVKNADGYKL 86

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 8/61 (13%)

Query: 82  DIKRHFEP-YGNVLHVRIRRN-------FAFVQFETQEEATKALESTDRSKLVDRVISVE 133
           ++    E  YG V  + +  N         +V+F  +E+A KA+   +      + I  E
Sbjct: 42  EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

Query: 134 Y 134
            
Sbjct: 102 L 102

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 16/88 (18%), Positives = 27/88 (30%), Gaps = 7/88 (7%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPY-----GNVLHVRIRRNFAFVQFETQEEAT 114
           +       + V    P    E  +  +FE       G VL  +       + F    +A 
Sbjct: 3   SGSSGGVAVEVRGLPPAVPDE-LLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAE 61

Query: 115 KALESTDRSKLVDRVISVEYALKDDSER 142
           + L   D  +L    +S+  A      R
Sbjct: 62  RVLAQAD-HELHGAQLSLRPAPPRAPAR 88

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 10/104 (9%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHF-EPYGNVLHVRI-------RRNFAFVQFET 109
           S  +  P  +LFV +  P    +  +   F + Y +    ++        + + FV+F  
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVD-DGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60

Query: 110 QEEATKALESTD-RSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           + E  +AL        L  + + +  A+   S        P  G
Sbjct: 61  ELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSSG 104

>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 = 36.6 bits (85), Expect = 8e-04
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 14/69 (20%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHF-----------EPYGNVLHVRIR--RNFAFVQFET 109
              + L+V N  P    E  +   F            P   VL V+I   +NFAF++F +
Sbjct: 4   GSARRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 62

Query: 110 QEEATKALE 118
            +E T+A+ 
Sbjct: 63  VDETTQAMA 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	240
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.95
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.94
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.94
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	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	99.94
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.93
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.93
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.93
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.92
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.92
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.92
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.92
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.91
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.91
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.9
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.89
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.89
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.88
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.83
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.81
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.8
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.8
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.78
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.77
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.77
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.76
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.76
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.75
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.75
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.74
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.74
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.74
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.73
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.72
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.72
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
1x5p_A	97	Negative elongation factor E; structure genomics,	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
2div_A	99	TRNA selenocysteine associated protein; structural	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.7
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.7
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.69
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.69
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.68
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.68
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.68
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.67
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.66
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.66
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.65
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.65
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.46
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.64
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.64
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.63
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.6
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.59
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.59
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.59
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.59
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.58
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.58
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.58
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.57
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.57
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.56
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.55
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.54
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.52
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.52
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.51
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.47
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.46
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.45
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.44
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.43
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.42
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.42
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.42
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.42
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.38
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.37
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.36
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.15
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.14
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.12
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.09
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.03
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.02
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.01
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.01
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.01
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.0
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.99
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.99
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.98
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.98
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.98
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.98
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.98
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.98
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.98
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.98
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.97
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.97
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.97
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.97
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.97
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.96
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.96
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.96
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.95
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.95
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.95
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.95
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.95
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.95
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.95
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.94
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.94
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.94
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.94
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.94
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.94
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.93
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.93
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.93
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.93
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.92
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.92
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.92
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.92
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.92
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.91
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.91
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.91
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.91
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.9
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.9
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.9
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.89
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.89
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.89
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.89
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.88
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.87
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.87
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.87
1x5p_A	97	Negative elongation factor E; structure genomics,	98.87
2div_A	99	TRNA selenocysteine associated protein; structural	98.86
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.86
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.86
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.86
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.86
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.86
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.85
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.85
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.85
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.84
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.84
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.84
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.84
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.84
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.83
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.81
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.81
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.81
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.8
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.8
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.8
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.79
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.78
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.78
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.78
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.78
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.77
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.76
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.76
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.76
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.76
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.76
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.75
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.74
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.73
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.2
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.73
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.72
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.72
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.72
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.71
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.7
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.69
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.68
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.67
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.66
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.66
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.65
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.63
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.63
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.61
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.58
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.58
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.55
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.52
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.46
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.33
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.27
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.2
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.14
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	97.97
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.9
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.84
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.84
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.82
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.68
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	97.53
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.53
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.01
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.88
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	96.59
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	96.08
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.62
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.53
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	95.12
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.38
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	93.05
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	92.28
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	92.2
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	83.71

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.95  E-value=1.1e-26  Score=176.79  Aligned_cols=122  Identities=21%  Similarity=0.430  Sum_probs=110.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      ++++++|||||+|.+.++|++|++.|||..|  .|+.|.|.++......         ...+..+|||+|| |..+++++
T Consensus        36 ~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~i~v~~~~~~~~~---------~~~~~~~l~v~nl-~~~~t~~~  103 (166)
T 3md3_A           36 KNNKNVNYAFVEYHQSHDANIALQTLNGKQI--ENNIVKINWAFQSQQS---------SSDDTFNLFVGDL-NVNVDDET  103 (166)
T ss_dssp             CC-CCEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCCCCCC---------CCTTCEEEEEESC-CTTCCHHH
T ss_pred             CCCCCCCEEEEEeCCHHHHHHHHHHcCCCcc--CCCeeEEEEcCCCCCC---------CCCCCceEEECCC-CCCCCHHH
Confidence            3466799999999999999999999999999  6999999999865432         3456789999999 88999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      |+++|++||.|..+.+.        +|+|||+|.+.++|++|+..|||..|+|+.|.|.||+
T Consensus       104 l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          104 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             HHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            99999999999999884        5799999999999999999999999999999999986

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.94  E-value=8e-27  Score=185.63  Aligned_cols=124  Identities=23%  Similarity=0.442  Sum_probs=111.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .|++++|||||+|.++++|++||+.||+..+  .|+.|.|.++......         ......+|||+|| |..+++++
T Consensus        52 ~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~--~g~~i~~~~~~~~~~~---------~~~~~~~l~v~nl-~~~~t~~~  119 (213)
T 4f02_A           52 ITRRSLGYAYVNFQQPADAERALDTMNFDVI--KGKPVRIMWSQRDPSL---------RKSGVGNIFIKNL-DKSIDNKA  119 (213)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCCCTHH---------HHHCTTEEEEESC-CTTCCHHH
T ss_pred             CCCCccccccceeCCHHHHHHHHHHhhhhhc--CCcccccccccccccc---------cccccccceECCc-ccccHHHH
Confidence            3678899999999999999999999999999  6999999998754432         1223578999999 89999999


Q ss_pred             HHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           83 IKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |+++|.+||.|..|.|.      +|||||+|.+.++|++||+.|||..|+|+.|.|.+|.++
T Consensus       120 l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          120 LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             HHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             HHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            99999999999999984      689999999999999999999999999999999999764

>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=1.3e-26  Score=178.48  Aligned_cols=123  Identities=22%  Similarity=0.380  Sum_probs=109.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .++.++|||||+|.++++|++|++ |||..|  .|++|.|.++......         ...+..+|||+|| |..+++++
T Consensus        49 ~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~--~g~~l~v~~~~~~~~~---------~~~~~~~l~v~nl-p~~~t~~~  115 (175)
T 1fje_B           49 RTGTNRKFGYVDFESAEDLEKALE-LTGLKV--FGNEIKLEKPKGRDSK---------KVRAARTLLAKNL-SFNITEDE  115 (175)
T ss_dssp             EEETTTTEEEEEESSHHHHHHHHH-GGGEEE--TTEEEEEECCCCSSCS---------TTGGGGEEEEESC-CSSCCHHH
T ss_pred             CCCccccEEEEEECCHHHHHHHHh-cCCCEe--CCeEEEEecCCCcccc---------ccccCCEEEEeCC-CCCCCHHH
Confidence            367789999999999999999995 999999  6999999999865432         3346789999999 88999999


Q ss_pred             HHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           83 IKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |+++|++||.|..+..   .+|||||+|.+.++|++|+..|||..|+|+.|.|.|+.++
T Consensus       116 l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          116 LKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHhcCeEEEecCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999999988821   3689999999999999999999999999999999999764

>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=99.94  E-value=3.9e-26  Score=174.39  Aligned_cols=118  Identities=29%  Similarity=0.468  Sum_probs=107.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++|||||+|.++++|++|++.|+|..|  +|++|.|.|+.+...           ..+..+|||+|| |..+++++|
T Consensus        41 ~~~~~g~afV~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~~~~~~~-----------~~~~~~l~v~nl-~~~~t~~~l  106 (168)
T 1b7f_A           41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYARPGGE-----------SIKDTNLYVTNL-PRTITDDQL  106 (168)
T ss_dssp             TTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCCCSS-----------TTTTCEEEEESC-CTTCCHHHH
T ss_pred             CCccceEEEEEECCHHHHHHHHHhcCCCEe--CCcEEEEEecCCCcc-----------cCCCCCEEEeCC-CCCCCHHHH
Confidence            667899999999999999999999999999  699999999986543           235789999999 889999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEe
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYA  135 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a  135 (240)
                      +++|++||.|..+.+.        +|+|||+|.+.++|++|+..|||..|.|  ++|.|.||
T Consensus       107 ~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999884        4799999999999999999999999988  99999986

>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=3.7e-26  Score=179.14  Aligned_cols=132  Identities=17%  Similarity=0.288  Sum_probs=112.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC---------CCCCCCCCCCCCEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD---------GSKSMANQRPTKTLFVINFD   74 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~---------~~~~~~~~~~~~~l~v~nl~   74 (240)
                      ++.++|||||+|.++++|++|+ .|||..|  .|++|.|.++.........         .........+.++|||+|| 
T Consensus        47 ~~~~~g~afV~F~~~~~A~~Al-~l~g~~~--~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-  122 (198)
T 2yh0_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL-  122 (198)
T ss_dssp             EETTTTEEEEEESCSHHHHHHG-GGTTEEE--TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECC-
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhcCCEE--cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCC-
Confidence            4567999999999999999999 8999999  6999999998865432211         0011223356799999999 


Q ss_pred             CCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           75 PIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        75 ~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      |..+++++|+++|.+||.|..|.+.        +|||||+|.+.++|++|+..|||..|+|+.|.|.++.+..
T Consensus       123 ~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             CTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            8899999999999999999999884        5799999999999999999999999999999999998764

>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=99.94  E-value=8e-26  Score=187.00  Aligned_cols=131  Identities=24%  Similarity=0.488  Sum_probs=111.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC--CCC------------------------
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR--DGS------------------------   56 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~--~~~------------------------   56 (240)
                      ++++++|||||+|.+.++|++|++.|||..|  .|+.|.|+|+........  .+.                        
T Consensus        47 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (282)
T 3pgw_A           47 RSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA  124 (282)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhcCCee--CCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhh
Confidence            4778899999999999999999999999999  699999999976442100  000                        


Q ss_pred             --------------------------------------------------------------------------CCCCCC
Q 026341           57 --------------------------------------------------------------------------KSMANQ   62 (240)
Q Consensus        57 --------------------------------------------------------------------------~~~~~~   62 (240)
                                                                                                ......
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (282)
T 3pgw_A          125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSEN  204 (282)
T ss_pred             ccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCC
Confidence                                                                                      000233


Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCccc-CcEEEEEEee
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLV-DRVISVEYAL  136 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~  136 (240)
                      .++++|||+|| +..+++++|+++|++||.|..|.|.   +|||||+|.+.++|++|+..|||..|. |+.|.|+|++
T Consensus       205 ~~~~~l~v~nl-~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          205 PPNHILFLTNL-PEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCEEEEeCC-CCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            46789999999 8899999999999999999999995   489999999999999999999999999 9999999986

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.94  E-value=8.2e-27  Score=185.31  Aligned_cols=133  Identities=19%  Similarity=0.326  Sum_probs=110.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++|||||+|.++++|++|++.||+..|  +|+.|.|.++..................+..+|||+|| |..+++++|
T Consensus        66 ~g~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-p~~~t~~~l  142 (216)
T 2qfj_A           66 TMKHKGFAFVEYEVPEAAQLALEQMNSVML--GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV-HQDLSDDDI  142 (216)
T ss_dssp             C-CCCSEEEEEESSHHHHHHHHHHHSSCCC--C-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECC-CTTCCHHHH
T ss_pred             CCccCceEEEEeCCHHHHHHHHHHccCCee--CCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCC-CCcCCHHHH
Confidence            677899999999999999999999999998  69999999887544221000000012245789999999 889999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      +++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|+|+.|.|.++....
T Consensus       143 ~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             HHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999984        5799999999999999999999999999999999998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.93  E-value=8.8e-26  Score=172.02  Aligned_cols=118  Identities=25%  Similarity=0.515  Sum_probs=106.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++|||||+|.++++|++|++.|||..|  .|++|.|.++.+...           ..+..+|||+|| |..+++++|
T Consensus        40 ~~~~~g~afV~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~~~~~~~-----------~~~~~~l~v~nl-~~~~t~~~l  105 (167)
T 1fxl_A           40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYARPSSA-----------SIRDANLYVSGL-PKTMTQKEL  105 (167)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCCCCG-----------GGTTCEEEEESC-CTTCCHHHH
T ss_pred             CCcceeEEEEEECCHHHHHHHHHHcCCCcc--CCceEEEEecCCCcc-----------cCCCCcEEECCC-CCcCCHHHH
Confidence            677899999999999999999999999999  699999999986543           234688999999 889999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCc--EEEEEEe
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDR--VISVEYA  135 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~--~l~v~~a  135 (240)
                      +++|++||.|..+.+.        +|+|||+|.+.++|++|++.|||..|.|+  +|.|.||
T Consensus       106 ~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999883        58999999999999999999999999996  4888876

>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=99.93  E-value=5.5e-26  Score=174.32  Aligned_cols=117  Identities=18%  Similarity=0.336  Sum_probs=105.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++|||||+|.++++|++|+ .|||..|  .|++|.|.++.....           .....+|||+|| |..+++++|
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~-~~~~~~~--~g~~i~v~~~~~~~~-----------~~~~~~l~v~nl-p~~~t~~~l  111 (172)
T 2g4b_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQSLKIRRPHDYQP-----------LPGAHKLFIGGL-PNYLNDDQV  111 (172)
T ss_dssp             EETTTTEEEEEESSHHHHHHHG-GGTTCEE--TTEECEEECCSSCCC-----------CTTTTCEEEECC-CTTCCHHHH
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhCCcEe--cCceeeecCCcccCC-----------CCCCCEEEEEcC-CCcCCHHHH
Confidence            4557999999999999999999 8999999  699999999875432           234789999999 889999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +++|++||.|..+.+.        +|+|||+|.+.++|++|+..|||..|+|+.|.|+||
T Consensus       112 ~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          112 KELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999983        579999999999999999999999999999999997

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.93  E-value=1.1e-25  Score=176.06  Aligned_cols=128  Identities=23%  Similarity=0.343  Sum_probs=104.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      ++.++|||||+|.++++|++||+. ++..|  .|+.|.|.++........     .....+.++|||+|| |..+++++|
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~-~~~~~--~g~~l~v~~~~~~~~~~~-----~~~~~~~~~l~V~nL-p~~~t~~~l  121 (196)
T 1l3k_A           51 TKRSRGFGFVTYATVEEVDAAMNA-RPHKV--DGRVVEPKRAVSREDSQR-----PGAHLTVKKIFVGGI-KEDTEEHHL  121 (196)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHT-CSCEE--TTEECEEEECCC----------------CCSEEEEECC-TTTCCHHHH
T ss_pred             CCCccceEEEEeCCHHHHHHHHhc-CCCEE--CCEEeeeecccCcccccc-----cccCCCcceEEEeCC-CCCCCHHHH
Confidence            677899999999999999999985 88888  699999999986543321     123445789999999 899999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCCC
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSE  141 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  141 (240)
                      +++|++||.|..|.|.        +|||||+|.+.++|++||.. ++..|+|+.|.|.++.++...
T Consensus       122 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          122 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            9999999999999884        57999999999999999986 899999999999999887654

>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=3.4e-25  Score=178.12  Aligned_cols=128  Identities=21%  Similarity=0.278  Sum_probs=109.4

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCC------------------------CCCCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDG------------------------SKSMANQR   63 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~------------------------~~~~~~~~   63 (240)
                      +|||||+|.++++|++|++.|||..|  .|+.|.|+++..........                        ........
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~--~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP  149 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBC--SSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCC
Confidence            79999999999999999999999999  69999999998542111000                        00012245


Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCccc-CcEEEEEEeecC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLV-DRVISVEYALKD  138 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~~~  138 (240)
                      +.++|||+|| |..+++++|+++|.+|| .|..|.+   .+|+|||+|.+.++|++|+..|||..|. |+.|.|.|++++
T Consensus       150 ~~~~l~V~nl-p~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          150 PSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             SCSEEEEECC-CTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCEEEEeCC-CccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            6799999999 88999999999999999 9999999   4799999999999999999999999999 999999999764

>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=99.93  E-value=1.1e-25  Score=169.51  Aligned_cols=133  Identities=18%  Similarity=0.193  Sum_probs=113.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhh-CCCcccCCCceEEEEeccCCCCCC-----CCCCCCCCCCCCCCEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGL-DNIPFGYDRRRLSVEWARGERGRH-----RDGSKSMANQRPTKTLFVINFDPI   76 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l-~g~~~~~~g~~l~v~~a~~~~~~~-----~~~~~~~~~~~~~~~l~v~nl~~~   76 (240)
                      +....+|+++|+|.+.++|++|++.| ||..|  +| +|.|.++.......     ...........+.++|||+|| |.
T Consensus         8 ~g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~--~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl-~~   83 (150)
T 2i2y_A            8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGV--DG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNL-GN   83 (150)
T ss_dssp             CCSSSCEEEEEECSSHHHHTTTHHHHHHHHTC--CC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESC-CS
T ss_pred             ccccccccceeeecCHHHHHHHHHHHhcCCCC--CC-ceecccccCccccccccccccccccccCCCCCCEEEEeCC-CC
Confidence            34566999999999999999999999 99999  68 99999887532111     111122335567899999999 88


Q ss_pred             CCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           77 RTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        77 ~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      .+++++|+++|.+||.|..|.|+   +|||||+|.+.++|+.|+..|||..|.|+.|.|+|+.++.
T Consensus        84 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           84 NGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             CCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999999995   7999999999999999999999999999999999998753

>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=3.5e-25  Score=173.89  Aligned_cols=128  Identities=21%  Similarity=0.282  Sum_probs=109.5

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC------------------------CCCCCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD------------------------GSKSMANQR   63 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~------------------------~~~~~~~~~   63 (240)
                      +|||||+|.++++|++|+..|||..|  .|++|.|.++.........                        ........+
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  118 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP  118 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCC--SSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCee--cCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCC
Confidence            79999999999999999999999999  6999999999854311100                        000112245


Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCccc-CcEEEEEEeecC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLV-DRVISVEYALKD  138 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~~~  138 (240)
                      +..+|||+|| |..+++++|+++|.+|| .|..|.+   .+|+|||+|.+.++|++|+..|||..|. |+.|.|.|++++
T Consensus       119 ~~~~l~v~nl-~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          119 PSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCCEEEECCC-CTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CccEEEEeCC-CCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            6899999999 88999999999999999 9999999   4699999999999999999999999999 999999999764

>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=99.92  E-value=4.2e-25  Score=174.58  Aligned_cols=126  Identities=17%  Similarity=0.227  Sum_probs=104.4

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCC------CC--------------C------CCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD------GS--------------K------SMA   60 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~------~~--------------~------~~~   60 (240)
                      .+|||||+|.++++|++||+.|||..|  .|++|.|.++......+..      +.              .      ...
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~  118 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFM--FGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR  118 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEE--CCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccc
Confidence            489999999999999999999999999  6999999999754321100      00              0      001


Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCe--EEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCc----
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDR----  128 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i--~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~----  128 (240)
                      ..+|+.+|||+|| |..+++++|+++|++||.|  ..+.+.      +|+|||+|.+.++|.+||..|||..|.|.    
T Consensus       119 ~~~p~~~l~v~NL-p~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~  197 (205)
T 3tyt_A          119 IQHPSNVLHFFNA-PLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY  197 (205)
T ss_dssp             CCCCCSEEEEEEE-CTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSS
T ss_pred             cCCCcceEEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCc
Confidence            2356789999999 8999999999999999998  788874      37999999999999999999999999885    


Q ss_pred             EEEEEEe
Q 026341          129 VISVEYA  135 (240)
Q Consensus       129 ~l~v~~a  135 (240)
                      ++.|.||
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            6777776

>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=3.5e-25  Score=168.05  Aligned_cols=135  Identities=24%  Similarity=0.235  Sum_probs=102.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC--CCCCCCCCCCCCCCCCEEEEeccCCCCCCH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG--RHRDGSKSMANQRPTKTLFVINFDPIRTRE   80 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~--~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~   80 (240)
                      +...++|||||+|.++++|++|+..+++.... ++ .+.+........  .............+..+|||+|| |..+++
T Consensus         8 n~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-~~~~~~   84 (158)
T 2kn4_A            8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGV-DG-EWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL-TYRTSP   84 (158)
T ss_dssp             ECSSCEEEEEEECSSHHHHHHHHHHHHHHHTC-CC-EEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESC-CTTCCH
T ss_pred             cCccccchhHHHHHHHHhHHHHHHhhcccCCC-CC-cccccCccccccccccccccccccCCCCCCEEEEeCC-CCCCCH
Confidence            34467999999999999999999988864432 23 222221111000  00001111223456789999999 899999


Q ss_pred             HHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           81 RDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        81 ~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ++|+++|++||.|..|.|.        +|||||+|.+.++|+.||..|||..|.|+.|.|.++.+...
T Consensus        85 ~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             HHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             HHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999984        57999999999999999999999999999999999987643

>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=99.92  E-value=1.6e-24  Score=179.39  Aligned_cols=126  Identities=20%  Similarity=0.280  Sum_probs=112.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCC-CCHHH
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIR-TRERD   82 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~~   82 (240)
                      ++.++|||||+|.+.++|++|+..|||..|  +|++|.|.|+.......        ...+..+|||+|| |.. +++++
T Consensus       133 ~g~~~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~i~v~~a~~~~~~~--------~~~~~~~l~v~nl-p~~~~~~~~  201 (284)
T 3smz_A          133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTDAGQLTP--------ALLHSRCLCVDRL-PPGFNDVDA  201 (284)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCGGGCCT--------TTTSCSEEEEECC-CTTCCCHHH
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCCCCc--------ccCCccEEEEecC-CcccCCHHH
Confidence            677899999999999999999999999999  69999999998755332        3356789999999 888 49999


Q ss_pred             HHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           83 IKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      |+++|+.||.|..+.|.       +|+|||+|.+.++|.+|+..|||..|.|+.|.|.|+.+...
T Consensus       202 l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999999999884       57999999999999999999999999999999999987653

>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=99.92  E-value=1.8e-24  Score=166.10  Aligned_cols=120  Identities=25%  Similarity=0.377  Sum_probs=104.1

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccC-CCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHH
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGY-DRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK   84 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~-~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~   84 (240)
                      .++|||||+|.++++|++|++.||+..+.. .+..|.|.++.....          ...+..+|||+|| |..+++++|+
T Consensus        45 ~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~l~v~nl-~~~~t~~~l~  113 (175)
T 3nmr_A           45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKN----------NAVEDRKLFIGMI-SKKCTENDIR  113 (175)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCC----------SCGGGSEEEEESC-CTTCCHHHHH
T ss_pred             CcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccccc----------ccCCCCeEEEcCC-CCcCCHHHHH
Confidence            679999999999999999999999987731 267888888775443          2235789999999 8999999999


Q ss_pred             HhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCccc---CcEEEEEEee
Q 026341           85 RHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLV---DRVISVEYAL  136 (240)
Q Consensus        85 ~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~---g~~l~v~~a~  136 (240)
                      ++|++||.|..+.+.       +|||||+|.+.++|++|++.|||..+.   +++|.|.||.
T Consensus       114 ~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          114 VMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999984       579999999999999999999998776   4999999973

>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=99.91  E-value=3.2e-24  Score=178.25  Aligned_cols=126  Identities=23%  Similarity=0.339  Sum_probs=107.1

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCC-CCHHHH
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIR-TRERDI   83 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~~l   83 (240)
                      +.++|||||+|.+.++|++|+..|||..|  +|+.|.|.++.+.......    .....+..+|||+|| |.. +++++|
T Consensus       156 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~~~~----~~~~~~~~~l~v~nl-p~~~~t~~~l  228 (292)
T 2ghp_A          156 NTSRRFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSNPLEKSKRT----DSATLEGREIMIRNL-STELLDENLL  228 (292)
T ss_dssp             ---CCEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCCC-------------CCTTTEEEEEEE-CTTTCCHHHH
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCcccccc----cccCCCCceEEEECC-CcccCCHHHH
Confidence            56799999999999999999999999999  6999999999876543221    124456899999999 889 999999


Q ss_pred             HHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           84 KRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      +++|.+||.|..|.|.         +|||||+|.+.++|++|+ .|||..|.|+.|.|.|+.++
T Consensus       229 ~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999999999999884         479999999999999999 99999999999999999865

>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=99.91  E-value=4.8e-25  Score=168.23  Aligned_cols=119  Identities=18%  Similarity=0.367  Sum_probs=104.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .++.++|||||+|.++++|++|+..  +..|  +|+.|.|.++.+...           ..+..+|||+|| |..+++++
T Consensus        40 ~~g~~~g~afV~f~~~~~a~~A~~~--~~~~--~g~~i~v~~~~~~~~-----------~~~~~~l~V~nl-p~~~t~~~  103 (167)
T 2cjk_A           40 ATGRSRGFGFLSFEKPSSVDEVVKT--QHIL--DGKVIDPKRAIPRDE-----------QDKTGKIFVGGI-GPDVRPKE  103 (167)
T ss_dssp             TTSSCCSCEEEEESSTHHHHHHHHS--CCEE--TTEECCCEECCCHHH-----------HHHCEEEEEEEE-CTTCCHHH
T ss_pred             CCCCccceEEEEEccHHHHHHHHhc--cccc--CCeEcccccccchhh-----------ccCCCeEEECCC-CCCCCHHH
Confidence            3678899999999999999999984  4566  699999998875432           224679999999 89999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |+++|++||.|..+.+.        +|||||+|.+.++|++|++ +++..|+|+.|.|.||.++
T Consensus       104 l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          104 FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999999999999984        4799999999999999998 8999999999999999864

>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=99.90  E-value=3.6e-23  Score=180.55  Aligned_cols=79  Identities=27%  Similarity=0.473  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| ++.+|+++|.++|.+||.|+.|.|+        +|||||+|.+.++|++||..|||..|+|+.|.|
T Consensus        98 ~~~~~~~lfV~nL-~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V  176 (437)
T 3pgw_S           98 QGDAFKTLFVARV-NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  176 (437)
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEE
Confidence            3456789999999 8999999999999999999999884        689999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +|+.+...
T Consensus       177 ~~a~~~~~  184 (437)
T 3pgw_S          177 DVERGRTV  184 (437)
T ss_pred             EEeCCCCC
Confidence            99987554

>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=99.89  E-value=7.2e-23  Score=169.38  Aligned_cols=115  Identities=21%  Similarity=0.350  Sum_probs=105.9

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHH
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK   84 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~   84 (240)
                      ++++|||||+|.++++|++|++.|||..|  .|++|.|+++.                 +..+|||+|| |..+++++|.
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v~~~~-----------------~~~~l~v~nl-p~~~t~~~l~  113 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRL--RERELSVQLQP-----------------TDALLCVANL-PPSLTQQQFE  113 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECC-----------------CSCEEEEESC-CTTCCHHHHH
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCee--CCeEEEEEecC-----------------CCCEEEEcCC-CCcCCHHHHH
Confidence            56799999999999999999999999998  69999999854                 2579999999 8999999999


Q ss_pred             HhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           85 RHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        85 ~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|.+||.|..+.+.        +|||||+|.+.++|..|+..|||..|.|+.|.|.++.+..
T Consensus       114 ~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             HHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             HHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            999999999999873        5799999999999999999999999999999999997654

>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=99.89  E-value=6.7e-23  Score=167.82  Aligned_cols=115  Identities=26%  Similarity=0.302  Sum_probs=103.4

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHH
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK   84 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~   84 (240)
                      ++.+|||||+|.+.++|++|+..|||..|  .|+.|.|.++.+                 ..+|||+|| |..+++++|+
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i--~g~~l~v~~a~~-----------------~~~l~v~nl-~~~~t~~~l~  114 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTIL--KSRPLRIRFATH-----------------GAALTVKNL-SPVVSNELLE  114 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCC-----------------SSEEEEESC-CTTCCHHHHH
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEE--CCceeEeeeccc-----------------CCcccccCC-CCCCCHHHHH
Confidence            34689999999999999999999999999  699999999873                 578999999 8899999999


Q ss_pred             HhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCC-ccc---CcEEEEEEeecCC
Q 026341           85 RHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRS-KLV---DRVISVEYALKDD  139 (240)
Q Consensus        85 ~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~-~~~---g~~l~v~~a~~~~  139 (240)
                      ++|..||.|..|.|.       +|||||+|.+.++|.+|+..||+. .+.   +++|.|.++....
T Consensus       115 ~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          115 QAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            999999999999984       689999999999999999999554 443   8999999998654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.88  E-value=3.6e-22  Score=165.78  Aligned_cols=111  Identities=21%  Similarity=0.300  Sum_probs=102.5

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHh
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRH   86 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~   86 (240)
                      ++|||||+|.++++|++|++ |||..|  +|+.|.|.++.                  .++|||+|| |..+++++|.++
T Consensus        80 ~~g~afV~f~~~~~A~~A~~-~~~~~~--~g~~i~v~~~~------------------~~~l~v~nl-p~~~t~~~l~~~  137 (292)
T 2ghp_A           80 NFRFARIEFARYDGALAAIT-KTHKVV--GQNEIIVSHLT------------------ECTLWMTNF-PPSYTQRNIRDL  137 (292)
T ss_dssp             SSEEEEEEESSHHHHHHHHT-TTTCEE--TTEECEEEECC------------------SCEEEEECC-CTTCCHHHHHHH
T ss_pred             CcEEEEEEECCHHHHHHHHH-hCCcEe--CCcEEEEEECC------------------CCEEEEECC-CCCCCHHHHHHH
Confidence            48999999999999999995 999999  69999999863                  689999999 899999999999


Q ss_pred             hccCC-CeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           87 FEPYG-NVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        87 f~~~G-~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      |.+|| .|..|.+       .+|||||+|.+.++|++|+..|||..|.|+.|.|.++.+..
T Consensus       138 f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          138 LQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             HHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             HHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            99999 9999998       36899999999999999999999999999999999988654

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.85  E-value=3.8e-21  Score=146.82  Aligned_cols=127  Identities=20%  Similarity=0.317  Sum_probs=72.5

Q ss_pred             EEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCC--------C-CCCCCCCCCCCCEEEEeccCCCCCCHHHH
Q 026341           13 VYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR--------D-GSKSMANQRPTKTLFVINFDPIRTRERDI   83 (240)
Q Consensus        13 V~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~--------~-~~~~~~~~~~~~~l~v~nl~~~~~~~~~l   83 (240)
                      .+|++.++|+.|+..|++....-.|+.+.+.++........        . ....+....+.++|||+|| |..+++++|
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nL-p~~~t~~~L   89 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI-HEEAQEDEI   89 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESC-CTTCCHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCC-CCCCCHHHH
Confidence            78999999999999999987743466666666433221110        0 1112334566789999999 889999999


Q ss_pred             HHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           84 KRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        84 ~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      +++|.+||.|..|.|.        +|||||+|.+.++|++||..|||..|.|+.|.|.|+.....
T Consensus        90 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           90 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             HHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             HHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999984        58999999999999999999999999999999999987653

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.83  E-value=6.1e-20  Score=129.15  Aligned_cols=82  Identities=26%  Similarity=0.477  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.++||||+|.+.++|++||+.||+..|.|+.|.|+|+.+...
T Consensus         7 ~~~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~i~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            7 GMAKVKVLFVRNL-ANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCCCEEEECC-CTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            4456789999999 889999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             CCC
Q 026341          141 ERD  143 (240)
Q Consensus       141 ~~~  143 (240)
                      ...
T Consensus        86 ~~~   88 (103)
T 2dgu_A           86 KRK   88 (103)
T ss_dssp             CCC
T ss_pred             cch
Confidence            443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.83  E-value=4.2e-21  Score=141.74  Aligned_cols=117  Identities=25%  Similarity=0.294  Sum_probs=73.9

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhc
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFE   88 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~   88 (240)
                      -++|++|++...|..||..|+|....  |.. .+.+..+           +....+.++|||+|| |..+++++|+++|+
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~--g~~-~~~~~~~-----------~~~~~~~~~l~V~nL-p~~~te~~L~~~F~   69 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQM--GRG-SMSYGRP-----------PPDVEGMTSLKVDNL-TYRTSPDTLRRVFE   69 (135)
T ss_dssp             ---------------------------------CCSCCS-----------CSSGGGCCCEEEECC-CSSCHHHHHHHHHG
T ss_pred             ccccccccCCCchhhhhhhccCCCCC--CCC-CCCcCCC-----------CCCCCCCCEEEEeCC-CCCCCHHHHHHHHH
Confidence            36788888888899999989887652  332 2222222           123445789999999 88999999999999


Q ss_pred             cCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           89 PYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        89 ~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      +||.|..|.|.        +|||||+|.+.++|++||..|||..|.|+.|.|+|+++...
T Consensus        70 ~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           70 KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             GGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             hcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999984        57999999999999999999999999999999999987543

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=3.2e-19  Score=126.56  Aligned_cols=76  Identities=24%  Similarity=0.324  Sum_probs=71.6

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC-CeEEEEecCHHHHHHHHHhcCCCcccC-----cEEEEEEe
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-NFAFVQFETQEEATKALESTDRSKLVD-----RVISVEYA  135 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k-g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~l~v~~a  135 (240)
                      ....++|||+|| |+.+++++|+++|.+||+|..|.|.. +||||+|.+.++|++||+.||+..|.|     +.|.|+++
T Consensus        12 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a   90 (108)
T 1x4c_A           12 RRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   90 (108)
T ss_dssp             CSCCCEEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEETTTEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEES
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEecCCEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeC
Confidence            345789999999 89999999999999999999999987 999999999999999999999999999     99999999


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      .+.
T Consensus        91 ~~~   93 (108)
T 1x4c_A           91 GPR   93 (108)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            874

>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=99.81  E-value=9.4e-20  Score=127.26  Aligned_cols=74  Identities=22%  Similarity=0.412  Sum_probs=69.2

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..+++|||+|| |..+++++|+++|++||+|..|.|.        +|||||+|.+.++|++|++.|||..|.|++|.|+|
T Consensus        17 ~~gt~lfV~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYL-PQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34788999999 8999999999999999999999884        57999999999999999999999999999999999


Q ss_pred             eec
Q 026341          135 ALK  137 (240)
Q Consensus       135 a~~  137 (240)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.8e-19  Score=122.57  Aligned_cols=78  Identities=31%  Similarity=0.485  Sum_probs=73.8

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.+.++||||+|.+.++|++|+..||+..|.|+.|.|+++.+...
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESC-CSSCCHHHHHHHHHTSSCEEEEEEETTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEECCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            456899999999 899999999999999999999999999999999999999999999999999999999999987654

>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=99.81  E-value=1.4e-19  Score=128.79  Aligned_cols=95  Identities=17%  Similarity=0.319  Sum_probs=80.4

Q ss_pred             CCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCC-CCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHH
Q 026341           36 DRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIR-TRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEAT  114 (240)
Q Consensus        36 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~  114 (240)
                      .|.+|.|..+......        ....+.++|||+|| |.. +++++|+++|.+||.|..|.|.++||||+|.+.++|+
T Consensus         6 ~g~~~~~~~s~~~~~~--------~~~~~~~~l~V~nl-~~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~   76 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKN--------DPKSINSRVFIGNL-NTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHAR   76 (110)
T ss_dssp             CSCCCCCCCCCSCCSC--------CCTTCSSEEEECSC-CCSSCCHHHHHHHHGGGSCCSEEEEETTEEEEECSSSHHHH
T ss_pred             CCcccccccCCCCCCC--------CCCCCCcEEEEeCC-CcccCCHHHHHHHHHhCCCeEEEEEeCCEEEEEECCHHHHH
Confidence            3556666655543222        13345689999999 888 9999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCcccCcEEEEEEeecCC
Q 026341          115 KALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus       115 ~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      +||+.||+..|+|+.|.|+++....
T Consensus        77 ~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           77 AAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HHHHHHTTCEETTEECCEEESCCCC
T ss_pred             HHHHHcCCCEECCeEEEEEECCCCC
Confidence            9999999999999999999998644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.9e-19  Score=122.36  Aligned_cols=79  Identities=23%  Similarity=0.452  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.+.++||||+|.+.++|++|+..||+..|.|+.|.|+++.+...
T Consensus         6 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A            6 SGKASTKLHVGNI-SPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             CCCSSEEEEEESC-CSSCCHHHHHHHHHTTSCCCEEEECSSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEECCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence            4456899999999 899999999999999999999999999999999999999999999999999999999999987654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.1e-19  Score=122.36  Aligned_cols=78  Identities=23%  Similarity=0.418  Sum_probs=73.5

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.+.++||||+|.+.++|++|+..|||..|.|+.|.|+++.+...
T Consensus         6 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~~~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A            6 SGNTWKIFVGNV-SAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             SCCSCCEEEESC-CTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHcCCCEEEEEEECCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            456789999999 889999999999999999999999999999999999999999999999999999999999987643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=2.1e-19  Score=124.79  Aligned_cols=79  Identities=25%  Similarity=0.578  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           61 NQRPTKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ...+.++|||+|| |. .+++++|+++|.+||.|..|.|++|||||+|.+.++|+.|+..|||..|.|+.|.|+++....
T Consensus         6 ~~~~~~~l~V~nl-p~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            6 NIPPKSRLFIGNL-PLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             ---CCEEEEEESS-TTSCCCHHHHHHHHTTTCCCCEEEEETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             cCCCCCEEEEeCC-CcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            4567899999999 87 999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             C
Q 026341          140 S  140 (240)
Q Consensus       140 ~  140 (240)
                      .
T Consensus        85 ~   85 (96)
T 2kvi_A           85 R   85 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.80  E-value=3.2e-19  Score=123.75  Aligned_cols=78  Identities=15%  Similarity=0.240  Sum_probs=72.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCc--ccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSK--LVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~--~~g~~l~v~~a~  136 (240)
                      ..+|+.+|||+|| |..+++++|.++|++||.|..|.+.  +|+|||+|++.++|++|++.|++..  |.|++|.|+|++
T Consensus        17 ~~~ps~~l~V~NL-p~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           17 KTPASPVVHIRGL-IDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCCCSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             cCCCCcEEEEeCC-CCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            5668999999999 8999999999999999999999986  7999999999999999999999876  789999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      .+.
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            653

>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=99.80  E-value=2.8e-19  Score=130.29  Aligned_cols=80  Identities=25%  Similarity=0.471  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|++||+.|||..|+|+.|.|
T Consensus        18 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           18 RSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCSSSEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4556889999999 8999999999999999999999984        789999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      +|+......
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1e-18  Score=121.88  Aligned_cols=78  Identities=31%  Similarity=0.448  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccC--CCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~--G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ...+.++|||+|| |..+++++|+++|.+|  |.|..|.++++||||+|.+.++|++||..|||..|.|+.|.|+++++.
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~g~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           11 TMSSVKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             CSSCCCEEEEESC-CTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             ccCCcCEEEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEEeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            4566899999999 8899999999999999  999999999999999999999999999999999999999999999875


Q ss_pred             C
Q 026341          139 D  139 (240)
Q Consensus       139 ~  139 (240)
                      .
T Consensus        90 ~   90 (99)
T 2cpd_A           90 D   90 (99)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=3.4e-19  Score=127.85  Aligned_cols=73  Identities=23%  Similarity=0.312  Sum_probs=65.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC-CeEEEEecCHHHHHHHHHhcCCCcccCcE-----EEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-NFAFVQFETQEEATKALESTDRSKLVDRV-----ISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k-g~afV~f~~~~~a~~A~~~l~g~~~~g~~-----l~v~~a~~  137 (240)
                      ..++|||+|| |+.+++++|+++|.+||+|..|.|.. +||||+|++.++|++||+.|||.+|+|+.     |.|..+.+
T Consensus        15 ~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           15 SENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             --CCEEEEEC-CSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             CCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEecCCEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence            4689999999 89999999999999999999999987 99999999999999999999999999988     55555443

>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=99.79  E-value=1.5e-18  Score=124.70  Aligned_cols=78  Identities=28%  Similarity=0.378  Sum_probs=72.0

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.|.       +|||||+|.+.++|++|++.|||..|.|+.|.|++
T Consensus         4 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGL-NRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECC-TTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            455789999999 8999999999999999999999995       48999999999999999999999999999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      +++...
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987643

>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=99.78  E-value=1.1e-18  Score=121.46  Aligned_cols=77  Identities=23%  Similarity=0.555  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           61 NQRPTKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..++.++|||+|| |. .+++++|+++|.+||.|..|.+++|||||+|.+.++|++|+..|||..|+|+.|.|++++..
T Consensus        18 ~~~~~~~l~V~nL-p~~~~t~~~L~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           18 GSHMKSRLFIGNL-PLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             -CCTTCEEEEESC-CSSCCCHHHHHHHHGGGSCEEEEEECSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCCEEEEeCC-CcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            5567899999999 87 99999999999999999999999999999999999999999999999999999999998764

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=9.4e-19  Score=122.40  Aligned_cols=78  Identities=18%  Similarity=0.316  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCC--cccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRS--KLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~--~~~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |+ .+++++|+++|++||.|..|.|.  ++||||+|++.++|++||+.||+.  .|.|++|.|+||
T Consensus        11 ~~~p~~~l~V~nL-p~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   89 (102)
T 1x4d_A           11 RVETRRVVHIMDF-QRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   89 (102)
T ss_dssp             CCCCCCEEEEESC-CCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCCEEEEeCC-CCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEEC
Confidence            3457899999999 88 99999999999999999999996  489999999999999999999864  599999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      ....
T Consensus        90 ~~~~   93 (102)
T 1x4d_A           90 QKYK   93 (102)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            8644

>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=99.78  E-value=2.3e-18  Score=121.08  Aligned_cols=81  Identities=16%  Similarity=0.232  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCC--cccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRS--KLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~--~~~g~~l~v~~a~  136 (240)
                      ...|.++|||+|| |+.+++++|+++|++||.|..|.|.  +|||||+|++.++|++|++.|++.  .|.|++|.|+|+.
T Consensus        11 ~~~p~~~l~V~nL-p~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           11 KVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESC-CSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            4567899999999 8999999999999999999999986  689999999999999999988654  5999999999998


Q ss_pred             cCCCCC
Q 026341          137 KDDSER  142 (240)
Q Consensus       137 ~~~~~~  142 (240)
                      .+....
T Consensus        90 ~~~~~~   95 (104)
T 1wex_A           90 SKRITR   95 (104)
T ss_dssp             SSSCCC
T ss_pred             CccccC
Confidence            765443

>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=99.78  E-value=2.5e-18  Score=122.06  Aligned_cols=79  Identities=25%  Similarity=0.426  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.     ++||||+|.+.++|++||+.||+..|+|+.|.|+|+
T Consensus        18 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           18 AGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCSSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            4556799999999 8899999999999999999999984     579999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      ++...
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.3e-19  Score=124.32  Aligned_cols=80  Identities=19%  Similarity=0.374  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCC--CcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDR--SKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g--~~~~g~~l~v~~a~  136 (240)
                      ...+.++|||+|| |+.+++++|+++|++||+|..|.|.  +|||||+|++.++|+.|++.|++  ..|.|++|.|+|++
T Consensus        12 ~~~~~~~LfV~nL-p~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~   90 (105)
T 1sjq_A           12 SGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN   90 (105)
T ss_dssp             CCCCCCEEEECSC-CTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcC
Confidence            4456899999999 8999999999999999999999997  69999999999999999998864  78999999999998


Q ss_pred             cCCCC
Q 026341          137 KDDSE  141 (240)
Q Consensus       137 ~~~~~  141 (240)
                      .+...
T Consensus        91 ~~~~~   95 (105)
T 1sjq_A           91 HKELK   95 (105)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            76543

>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=4.7e-18  Score=119.36  Aligned_cols=80  Identities=31%  Similarity=0.514  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|++||..||+..|+|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           11 SKSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CSCCCCEEEEESC-CTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4556899999999 8999999999999999999999996      78999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 026341          135 ALKDDSE  141 (240)
Q Consensus       135 a~~~~~~  141 (240)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876543

>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=3.4e-18  Score=118.28  Aligned_cols=77  Identities=22%  Similarity=0.395  Sum_probs=71.5

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++.|||..|.|+.|.|++
T Consensus         3 ~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSL-HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            46789999999 8899999999999999999999984        57999999999999999999999999999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      +.++..
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            987653

>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=2.9e-18  Score=120.49  Aligned_cols=79  Identities=23%  Similarity=0.468  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|++||..|||..|.|+.|.|.|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNL-DDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4456889999999 8899999999999999999999986      68999999999999999999999999999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            987654

>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=99.78  E-value=3.4e-18  Score=120.07  Aligned_cols=80  Identities=23%  Similarity=0.380  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|++||..||+..|.|+.|.|+|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           11 DDGQPRTLYVGNL-SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             CSCCCCEEEEESC-CTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCC-CccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            4566899999999 8899999999999999999999995      48999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 026341          135 ALKDDSE  141 (240)
Q Consensus       135 a~~~~~~  141 (240)
                      +.+....
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9886543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.77  E-value=7.9e-19  Score=117.83  Aligned_cols=73  Identities=18%  Similarity=0.222  Sum_probs=68.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ....-|||+|| ++.+++++|+++|.+||+|..+.+  ++|||||+|.+.++|++|++.||+.++.|++|.|++|.
T Consensus         5 ~~~~wL~VgNL-~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            5 WGSSWLLLKNL-TAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCCEEEEECC-CTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CccceEEEeCC-CccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            44678999999 889999999999999999999988  58999999999999999999999999999999999984

>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=1.4e-18  Score=123.63  Aligned_cols=76  Identities=22%  Similarity=0.307  Sum_probs=70.5

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      .++.++|||+|| ++.+++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+.|||..|+|+.|.|+
T Consensus         3 ~~p~~~lfV~nL-~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~   81 (110)
T 3s8s_A            3 QIPLKEVTFARL-NDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ   81 (110)
T ss_dssp             CSCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEECC-CCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            356789999999 8999999999999999999999983        5899999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ++...
T Consensus        82 ~a~~~   86 (110)
T 3s8s_A           82 LDIKG   86 (110)
T ss_dssp             ECSTT
T ss_pred             ECCCC
Confidence            98654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.77  E-value=5.8e-19  Score=125.50  Aligned_cols=74  Identities=18%  Similarity=0.184  Sum_probs=69.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..++|||+|| |+.+++++|+++|.+|| +|..+.|.    +|||||+|.+.++|++||+.|||..|+|+.|.|+++...
T Consensus        27 ~~~~l~VgnL-p~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           27 KRYRITMKNL-PEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CCEEEEEECS-SCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCEEEEECC-CCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            4689999999 99999999999999999 89999984    799999999999999999999999999999999998754

>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=99.77  E-value=1.9e-18  Score=119.87  Aligned_cols=77  Identities=25%  Similarity=0.282  Sum_probs=71.9

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHH----HhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIK----RHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~----~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ....++|||+|| |+.+++++|+    ++|++||.|..|.|+     ++||||+|.+.++|++||+.|||..|+|+.|.|
T Consensus         6 ~~~~~~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            6 SGNGADVQVSNI-DYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             CSSCEEEEEESC-CTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345789999999 8999999999    999999999999997     899999999999999999999999999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      +++++..
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.77  E-value=6.5e-18  Score=118.09  Aligned_cols=80  Identities=20%  Similarity=0.370  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc--CCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST--DRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l--~g~~~~g~~l~v~~a~  136 (240)
                      ..++.++|||+|| |+.+++++|+++|++||.|..|.|.  +|||||+|++.++|++|++.|  ++..|.|++|.|+|++
T Consensus        11 ~~~p~~~l~V~nL-p~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           11 DGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             CSSCCSEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            4567899999999 8999999999999999999999986  589999999999999999987  4678999999999998


Q ss_pred             cCCCC
Q 026341          137 KDDSE  141 (240)
Q Consensus       137 ~~~~~  141 (240)
                      .+...
T Consensus        90 ~~~~~   94 (101)
T 2cq1_A           90 HKELK   94 (101)
T ss_dssp             CSSCC
T ss_pred             cccCc
Confidence            76544

>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=99.77  E-value=2.7e-18  Score=123.14  Aligned_cols=81  Identities=19%  Similarity=0.363  Sum_probs=73.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcC--CCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTD--RSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~--g~~~~g~~l~v~~a~  136 (240)
                      ..++.++|||+|| |+.+++++|+++|++||.|..|.|.  +|||||+|++.++|++|++.|+  +..|.|++|.|+|++
T Consensus        27 ~~~ps~~LfVgNL-p~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  105 (119)
T 2ad9_A           27 AGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN  105 (119)
T ss_dssp             CSSCCSEEEEESC-CTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEcc
Confidence            4567899999999 8999999999999999999999996  6999999999999999999987  468999999999998


Q ss_pred             cCCCCC
Q 026341          137 KDDSER  142 (240)
Q Consensus       137 ~~~~~~  142 (240)
                      .+..+.
T Consensus       106 ~k~~~~  111 (119)
T 2ad9_A          106 HKELKT  111 (119)
T ss_dssp             SSSCCC
T ss_pred             CCCCCc
Confidence            766543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.77  E-value=1.3e-18  Score=123.32  Aligned_cols=78  Identities=31%  Similarity=0.573  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.+.+|||||+|.+.++|++|+..|||..|+|+.|.|+++.+..
T Consensus        27 ~~~~~~~l~V~nL-p~~~t~~~L~~~F~~~G~i~~v~i~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           27 GELSNTRLFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             -CCSCSEEEECSS-CTTCCHHHHHHHHTTTSCCCEEEEETTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            4456899999999 89999999999999999999999999999999999999999999999999999999999998754

>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=99.77  E-value=5e-18  Score=119.63  Aligned_cols=79  Identities=23%  Similarity=0.335  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||..||+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           11 ERNQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCTTTEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            4567899999999 8999999999999999999999983        579999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .++.+...
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987654

>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=8.8e-18  Score=120.35  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||+.|||..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           11 DTSNHFHVFVGDL-SPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CSTTCEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4456899999999 8999999999999999999999984        479999999999999999999999999999999


Q ss_pred             EEeecCCCCCC
Q 026341          133 EYALKDDSERD  143 (240)
Q Consensus       133 ~~a~~~~~~~~  143 (240)
                      .|+........
T Consensus        90 ~~a~~~~~~~~  100 (115)
T 2dgo_A           90 NWATRKPPAPK  100 (115)
T ss_dssp             EESSCCCCCSC
T ss_pred             EEccCCCCCCc
Confidence            99987665433

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4.5e-18  Score=119.25  Aligned_cols=79  Identities=28%  Similarity=0.445  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        ++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus         8 ~~~~~~~l~v~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            8 MASDEGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCSEEEEESC-CTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            4456899999999 8999999999999999999999984        579999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.+...
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            99987654

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=5.7e-18  Score=118.06  Aligned_cols=78  Identities=27%  Similarity=0.422  Sum_probs=72.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||..|||..|.|+.|.|.
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            5 SSGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCSCEEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            456789999999 8899999999999999999999983        5899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      ++.+...
T Consensus        84 ~a~~~~~   90 (99)
T 1whw_A           84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             EcCCCcc
Confidence            9988654

>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=99.77  E-value=3.9e-18  Score=116.17  Aligned_cols=75  Identities=21%  Similarity=0.384  Sum_probs=70.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..++|||+|| |..+++++|+++|.+||.|..+.+         .+|||||+|.+.++|++|+..|||..|+|+.|.|++
T Consensus         3 ~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            3 KPTKVHIGRL-TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            4679999999 899999999999999999999988         578999999999999999999999999999999999


Q ss_pred             eecCC
Q 026341          135 ALKDD  139 (240)
Q Consensus       135 a~~~~  139 (240)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            97654

>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=99.77  E-value=1.7e-18  Score=122.87  Aligned_cols=79  Identities=20%  Similarity=0.346  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEeccCCCC-CCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcC--CCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIR-TRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTD--RSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~-~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~--g~~~~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |+. +++++|+++|.+||+|..|.|.  +|||||+|++.++|+.||+.||  +..|.|++|.|+|+
T Consensus        21 ~~~p~~~l~V~NL-p~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a   99 (112)
T 1x4f_A           21 KQELGRVIHLSNL-PHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   99 (112)
T ss_dssp             SSCCCCEEEEESC-CCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCC-CCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEC
Confidence            4567899999999 887 9999999999999999999996  6999999999999999999886  45699999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      .....
T Consensus       100 ~~~~~  104 (112)
T 1x4f_A          100 EKYKK  104 (112)
T ss_dssp             CSCSS
T ss_pred             ccccc
Confidence            86543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.1e-18  Score=120.28  Aligned_cols=79  Identities=34%  Similarity=0.438  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        ++||||+|.+.++|++||..|||..|+|+.|.|
T Consensus         9 ~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            9 DVDGMITLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             CCSCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCeEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            4566899999999 8999999999999999999999984        589999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.....
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99987543

>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=7.5e-18  Score=117.47  Aligned_cols=79  Identities=23%  Similarity=0.447  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||+ ||+..|.|+.|.|
T Consensus         6 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            6 SGSKSNKIFVGGI-PHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCSSCCEEEEESC-CSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            4456899999999 8999999999999999999999983        6899999999999999999 9999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      .++.++...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2dgs_A           84 KRAEPRDSK   92 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCccc
Confidence            999876543

>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=4.5e-18  Score=119.50  Aligned_cols=79  Identities=25%  Similarity=0.495  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|++||..|||..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           11 RADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCSSSEEEEEESC-CTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            4556899999999 8899999999999999999999984        469999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.+...
T Consensus        90 ~~a~~~~~   97 (103)
T 2cq0_A           90 EWAKPSTN   97 (103)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99987653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=8.4e-18  Score=124.50  Aligned_cols=80  Identities=23%  Similarity=0.449  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|+.||+|..|.|.        +|||||+|.+.++|++||+.|||..|.|+.|.|
T Consensus        38 ~~~~~~~l~V~nL-p~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           38 EPDVLRNLMVNYI-PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CTTTTSEEEEESC-STTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            4456789999999 8999999999999999999999884        679999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      +++......
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.76  E-value=2e-18  Score=123.85  Aligned_cols=74  Identities=27%  Similarity=0.487  Sum_probs=69.3

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..+|||+|| |..+++++|+++|.+||.|..|.|.      +|||||+|.+.++|++||+.|||..|+|+.|.|.++...
T Consensus         5 ~~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCC-CCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            568999999 8999999999999999999999984      689999999999999999999999999999999999765


Q ss_pred             C
Q 026341          139 D  139 (240)
Q Consensus       139 ~  139 (240)
                      .
T Consensus        84 ~   84 (115)
T 4f25_A           84 K   84 (115)
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=99.76  E-value=2.5e-18  Score=119.17  Aligned_cols=77  Identities=27%  Similarity=0.529  Sum_probs=71.0

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEE-EEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV-RIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~-~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..| .|+        +|||||+|.+.++|++|+..|||..|.|+.|.|+
T Consensus         3 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECC-CTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45789999999 8899999999999999999988 773        5899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      ++.+...
T Consensus        82 ~a~~~~~   88 (96)
T 1x5t_A           82 YAFKKDS   88 (96)
T ss_dssp             ESCCCCC
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=3.3e-18  Score=119.94  Aligned_cols=80  Identities=28%  Similarity=0.502  Sum_probs=73.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus         8 ~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2cqb_A            8 MATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   86 (102)
T ss_dssp             SCCCCSCEEEESC-CSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            4456899999999 8899999999999999999999983        689999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      .++.+....
T Consensus        87 ~~a~~~~~~   95 (102)
T 2cqb_A           87 NLAKPMRIK   95 (102)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999876543

>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=4e-18  Score=115.39  Aligned_cols=74  Identities=30%  Similarity=0.579  Sum_probs=69.5

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.+        .+|||||+|.+.++|++|++.|||..|+|+.|.|+
T Consensus         4 ~~~~~~l~V~nl-~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            4 ATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCSSEEEEECC-CTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            456899999999 889999999999999999999988        47899999999999999999999999999999999


Q ss_pred             Eee
Q 026341          134 YAL  136 (240)
Q Consensus       134 ~a~  136 (240)
                      ||+
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            985

>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=99.76  E-value=3.5e-18  Score=129.07  Aligned_cols=79  Identities=23%  Similarity=0.391  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||+|..|.|+        ++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        35 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           35 LLKKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTCCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            4456899999999 8999999999999999999999983        579999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +|+.+...
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99987543

>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=99.76  E-value=7.3e-18  Score=118.76  Aligned_cols=80  Identities=25%  Similarity=0.423  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccC---cEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVD---RVI  130 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g---~~l  130 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++||+.|||..|.|   +.|
T Consensus        11 ~~~~~~~l~v~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGML-NKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            3456899999999 8999999999999999999999985       5899999999999999999999999998   999


Q ss_pred             EEEEeecCCCC
Q 026341          131 SVEYALKDDSE  141 (240)
Q Consensus       131 ~v~~a~~~~~~  141 (240)
                      .|.++.....+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999887643

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=6e-18  Score=118.18  Aligned_cols=79  Identities=19%  Similarity=0.407  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++|++.|||..|.|+.|.|.
T Consensus        13 ~~~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGL-PFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4456789999999 8999999999999999999999985       4899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      ++.+...
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9987653

>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=99.75  E-value=6.8e-18  Score=117.27  Aligned_cols=78  Identities=24%  Similarity=0.404  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCccc--CcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLV--DRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~a~  136 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.+.  ++||||+|.+.++|++|++.||+..|.  |+.|.|+|++
T Consensus        13 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           13 KANPTTRLWVGGL-GPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECC-CSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            3456789999999 8899999999999999999999996  579999999999999999999999999  9999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      ++.
T Consensus        92 ~~~   94 (97)
T 1why_A           92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.6e-18  Score=117.70  Aligned_cols=78  Identities=18%  Similarity=0.352  Sum_probs=70.1

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCC-eEEEEE-eCCeEEEEecCHHHHHHHHHhcCC-CcccCcEEEEEEeecC
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGN-VLHVRI-RRNFAFVQFETQEEATKALESTDR-SKLVDRVISVEYALKD  138 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~-i~~~~~-~kg~afV~f~~~~~a~~A~~~l~g-~~~~g~~l~v~~a~~~  138 (240)
                      ..+.++|||+|| |..+++++|+++|.+||. |..+.+ .++||||+|.+.++|++|++.||| ..|+|+.|.|+++.+.
T Consensus         5 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~vv~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            5 SSGMNKLYIGNL-SPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCCEEEECC-CTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHHcCCceEEEEEcCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            346789999999 899999999999999998 665555 589999999999999999999999 9999999999999875


Q ss_pred             CC
Q 026341          139 DS  140 (240)
Q Consensus       139 ~~  140 (240)
                      ..
T Consensus        84 ~~   85 (93)
T 2cqh_A           84 KL   85 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.75  E-value=5.4e-18  Score=114.21  Aligned_cols=74  Identities=24%  Similarity=0.483  Sum_probs=69.0

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      +.+|||+|| |..+++++|+++|.+||.|..+.+.        +|||||+|.+.++|++|+..|||..|.|+.|.|+++.
T Consensus         1 t~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   79 (83)
T 3md1_A            1 TFNLFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA   79 (83)
T ss_dssp             CEEEEEECC-CTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CeEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecC
Confidence            368999999 8899999999999999999999884        6899999999999999999999999999999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      ++.
T Consensus        80 ~~~   82 (83)
T 3md1_A           80 KLE   82 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>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=99.75  E-value=1.2e-17  Score=116.53  Aligned_cols=79  Identities=29%  Similarity=0.439  Sum_probs=73.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.+.  ++||||+|.+.++|++|++.|||..|.|+.|.|.++.+.
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           11 TFTQRSRLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCCCTTEEEEESC-CTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            4456789999999 8899999999999999999999996  599999999999999999999999999999999999875


Q ss_pred             CC
Q 026341          139 DS  140 (240)
Q Consensus       139 ~~  140 (240)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpj_A           90 AS   91 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=8.5e-18  Score=115.99  Aligned_cols=75  Identities=28%  Similarity=0.506  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..++.++|||+|| |..+++++|+++|.+||.|..|.+.        ++||||+|.+.++|++|++.||+..|.|+.|.|
T Consensus        12 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           12 LAPSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             CCCCTTSEEEESC-CTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            4556889999999 8999999999999999999999984        579999999999999999999999999999999


Q ss_pred             EEee
Q 026341          133 EYAL  136 (240)
Q Consensus       133 ~~a~  136 (240)
                      +||+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>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=6.9e-18  Score=117.40  Aligned_cols=77  Identities=23%  Similarity=0.384  Sum_probs=70.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..|.|.           ++||||+|.+.++|++||..|||..|.|+.|.
T Consensus         3 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            45789999999 8999999999999999999999884           36999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q 026341          132 VEYALKDDS  140 (240)
Q Consensus       132 v~~a~~~~~  140 (240)
                      |.++.....
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999987653

>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=99.75  E-value=4.6e-18  Score=115.62  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=67.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+..+|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++.|||..|+|+.|.|+|
T Consensus         4 ~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            4 GSHFHVFVGDL-SPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             --CEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCceEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            45789999999 8899999999999999999999984        47999999999999999999999999999999999


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      +.++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9764

>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=6.6e-18  Score=117.12  Aligned_cols=75  Identities=20%  Similarity=0.465  Sum_probs=70.4

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      |.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.|||..|+|+.|.|.++
T Consensus         1 P~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   79 (96)
T 2x1f_A            1 PSRVVYLGSI-PYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEc
Confidence            4689999999 8999999999999999999999984        689999999999999999999999999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      .+..
T Consensus        80 ~~~~   83 (96)
T 2x1f_A           80 SNSD   83 (96)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8754

>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=99.75  E-value=1.4e-17  Score=117.13  Aligned_cols=77  Identities=27%  Similarity=0.446  Sum_probs=70.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+.++|||+|| |..+++++|+++|.+|| |..|.|+         +|||||+|.+.++|++|| .||+..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           11 PKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CSSSCEEEEEESC-CSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCEEEEeCC-CCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            3456799999999 89999999999999999 9999984         579999999999999999 9999999999999


Q ss_pred             EEEeecCCC
Q 026341          132 VEYALKDDS  140 (240)
Q Consensus       132 v~~a~~~~~  140 (240)
                      |+++.++..
T Consensus        88 V~~a~~~~~   96 (104)
T 1wi8_A           88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999987654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.75  E-value=5.8e-18  Score=116.38  Aligned_cols=78  Identities=27%  Similarity=0.377  Sum_probs=72.2

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|++|+..||+..|.|+.|.|+++
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNL-PFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSC-CTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            456889999999 8999999999999999999999985      589999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      ++...
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            87653

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-18  Score=119.69  Aligned_cols=75  Identities=24%  Similarity=0.468  Sum_probs=67.3

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEEe--------CCeEEEEecCHHHHHHHHHhcC-CCcccCcEEEEEE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIR--------RNFAFVQFETQEEATKALESTD-RSKLVDRVISVEY  134 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~-g~~~~g~~l~v~~  134 (240)
                      +++|||+|| |..+|+++|+++|++|| +|..|.|+        +|||||+|.+.++|++||+.|+ +..|+|++|.|+|
T Consensus         1 S~~i~v~nL-p~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRML-PQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY   79 (91)
T ss_dssp             CCEEEEETC-CSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEEC
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEE
Confidence            368999999 99999999999999999 89988873        6899999999999999999874 5679999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      |.++..
T Consensus        80 a~~~~~   85 (91)
T 2lxi_A           80 SDPKPK   85 (91)
T ss_dssp             CCSCCC
T ss_pred             cCCCCC
Confidence            987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.2e-18  Score=119.01  Aligned_cols=78  Identities=26%  Similarity=0.483  Sum_probs=72.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|.|+.|.|
T Consensus        19 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           19 RSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CBTTBEEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            4456789999999 8899999999999999999999984        589999999999999999999999999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      +++.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998754

>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=6.1e-18  Score=121.21  Aligned_cols=79  Identities=20%  Similarity=0.441  Sum_probs=72.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        ++||||+|.+.++|++||+.||+..|.|+.|.|
T Consensus        21 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           21 EGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCSTTCCEEEESC-CSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4456789999999 8999999999999999999999884        479999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +|++++..
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99987654

>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=99.75  E-value=1.6e-17  Score=118.16  Aligned_cols=79  Identities=30%  Similarity=0.481  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcC------CCccc
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTD------RSKLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~------g~~~~  126 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||..||      +..|+
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           11 DVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             cCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            4556889999999 8999999999999999999999984        6899999999999999999999      99999


Q ss_pred             CcEEEEEEeecCCC
Q 026341          127 DRVISVEYALKDDS  140 (240)
Q Consensus       127 g~~l~v~~a~~~~~  140 (240)
                      |+.|.|.++.+...
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.2e-17  Score=117.64  Aligned_cols=78  Identities=19%  Similarity=0.387  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        ++||||+|.+.++|++||..|++ .|.|+.|.|
T Consensus        13 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           13 KDTTFTKIFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CSCSSSEEEEECC-CSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            4556899999999 8999999999999999999999984        57999999999999999999998 899999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.....
T Consensus        91 ~~a~~~~~   98 (116)
T 2cqd_A           91 NLAYLGAK   98 (116)
T ss_dssp             EESTTTCC
T ss_pred             EEcccCCC
Confidence            99976543

>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=99.74  E-value=9.3e-18  Score=113.61  Aligned_cols=75  Identities=24%  Similarity=0.454  Sum_probs=69.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc-CCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST-DRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l-~g~~~~g~~l~v~~a~  136 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.+.  +|||||+|.+.++|++|+..| ++..|.|+.|.|+|++
T Consensus         8 ~~~~~~~l~V~~l-~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGL-GDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECC-TTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCC-CCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            4456789999999 8899999999999999999999996  599999999999999999999 9999999999999974

>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=119.13  Aligned_cols=79  Identities=22%  Similarity=0.467  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|.|+.|.|
T Consensus        22 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           22 RSVEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CBTTBEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            4456789999999 8899999999999999999999984        689999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .|+.+...
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99987653

>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=1.1e-17  Score=118.76  Aligned_cols=79  Identities=18%  Similarity=0.443  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.  ++||||+|.+.++|++|+..|||..|.|+.|.|.|+++.
T Consensus        21 ~~~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   99 (109)
T 1x4g_A           21 SSPKNCTVYCGGI-ASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             SCSSCCEEEEECC-SSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            3456789999999 8899999999999999999999996  699999999999999999999999999999999999876


Q ss_pred             CC
Q 026341          139 DS  140 (240)
Q Consensus       139 ~~  140 (240)
                      ..
T Consensus       100 ~~  101 (109)
T 1x4g_A          100 PD  101 (109)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=7.2e-18  Score=118.59  Aligned_cols=80  Identities=19%  Similarity=0.324  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhcc-CCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCc-ccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEP-YGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSK-LVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~-~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~-~~g~~l~  131 (240)
                      ...+.++|||+|| |..+++++|+++|.+ ||.|..|.|.       +|||||+|.+.++|++||..||+.. |.|+.|.
T Consensus         5 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDL-TPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECC-CTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999 889999999999999 9999999984       6899999999999999999999999 9999999


Q ss_pred             EEEeecCCCC
Q 026341          132 VEYALKDDSE  141 (240)
Q Consensus       132 v~~a~~~~~~  141 (240)
                      |+++.+....
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999776543

>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=2.4e-17  Score=116.44  Aligned_cols=79  Identities=29%  Similarity=0.584  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhc-CCCcccCcEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALEST-DRSKLVDRVI  130 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l-~g~~~~g~~l  130 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.         +|||||+|.+.++|++||..| |+..|.|+.|
T Consensus        11 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           11 KKQTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CSSCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             cCCCCCEEEEeCC-CCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            4566899999999 8999999999999999999999983         579999999999999999999 9999999999


Q ss_pred             EEEEeecCCC
Q 026341          131 SVEYALKDDS  140 (240)
Q Consensus       131 ~v~~a~~~~~  140 (240)
                      .|+|+.+...
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987654

>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=99.74  E-value=9e-18  Score=118.72  Aligned_cols=75  Identities=21%  Similarity=0.337  Sum_probs=70.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++||+.|||..|.|+.|.|+
T Consensus        25 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            4567899999999 8999999999999999999999985       6799999999999999999999999999999999


Q ss_pred             Eee
Q 026341          134 YAL  136 (240)
Q Consensus       134 ~a~  136 (240)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>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=4.5e-17  Score=116.40  Aligned_cols=78  Identities=27%  Similarity=0.326  Sum_probs=71.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       ++||||+|.+.++|++||+.||+..|+|+.|.|+
T Consensus        11 ~~~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANL-DYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            4556899999999 8999999999999999999999984       5799999999999999999999999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            987644

>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=99.74  E-value=1.5e-17  Score=117.34  Aligned_cols=79  Identities=25%  Similarity=0.427  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcc---cCcE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKL---VDRV  129 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~---~g~~  129 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+.||+..+   .|+.
T Consensus         9 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            9 KDHDAIKLFIGQI-PRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCTTCEEEEEESC-CTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            4456889999999 8999999999999999999999984        58999999999999999999999988   8999


Q ss_pred             EEEEEeecCCC
Q 026341          130 ISVEYALKDDS  140 (240)
Q Consensus       130 l~v~~a~~~~~  140 (240)
                      |.|.++.....
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999987654

>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=8.2e-18  Score=119.44  Aligned_cols=77  Identities=34%  Similarity=0.564  Sum_probs=72.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.      +|||||+|.+.++|++|+..|||..|+|+.|.|++
T Consensus        25 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           25 NKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             CTTCCCEEEEESC-CTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECC-CCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556899999999 8899999999999999999999995      78999999999999999999999999999999999


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9764

>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=99.74  E-value=1.4e-17  Score=115.63  Aligned_cols=78  Identities=28%  Similarity=0.543  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHH----HhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIK----RHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~----~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+.++|||+|| |..+++++|+    ++|.+||.|..|.+.     +|||||+|.+.++|+.|+..|||..|.|+.|.
T Consensus         4 ~~~~~~~l~V~nL-p~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            4 ETRPNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             --CCCSEEEEESC-CTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            4467899999999 8999999999    999999999999985     79999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |+|+.+..
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99998754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=8.9e-18  Score=116.08  Aligned_cols=76  Identities=36%  Similarity=0.504  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.+.        ++||||+|.+.++|++|+..|||..|.|+.|.|
T Consensus        11 ~~~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           11 NPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             SCCGGGCEEEESC-CSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4566899999999 8899999999999999999999984        479999999999999999999999999999999


Q ss_pred             EEeec
Q 026341          133 EYALK  137 (240)
Q Consensus       133 ~~a~~  137 (240)
                      +|++.
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=121.37  Aligned_cols=78  Identities=14%  Similarity=0.305  Sum_probs=70.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHH----HhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIK----RHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~----~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+.++|||+|| ++.+++++|+    ++|++||.|..|.+.     +|||||+|.+.++|+.|+..|||..|.|++|.
T Consensus        25 ~~~p~~~LfV~nL-~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           25 HTEPSQVVLITNI-NPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CCSCCSEEEEESC-CTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            4456889999999 8899998866    699999999999884     68999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |.|++...
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99998653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=115.90  Aligned_cols=77  Identities=23%  Similarity=0.375  Sum_probs=69.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .....++|||+|| |..+++++|+++|.+||.|. +.+.    +|||||+|.+.++|++|+..|||..|.|+.|.|+++.
T Consensus        15 ~~~~~~~l~V~nL-~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   92 (97)
T 2e5j_A           15 GAPLAADVYVGNL-PRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR   92 (97)
T ss_dssp             SSCCCCEEEEECC-CTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECC
T ss_pred             CCCCCCEEEEeCC-CCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            3445789999999 89999999999999999986 4543    7999999999999999999999999999999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      ++.
T Consensus        93 ~~~   95 (97)
T 2e5j_A           93 QQR   95 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=6.9e-18  Score=116.69  Aligned_cols=74  Identities=26%  Similarity=0.424  Sum_probs=66.1

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCC--eEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCc----ccCc
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGN--VLHVRIR--------RNFAFVQFETQEEATKALESTDRSK----LVDR  128 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~--i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~----~~g~  128 (240)
                      ..-.+|||+|| |+.+|+++|+++|++||.  |..|.++        +|||||+|.+.++|++||+.|||..    |+|+
T Consensus         7 ~~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            7 HHMDTIILRNI-APHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             CCCCEEEEESC-CTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CccCEEEEeCC-CCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            34679999999 889999999999999995  5677763        6899999999999999999999974    8999


Q ss_pred             EEEEEEeec
Q 026341          129 VISVEYALK  137 (240)
Q Consensus       129 ~l~v~~a~~  137 (240)
                      +|.|+||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999975

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=115.78  Aligned_cols=76  Identities=18%  Similarity=0.280  Sum_probs=69.8

Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--------EEEe--------CCeEEEEecCHHHHHHHHHhcCCC
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--------VRIR--------RNFAFVQFETQEEATKALESTDRS  123 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--------~~~~--------kg~afV~f~~~~~a~~A~~~l~g~  123 (240)
                      ....+.++|||+|| |..+++++|+++|++||.|..        +.+.        +|||||+|.+.++|++|++.|||.
T Consensus         8 ~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            8 HSHSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CSCCCCSEEEEECC-CSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            35567899999999 899999999999999999998        7773        579999999999999999999999


Q ss_pred             cccCcEEEEEEee
Q 026341          124 KLVDRVISVEYAL  136 (240)
Q Consensus       124 ~~~g~~l~v~~a~  136 (240)
                      .|.|+.|.|++|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999974

>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=115.68  Aligned_cols=78  Identities=23%  Similarity=0.347  Sum_probs=69.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE----eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI----RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~----~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|.-+..    .++||||+|.+.++|++||..||+..|.|+.|.|+|+.
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           11 WSGESKTLVLSNL-SYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CSCCCSEEEEESC-CTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            4456899999999 889999999999999998843322    47899999999999999999999999999999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      +..
T Consensus        90 ~~~   92 (101)
T 2fc9_A           90 PRG   92 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=3.5e-17  Score=114.90  Aligned_cols=77  Identities=29%  Similarity=0.463  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+|| |..|.|+        +|||||+|.+.++|++|| .||+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   87 (103)
T 2dng_A           11 PTEPPYTAYVGNL-PFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRV   87 (103)
T ss_dssp             CSSSCEEEEEESC-CTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEE
T ss_pred             CCCCCeEEEEeCC-CCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEE
Confidence            4456899999999 99999999999999997 9999884        579999999999999999 89999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2dng_A           88 DIAEGRKQ   95 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEecCCCC
Confidence            99987543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=118.20  Aligned_cols=79  Identities=20%  Similarity=0.246  Sum_probs=71.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeE--------EEEEe--------CCeEEEEecCHHHHHHHHHhcCCCc
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL--------HVRIR--------RNFAFVQFETQEEATKALESTDRSK  124 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~--------~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~  124 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|.        .|.|.        +|||||+|.+.++|++||+.|||..
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           11 EDSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCEEEEECC-CTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             cCCCCCEEEEcCC-CCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            4456899999999 89999999999999999998        57773        6899999999999999999999999


Q ss_pred             ccCcEEEEEEeecCCC
Q 026341          125 LVDRVISVEYALKDDS  140 (240)
Q Consensus       125 ~~g~~l~v~~a~~~~~  140 (240)
                      |.|+.|.|.++.....
T Consensus        90 ~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPP  105 (113)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             cCCCEEEEEECCCCCC
Confidence            9999999999987654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=8.4e-18  Score=117.66  Aligned_cols=73  Identities=26%  Similarity=0.404  Sum_probs=69.0

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|||+|| |..+++++|+++|++||+|..|.+.   ++||||+|.+.++|++|++.|||..|.|+.|.|+++.+..
T Consensus         1 ~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNL-GTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECC-CSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            47999999 8899999999999999999999994   7899999999999999999999999999999999998765

>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=99.73  E-value=3e-17  Score=117.52  Aligned_cols=80  Identities=26%  Similarity=0.471  Sum_probs=71.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCe----EEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV----LHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i----~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|    ..+.+.    +|||||+|.+.++|++||..|||..|.|+.|.|
T Consensus        21 ~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   99 (115)
T 2cpx_A           21 PGEPNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   99 (115)
T ss_dssp             CCSCCSEEEEECC-CTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4557899999999 8999999999999999988    555553    689999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 026341          133 EYALKDDSE  141 (240)
Q Consensus       133 ~~a~~~~~~  141 (240)
                      +|+.+....
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpx_A          100 EFGKNKKQR  108 (115)
T ss_dssp             EECCCCSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>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=99.73  E-value=2.2e-17  Score=117.06  Aligned_cols=78  Identities=23%  Similarity=0.414  Sum_probs=71.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|+.|++.|||..|.|+.|.|
T Consensus        22 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           22 GSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             SCSSCEEEEEECC-CSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4556789999999 8899999999999999999999984        579999999999999999999999999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      ++++++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998653

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=118.50  Aligned_cols=75  Identities=24%  Similarity=0.288  Sum_probs=70.2

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ..++|||+|| |..+++++|+++|.+||.|..|.|+  ++||||+|.+.++|+.||..|||..|.|+.|.|+|+....
T Consensus         9 ~~~~l~V~nL-p~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            3679999999 8999999999999999999999984  7899999999999999999999999999999999998643

>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=99.73  E-value=1.1e-17  Score=122.45  Aligned_cols=79  Identities=35%  Similarity=0.569  Sum_probs=72.9

Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ....+.++|||+|| |..+++++|+++|.+||+|..|.|.        +|||||+|.+.++|++||+.|||..|+|+.|.
T Consensus        41 ~~~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           41 ANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SCCCCSSCBCEETC-TTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            35567899999999 8999999999999999999999984        58999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |+|+.++.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99998754

>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=99.73  E-value=2e-18  Score=127.60  Aligned_cols=118  Identities=19%  Similarity=0.258  Sum_probs=67.6

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhh
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF   87 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f   87 (240)
                      +|+||.+|.-++.+-.|+..+..+.   +|...--......         .........+|||+|| |+.+++++|+++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~---gg~~~g~~~g~~~---------~~~~~~~~~~lfV~nL-p~~~te~dL~~~F   67 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASMT---GGQQMGRGSGDSE---------FTVQSTTGHCVHMRGL-PYKATENDIYNFF   67 (139)
T ss_dssp             --------------------------------------------------------CCCCEECCSC-CTTCCHHHHHHHH
T ss_pred             CCcccccccCccccchhcccchhcc---CCCCCCCCCCCcc---------cCCCCCCCCEEEEeCC-CCCCCHHHHHHHH
Confidence            4789999999988877777655552   2333211111100         1123345789999999 9999999999999


Q ss_pred             ccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           88 EPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        88 ~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ++|| |..|.|+       +|||||+|++.++|++|| .+|+..|.|+.|.|.++.....
T Consensus        68 ~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           68 SPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             HhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            9999 6688884       689999999999999999 7899999999999999887654

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-17  Score=118.04  Aligned_cols=78  Identities=17%  Similarity=0.323  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHH---HhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIK---RHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~---~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      ...+.++|||+|| |+.+++++|+   ++|.+||+|..|.|.           +|||||+|.+.++|++||+.|||..|+
T Consensus        11 r~~~~~~l~V~nL-p~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           11 RVVQKNLVFVVGL-SQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCSSCEEEEEE-CTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             cccCCCEEEEECC-CCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            3445789999999 8999999999   999999999999985           269999999999999999999999999


Q ss_pred             CcEEEEEEeecCC
Q 026341          127 DRVISVEYALKDD  139 (240)
Q Consensus       127 g~~l~v~~a~~~~  139 (240)
                      |+.|.|+||.++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998765

>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=99.72  E-value=1.3e-17  Score=115.27  Aligned_cols=76  Identities=28%  Similarity=0.377  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||+|..|.|.       ++||||+|.+.++|++|++.||+..|.|+.|.|+
T Consensus        12 ~~~~~~~l~v~nl-p~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNL-EARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            4456789999999 8899999999999999999999984       5799999999999999999999999999999999


Q ss_pred             Eeec
Q 026341          134 YALK  137 (240)
Q Consensus       134 ~a~~  137 (240)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9863

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=6.9e-17  Score=116.72  Aligned_cols=73  Identities=22%  Similarity=0.212  Sum_probs=66.3

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCe-EEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeecCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNF-AFVQFETQEEATKALESTDRSKLVD--RVISVEYALKDD  139 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~-afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~  139 (240)
                      ..|||+|| ++.+++++|+++|++||.|..|.|.  .|| |||+|.+.++|+.|++.|||..|.|  +.|.|++|++..
T Consensus        26 l~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           26 LLLSIQNP-LYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEEEESC-CSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEEEcCc-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            34679999 9999999999999999999999884  386 9999999999999999999999988  699999998764

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.2e-17  Score=117.20  Aligned_cols=79  Identities=15%  Similarity=0.214  Sum_probs=71.0

Q ss_pred             CCCCCCEEEE--eccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcc-----cCcEEE
Q 026341           61 NQRPTKTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKL-----VDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v--~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~-----~g~~l~  131 (240)
                      ...|+.+|||  +|| ++.+++++|+++|++||.|..|.|+  +|||||+|.+.++|++|++.|||.+|     .|.+|.
T Consensus        21 ~~~pt~~L~V~Ng~L-~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGL-GNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTG-GGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCC-CCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            3456889999  779 8999999999999999999999986  68999999999999999999999988     689999


Q ss_pred             EEEeecCCC
Q 026341          132 VEYALKDDS  140 (240)
Q Consensus       132 v~~a~~~~~  140 (240)
                      |.|+.....
T Consensus       100 v~~a~~~p~  108 (114)
T 2cq2_A          100 LNFVEKVQW  108 (114)
T ss_dssp             EEEESCCCC
T ss_pred             EEecccCcc
Confidence            999986543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.72  E-value=2.6e-17  Score=118.39  Aligned_cols=75  Identities=21%  Similarity=0.466  Sum_probs=69.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++|++.|||..|+|+.|.|
T Consensus        36 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           36 EGPEGCNLFIYHL-PQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCSEEEEEECS-CTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4566799999999 8999999999999999999999984        689999999999999999999999999999999


Q ss_pred             EEee
Q 026341          133 EYAL  136 (240)
Q Consensus       133 ~~a~  136 (240)
                      +|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9974

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=9.7e-18  Score=117.21  Aligned_cols=74  Identities=16%  Similarity=0.255  Sum_probs=69.1

Q ss_pred             CCCEEEEeccCCC------CCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC-c
Q 026341           64 PTKTLFVINFDPI------RTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD-R  128 (240)
Q Consensus        64 ~~~~l~v~nl~~~------~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g-~  128 (240)
                      ..++|||+|| |+      .+++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+.|||..|.| +
T Consensus         5 ~~~~vfV~nL-p~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            5 SDQYIVVNGA-PVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             GGGEEEEESC-CCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             cCcEEEEeCC-CcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3689999999 99      99999999999999999999983        6999999999999999999999999999 9


Q ss_pred             EEEEEEeecC
Q 026341          129 VISVEYALKD  138 (240)
Q Consensus       129 ~l~v~~a~~~  138 (240)
                      .|.|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999999753

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.72  E-value=9.2e-18  Score=117.44  Aligned_cols=74  Identities=18%  Similarity=0.352  Sum_probs=69.6

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...++|||+|| |..+++++|+++|.+||.|..|.+.  +|||||+|.+.++|++|+..|||..|+|+.|.|.|+++
T Consensus        25 ~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           25 PRVTTAYIGNI-PHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SSCCEEEEESC-CTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCEEEEcCC-CcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            44689999999 8899999999999999999999985  79999999999999999999999999999999999875

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5e-17  Score=113.82  Aligned_cols=79  Identities=25%  Similarity=0.430  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-----eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-----RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-----~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |..+++++|+++|..|+.|..+..     .++||||+|.+.++|++||+.||+..|.|+.|.|+|+
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           11 RSQPSKTLFVKGL-SEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             SSCCCSSEEEECC-CTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCC-CCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            4566899999999 899999999999999875554433     2589999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      +++..
T Consensus        90 ~~~~~   94 (102)
T 2fc8_A           90 KPKGE   94 (102)
T ss_dssp             CCCCS
T ss_pred             cCCCC
Confidence            87654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.1e-16  Score=111.04  Aligned_cols=77  Identities=26%  Similarity=0.440  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ...+.++|||+||   .+++++|+++|.+||.|..|.|.  ++||||+|.+.++|++||..|||..|.|+.|.|.|+.+.
T Consensus        11 ~~~~~~~l~V~n~---~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           11 APRKGNTLYVYGE---DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCCCSEEEEECS---SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCCCEEEEcCC---CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            3456789999997   69999999999999999999985  799999999999999999999999999999999999876


Q ss_pred             CC
Q 026341          139 DS  140 (240)
Q Consensus       139 ~~  140 (240)
                      ..
T Consensus        88 ~~   89 (97)
T 1x5p_A           88 PM   89 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=9.6e-17  Score=116.49  Aligned_cols=79  Identities=20%  Similarity=0.302  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++|+..|||..|.|+.|.|+
T Consensus        31 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESC-CSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            4566789999999 8999999999999999999999984       6899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      +|.....
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9987553

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.3e-17  Score=114.91  Aligned_cols=78  Identities=22%  Similarity=0.343  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeE-EEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcE--
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL-HVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRV--  129 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~-~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~--  129 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|. .|.|.        +|||||+|.+.++|++|++.|||..|.|+.  
T Consensus         5 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            5 SSGMAASLWMGDL-EPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCSSSSEEEECSC-CTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCccEEEEeCC-CCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            3456899999999 88999999999999999999 98884        479999999999999999999999999999  


Q ss_pred             --EEEEEeecCC
Q 026341          130 --ISVEYALKDD  139 (240)
Q Consensus       130 --l~v~~a~~~~  139 (240)
                        |.|+|+.+..
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              9999987653

>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=3.2e-17  Score=115.57  Aligned_cols=76  Identities=17%  Similarity=0.275  Sum_probs=69.7

Q ss_pred             CCCCCEEEEeccCCCCC------CHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCc-
Q 026341           62 QRPTKTLFVINFDPIRT------RERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDR-  128 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~------~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~-  128 (240)
                      ....++|||+|| |+.+      ++++|+++|++||.|..|.|+      +|||||+|.+.++|++||..|||..|.|+ 
T Consensus        12 ~~~~~~l~V~nL-p~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           12 DGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CSCCSEEEEESC-CCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCEEEEeCC-CcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            345789999999 8888      789999999999999999985      68999999999999999999999999998 


Q ss_pred             EEEEEEeecC
Q 026341          129 VISVEYALKD  138 (240)
Q Consensus       129 ~l~v~~a~~~  138 (240)
                      .|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999998754

>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=2.2e-17  Score=114.81  Aligned_cols=77  Identities=19%  Similarity=0.213  Sum_probs=68.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .....++|||+|| |..+++++|+++|.+||.|..+.+        .+|||||+|.+.++|++||+.|||..|.|+.|.|
T Consensus        11 ~~~~~~~l~v~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   89 (98)
T 2cqp_A           11 GKPGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (98)
T ss_dssp             CCCSSEEEEEESC-CTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3455789999999 999999999999999999875544        2689999999999999999999999999999999


Q ss_pred             EEeecC
Q 026341          133 EYALKD  138 (240)
Q Consensus       133 ~~a~~~  138 (240)
                      +++...
T Consensus        90 ~~a~~~   95 (98)
T 2cqp_A           90 VLGSGP   95 (98)
T ss_dssp             EESSCS
T ss_pred             EEcCCC
Confidence            998754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4.5e-17  Score=110.34  Aligned_cols=76  Identities=22%  Similarity=0.389  Sum_probs=67.5

Q ss_pred             CCCCCE-EEEeccCCCCCCHHH----HHHhhccCC-CeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           62 QRPTKT-LFVINFDPIRTRERD----IKRHFEPYG-NVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        62 ~~~~~~-l~v~nl~~~~~~~~~----l~~~f~~~G-~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .+|+.+ |||+|| |+.+++++    |.++|.+|| +|..|  ..|+|||+|.+.++|++|++.|||..|.|++|.|+||
T Consensus         5 ~~p~~T~lYV~NL-~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A   81 (96)
T 2diu_A            5 SSGCHTLLYVYNL-PANKDGKSVSNRLRRLSDNCGGKVLSI--TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFT   81 (96)
T ss_dssp             CCCSSEEEEEESC-CTTSCHHHHHHHHHHHHHTTTCCEEEC--CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESS
T ss_pred             CCCcceEEEEeCC-CCcCCHHHHHHHHHHHHHHcCCeeEEE--ecCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEec
Confidence            345666 999999 99999888    558999995 99888  4599999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      +....
T Consensus        82 ~~~sd   86 (96)
T 2diu_A           82 PKNRE   86 (96)
T ss_dssp             CCSCC
T ss_pred             CCCcc
Confidence            87654

>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=99.70  E-value=5.9e-18  Score=115.97  Aligned_cols=74  Identities=18%  Similarity=0.307  Sum_probs=63.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCC--CeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYG--NVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G--~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .+|||+|| |+.+++++|+++|++||  .|..+.+.        +|||||+|.+.++|++||+.|||..|+|+.|.|.++
T Consensus         2 ~~l~V~nL-~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESC-CTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC
T ss_pred             eEEEEeCC-CCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEEC
Confidence            47999999 89999999999999999  99998873        579999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      .+...
T Consensus        81 ~~~~~   85 (90)
T 3p5t_L           81 NKLEH   85 (90)
T ss_dssp             -----
T ss_pred             CCCcc
Confidence            87643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.9e-17  Score=114.69  Aligned_cols=73  Identities=26%  Similarity=0.448  Sum_probs=68.2

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .+..+|||+|| |..+++++|+++|++||+|..|.|+       +|||||+|.+.++|++||. +++..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~L-p~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECC-CTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            44689999999 8999999999999999999999995       6899999999999999999 8999999999999998


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.70  E-value=7.2e-17  Score=115.54  Aligned_cols=77  Identities=21%  Similarity=0.411  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.|.     +|||||+|.+.++|++|+..|||..|+|+.|.|.|+.
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            5 PEVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TTCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            346789999999 8999999999999999999999984     5899999999999999999999999999999999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      +..
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            643

>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=1.1e-17  Score=117.60  Aligned_cols=76  Identities=25%  Similarity=0.506  Sum_probs=70.4

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++.|||..|.|+.|.|.+
T Consensus         6 ~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            6 RSLRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHSCEEEESC-CTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCccEEEEeCC-CCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34689999999 8999999999999999999999884        68999999999999999999999999999999999


Q ss_pred             eecCC
Q 026341          135 ALKDD  139 (240)
Q Consensus       135 a~~~~  139 (240)
                      +.+..
T Consensus        85 a~~~~   89 (104)
T 1p1t_A           85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCcc
Confidence            98654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=7.1e-17  Score=117.22  Aligned_cols=75  Identities=19%  Similarity=0.309  Sum_probs=68.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCe-EEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNF-AFVQFETQEEATKALESTDRSKLVD--RVISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~-afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~  137 (240)
                      +...|||+|| ++.+++++|.++|++||+|..|.+.   +++ |||+|.+.++|+.|++.|||..|.|  +.|.|+|++.
T Consensus        27 ~VL~I~V~NL-~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           27 PVLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             SEEEEEEESC-CSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             ceEEEEECCC-CCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            4566789999 8999999999999999999999884   567 9999999999999999999999998  9999999987


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus       106 ~~  107 (130)
T 3zzy_A          106 TS  107 (130)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>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=7e-17  Score=114.48  Aligned_cols=78  Identities=26%  Similarity=0.360  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCC-eEEEEEe---------CCeEEEEecCHHHHHHHHHhcC--CCcccCcE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGN-VLHVRIR---------RNFAFVQFETQEEATKALESTD--RSKLVDRV  129 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~-i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~--g~~~~g~~  129 (240)
                      ..+.++|||+|| |..+++++|+++|.+||. |..|.+.         +|||||+|.+.++|+.|+..||  +..|.|+.
T Consensus         5 s~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            5 SSGNCRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCCSEEEEEECC-CTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             ccCCCEEEEeCC-CCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            345789999999 899999999999999998 9999885         5899999999999999999996  58999999


Q ss_pred             EEEEEeecCCC
Q 026341          130 ISVEYALKDDS  140 (240)
Q Consensus       130 l~v~~a~~~~~  140 (240)
                      |.|+|+.+...
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999987654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.1e-17  Score=115.57  Aligned_cols=78  Identities=24%  Similarity=0.339  Sum_probs=71.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||+|..|.|.        +|||||+|.+.++|++||.. |+..|+|+.|.|
T Consensus        12 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           12 GADEIGKLFVGGL-DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CSSSSSEECCBSC-CTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            4566899999999 8999999999999999999999984        47999999999999999998 999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 2dh8_A           90 KPCTPRGM   97 (105)
T ss_dssp             CCSCCSSC
T ss_pred             EEccCCCC
Confidence            99987654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.2e-16  Score=109.47  Aligned_cols=75  Identities=23%  Similarity=0.378  Sum_probs=69.1

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .....+|||+|| |+.+++++|+++|.+| .|..|.|+       +|||||+|.+.++|++||. |||..|.|+.|.|.+
T Consensus         7 ~~~~~~l~v~nL-p~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGA-PFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECC-CSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECC-CCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            445789999999 9999999999999999 89999884       5799999999999999999 999999999999999


Q ss_pred             eecCC
Q 026341          135 ALKDD  139 (240)
Q Consensus       135 a~~~~  139 (240)
                      +....
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>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=99.70  E-value=6.7e-17  Score=110.26  Aligned_cols=72  Identities=25%  Similarity=0.439  Sum_probs=67.5

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.++|++|+ .|||..|.|+.|.|++++
T Consensus         6 ~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            6 ARSIYVGNV-DYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESC-CTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            578999999 8999999999999999999999884        679999999999999999 899999999999999987


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      +.
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=6.1e-17  Score=112.14  Aligned_cols=78  Identities=23%  Similarity=0.408  Sum_probs=70.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..+..   .+|||||+|.+.++|++|+..|||..|.|+.|.|+++.+
T Consensus        12 ~~~~~~~l~V~nL-~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           12 KVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESC-CSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            3456899999999 899999999999999998887722   468999999999999999999999999999999999977


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus        91 ~~   92 (96)
T 1fjc_A           91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.69  E-value=7.7e-17  Score=121.34  Aligned_cols=75  Identities=17%  Similarity=0.255  Sum_probs=68.7

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEeec
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYALK  137 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~  137 (240)
                      ....|||+|| ++.+++++|+++|++||+|..|.|.    ++||||+|.+.++|++|++.|||..|.|  +.|.|+|++.
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~  123 (164)
T 1sjr_A           45 PVLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  123 (164)
T ss_dssp             CEEEEEECSC-CSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSS
T ss_pred             ceEEEEEeCc-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecC
Confidence            3567899999 8999999999999999999999984    4699999999999999999999999966  9999999987


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus       124 ~~  125 (164)
T 1sjr_A          124 TS  125 (164)
T ss_dssp             SS
T ss_pred             Cc
Confidence            64

>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=99.69  E-value=1.9e-17  Score=114.47  Aligned_cols=74  Identities=20%  Similarity=0.215  Sum_probs=65.5

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ++.++|||+|| |+.+++++|+++|.+||.|..+.+        .++||||+|.+.++|++||+.||+..|.|+.|.|++
T Consensus        13 ~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           13 PGPTVIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             --CEEEEEECC-CTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            45689999999 999999999999999999876555        258999999999999999999999999999999998


Q ss_pred             eec
Q 026341          135 ALK  137 (240)
Q Consensus       135 a~~  137 (240)
                      +..
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            753

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.1e-16  Score=114.81  Aligned_cols=76  Identities=21%  Similarity=0.438  Sum_probs=69.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++||.. ++..|+|+.|.|.+
T Consensus        25 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           25 EQFRKLFIGGL-SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHTEEEEECC-TTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            34689999999 8999999999999999999999984        57999999999999999997 99999999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      +.++..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            987654

>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=99.69  E-value=1.3e-16  Score=108.37  Aligned_cols=73  Identities=29%  Similarity=0.530  Sum_probs=66.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++ +++..|+|+.|.|
T Consensus         7 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v   84 (87)
T 3s7r_A            7 NEEDAGKMFVGGL-SWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDP   84 (87)
T ss_dssp             CCSCTTEEEEECC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEE
Confidence            3456889999999 8999999999999999999999984        5799999999999999996 5888999999999


Q ss_pred             EEe
Q 026341          133 EYA  135 (240)
Q Consensus       133 ~~a  135 (240)
                      ++|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            886

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=7.5e-17  Score=121.68  Aligned_cols=74  Identities=18%  Similarity=0.286  Sum_probs=67.9

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC--CeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG--NVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G--~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+|||+|| |+.+++++|+++|.+||  .|..|.|.        +|||||+|.+.++|++||..|||..|+|+.|.|.
T Consensus        54 ~~~~lfVgnL-p~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSF-SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECC-CTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            4579999999 99999999999999999  99999984        5799999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ++.+.
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99753

>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=99.68  E-value=4.9e-17  Score=116.25  Aligned_cols=74  Identities=26%  Similarity=0.449  Sum_probs=68.9

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++|| .|||..|.|+.|.|+++
T Consensus        24 ~~~~l~V~nl-p~~~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 DARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHTEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            4579999999 8999999999999999999999984        589999999999999999 99999999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      ....
T Consensus       102 ~~~~  105 (114)
T 2cq4_A          102 QAEK  105 (114)
T ss_dssp             HHHH
T ss_pred             CCCc
Confidence            7643

>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=99.68  E-value=1.8e-16  Score=111.11  Aligned_cols=76  Identities=24%  Similarity=0.385  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+..+|||+|| |+.+++++|+++|.+||.| .|.|+       +|||||+|.+.++|++||+ +|+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGL-PYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESC-CTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            4456789999999 9999999999999999954 77773       6799999999999999995 79999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987654

>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=1.8e-17  Score=112.17  Aligned_cols=72  Identities=18%  Similarity=0.405  Sum_probs=66.3

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.|||..|.|+.|+|.+
T Consensus         3 ~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESC-CTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            46789999999 8999999999999999999999984        68999999999999999999999999999887765


Q ss_pred             e
Q 026341          135 A  135 (240)
Q Consensus       135 a  135 (240)
                      +
T Consensus        82 ~   82 (85)
T 1x4e_A           82 P   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=3.3e-16  Score=109.87  Aligned_cols=77  Identities=29%  Similarity=0.528  Sum_probs=69.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|++||.  ++..|+|+.|.|
T Consensus        11 ~~~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v   87 (103)
T 2cqg_A           11 AVQKTSDLIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDC   87 (103)
T ss_dssp             CCCCCCCEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEE
T ss_pred             ccCCCCEEEEEcC-CCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEE
Confidence            4456789999999 8999999999999999999999884        4699999999999999998  467899999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqg_A           88 KLPNSKQS   95 (103)
T ss_dssp             ECCCTTCC
T ss_pred             EecCCCCc
Confidence            99987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.68  E-value=1.5e-16  Score=115.45  Aligned_cols=74  Identities=19%  Similarity=0.407  Sum_probs=68.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|++|| .|||..|+|+.|.|+++
T Consensus        35 ~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           35 DKRSVYVGNV-DYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHTEEEEEEE-CTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            3689999999 8999999999999999999999884        579999999999999999 79999999999999998


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      +...
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1.9e-16  Score=112.40  Aligned_cols=78  Identities=22%  Similarity=0.377  Sum_probs=67.5

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||..+ +..|+|+.|.|
T Consensus        21 ~~~~~~~lfV~nL-p~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           21 MGSSGCKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             -----CCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            3456789999999 8999999999999999999999984        589999999999999999976 59999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .++.+...
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>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=4e-16  Score=111.47  Aligned_cols=77  Identities=17%  Similarity=0.445  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcc--------
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKL--------  125 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~--------  125 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++||..|||..|        
T Consensus        21 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            3456789999999 8899999999999999999999984       57999999999999999999999999        


Q ss_pred             cCcEEEEEEeecC
Q 026341          126 VDRVISVEYALKD  138 (240)
Q Consensus       126 ~g~~l~v~~a~~~  138 (240)
                      .+++|.|.|+.+.
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999854

>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=99.68  E-value=5.8e-17  Score=119.30  Aligned_cols=115  Identities=12%  Similarity=0.124  Sum_probs=69.2

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhh
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF   87 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f   87 (240)
                      +|++|.+|..++.+-.....+..+.   +|...  ...         ...........++|||+|| |+.+|+++|+++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~---gg~~~--g~g---------~~~~~~~~~~~~~lfVgnL-p~~~te~dL~~~F   65 (136)
T 2hgl_A            1 MGSSHHHHHHSSGLVPRGSHMASMT---GGQQM--GRG---------SMMLGPEGGEGFVVKLRGL-PWSCSVEDVQNFL   65 (136)
T ss_dssp             ------------------------------------------------CCSCSSCCTTCEEEEESC-CTTCCHHHHHHHT
T ss_pred             CccccccccchHHHHhhccCCCccc---CCCCC--CCC---------CCCCCCCCCCCCEEEEeCC-CCCCCHHHHHHHH
Confidence            4788888888877665555433332   12110  000         0001123345789999999 9999999999999


Q ss_pred             ccCCC---eEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           88 EPYGN---VLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        88 ~~~G~---i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ++||.   |..|.|.       +|||||+|.+.++|++||+ ||+..|+|+.|.|.++...
T Consensus        66 ~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           66 SDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             TTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHH
T ss_pred             HHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChH
Confidence            99998   7788774       6899999999999999999 9999999999999998653

>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=99.68  E-value=2.8e-16  Score=110.53  Aligned_cols=76  Identities=22%  Similarity=0.312  Sum_probs=68.7

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE-EEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~-~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ....++|||+|| |+.+++++|+++|.+||.|.. |.|       .+|||||+|.+.++|++||.. |+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESC-CTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345789999999 999999999999999999987 766       378999999999999999997 9999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

>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=99.68  E-value=9.7e-17  Score=109.37  Aligned_cols=73  Identities=16%  Similarity=0.297  Sum_probs=68.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..++|||+|| |..+++++|+++|.+| .|..+.+  .+|||||+|.+.++|++|++.|||..|.|+.|.|+++...
T Consensus         4 ~~~~l~V~nL-p~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            4 GSSGILVKNL-PQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESC-CSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            4688999999 8999999999999999 9998887  4799999999999999999999999999999999998654

>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=99.68  E-value=5.9e-17  Score=113.16  Aligned_cols=76  Identities=29%  Similarity=0.458  Sum_probs=66.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      .....++|||+|| |..+++++|+++|++|| |..|.|.         +|||||+|.+.++|++|| .|||..|+|+.|.
T Consensus        15 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~   91 (100)
T 2j76_E           15 PKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIR   91 (100)
T ss_dssp             -----CEEEESCC-SSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCC
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEE
Confidence            4456899999999 89999999999999999 9999983         579999999999999999 8999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |+++.+..
T Consensus        92 V~~a~~~~   99 (100)
T 2j76_E           92 VDVADQAQ   99 (100)
T ss_dssp             CEECCCSC
T ss_pred             EEeccCCC
Confidence            99997653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.67  E-value=6.7e-17  Score=108.43  Aligned_cols=66  Identities=20%  Similarity=0.364  Sum_probs=61.6

Q ss_pred             CEEEEeccCCCCC------CHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCc-EEEE
Q 026341           66 KTLFVINFDPIRT------RERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDR-VISV  132 (240)
Q Consensus        66 ~~l~v~nl~~~~~------~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~-~l~v  132 (240)
                      ++|||+|| |..+      ++++|+++|++||.|..|.|+      +|||||+|.+.++|++|+..|||..|+|+ +|.|
T Consensus         2 ~~l~V~nL-p~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESC-CCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCC-CCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            68999999 8888      679999999999999999985      69999999999999999999999999999 8866

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=1.1e-16  Score=117.32  Aligned_cols=77  Identities=26%  Similarity=0.421  Sum_probs=70.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--EEE--------eCCeEEEEecCHHHHHHHHHhcCCC----ccc
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--VRI--------RRNFAFVQFETQEEATKALESTDRS----KLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--~~~--------~kg~afV~f~~~~~a~~A~~~l~g~----~~~  126 (240)
                      ...+.++|||+|| |+.+++++|+++|.+||.|..  |.|        .+|||||+|.+. +|++||..|||.    .|+
T Consensus        19 ~~~~~~~lfV~nL-~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           19 SENANDTIILRNL-NPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             CSCCCCEEEECSC-CTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            4466889999999 999999999999999999966  777        369999999999 999999999999    999


Q ss_pred             CcEEEEEEeecCC
Q 026341          127 DRVISVEYALKDD  139 (240)
Q Consensus       127 g~~l~v~~a~~~~  139 (240)
                      |+.|.|+++.+..
T Consensus        97 gr~l~V~~a~~~~  109 (131)
T 2m2b_A           97 GKTINVEFAKGSK  109 (131)
T ss_dssp             GCCCCCEECCCSC
T ss_pred             CEEEEEEECCCCC
Confidence            9999999998754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.67  E-value=2.6e-16  Score=116.36  Aligned_cols=75  Identities=29%  Similarity=0.580  Sum_probs=69.0

Q ss_pred             CCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           60 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        60 ~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ....+..+|||+|| |..+++++|+++|.+||.|..+.|+        +|||||+|.+.++|++|++.|||..|.|+.|.
T Consensus        58 ~~~~~~~~l~v~nl-p~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           58 GSATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             SSCSSCCEEEEECC-CTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCCCCcEEEEEeC-CCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34567899999999 8899999999999999999999983        68999999999999999999999999999999


Q ss_pred             EEEe
Q 026341          132 VEYA  135 (240)
Q Consensus       132 v~~a  135 (240)
                      |++|
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3.5e-16  Score=108.26  Aligned_cols=76  Identities=17%  Similarity=0.277  Sum_probs=69.1

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEE-Ee----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVR-IR----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~-~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...++|||+|| |+.+++++|+++|.+||.|..|. |+    .+.|||+|.+.++|++|+..|||..|.|+.|.|+++.+
T Consensus        13 ~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           13 QRIRKLQIRNI-PPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CSCCCEEEEEE-CSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCEEEEEcC-CCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            34789999999 89999999999999999999994 64    34599999999999999999999999999999999987


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ++
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            63

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=4.3e-16  Score=107.46  Aligned_cols=75  Identities=19%  Similarity=0.319  Sum_probs=66.7

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC--C-eEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--N-FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k--g-~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ....+|||+|| |+.+++++|+++|.+||.|..|.+.+  + ||||+|.+.++|++||. |||..|+|+.|.|+++....
T Consensus         6 ~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            6 SGLRSVFVSGF-PRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TTCCEEEEECC-CTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            34679999999 89999999999999999999984432  1 99999999999999999 99999999999999886544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.67  E-value=7.2e-17  Score=106.56  Aligned_cols=67  Identities=27%  Similarity=0.494  Sum_probs=62.7

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +|||+|| |..+++++|+++|++||+|..|.++        +|||||+|.+.++|++|++ ||+..|+|+.|.|++|
T Consensus         1 ~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGL-SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECC-CSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            4899999 8999999999999999999999883        5899999999999999998 9999999999999875

>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=99.66  E-value=1.7e-16  Score=113.53  Aligned_cols=77  Identities=22%  Similarity=0.243  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCe-EEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV-LHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i-~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+..+|||+|| |+.+++++|+++|.+||.| ..|.|       .+|||||+|.+.++|++||.. |+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESC-CTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCc-CCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            3456789999999 9999999999999999999 77777       379999999999999999987 999999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      .++....
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998654

>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=99.66  E-value=1.1e-16  Score=116.17  Aligned_cols=76  Identities=17%  Similarity=0.275  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEE-EE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV-RI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~-~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ......+|||+|| |+.+++++|+++|..||.|..+ .+       .+|||||+|.+.++|++||. ||+..|+|+.|.|
T Consensus        21 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   98 (124)
T 1wel_A           21 PHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   98 (124)
T ss_dssp             CCCCCCEEEEECC-CTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            3455789999999 9999999999999999998652 33       36899999999999999999 9999999999999


Q ss_pred             EEeecC
Q 026341          133 EYALKD  138 (240)
Q Consensus       133 ~~a~~~  138 (240)
                      .++..+
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            999754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.66  E-value=2.9e-16  Score=120.94  Aligned_cols=77  Identities=21%  Similarity=0.324  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|++||+.|||..|+|+.|.|+
T Consensus        84 ~~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECC-CSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4456789999999 8999999999999999999999984       5899999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ||...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            99764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.66  E-value=6.9e-17  Score=112.94  Aligned_cols=77  Identities=23%  Similarity=0.304  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+..+|||+|| |..+++++|+++|.+||.|..+.+       .+|||||+|.+.++|++||+ |||..|.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           13 ESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   90 (101)
T ss_dssp             TCSCSEEEEEECC-CTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEE
Confidence            3446789999999 899999999999999997755211       37999999999999999999 99999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++.+..
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            998754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=1.7e-16  Score=114.23  Aligned_cols=75  Identities=20%  Similarity=0.245  Sum_probs=68.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCC---eEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGN---VLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~---i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ....++|||+|| |+.+++++|+++|..||.   |..|.|.       +|||||+|.+.++|++||+ ||+..|+|+.|.
T Consensus        14 ~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGL-PWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESC-CTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345789999999 999999999999999998   7888874       6899999999999999999 999999999999


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      |.++...
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998654

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.66  E-value=1.9e-16  Score=117.73  Aligned_cols=79  Identities=23%  Similarity=0.409  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--------EEE-----eCCeEEEEecCHHHHHHHHHhcCCCcccC
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--------VRI-----RRNFAFVQFETQEEATKALESTDRSKLVD  127 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--------~~~-----~kg~afV~f~~~~~a~~A~~~l~g~~~~g  127 (240)
                      ...+.++|||+|| |+.+++++|+++|.+||.|..        +.+     .+|||||+|.+.++|++||..|||..|.|
T Consensus        41 ~~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           41 PGEPNCRIYVKNL-AKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CCSCCSEEEEEEE-CTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            3456899999999 899999999999999998865        333     26899999999999999999999999999


Q ss_pred             cEEEEEEeecCCC
Q 026341          128 RVISVEYALKDDS  140 (240)
Q Consensus       128 ~~l~v~~a~~~~~  140 (240)
                      +.|.|.+++....
T Consensus       120 ~~l~V~~a~~~~~  132 (143)
T 3egn_A          120 KPMVVQFARSARP  132 (143)
T ss_dssp             EECEEEECCCSCC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999986543

>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=99.66  E-value=4.3e-16  Score=122.78  Aligned_cols=76  Identities=16%  Similarity=0.208  Sum_probs=70.7

Q ss_pred             CCCCEEEEeccCC-CCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           63 RPTKTLFVINFDP-IRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        63 ~~~~~l~v~nl~~-~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      .++++|||+|| + +.+++++|+++|++||.|..|.|.   +|||||+|.+.++|+.||+.|||..|.|+.|.|.+++..
T Consensus         2 ~~~~~l~V~nL-~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A            2 ADSPVLMVYGL-DQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             CCCSEEEEECC-CTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCC-CcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            45789999999 6 899999999999999999999985   699999999999999999999999999999999999754


Q ss_pred             C
Q 026341          139 D  139 (240)
Q Consensus       139 ~  139 (240)
                      .
T Consensus        81 ~   81 (205)
T 3tyt_A           81 A   81 (205)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.65  E-value=5.8e-17  Score=110.89  Aligned_cols=72  Identities=22%  Similarity=0.494  Sum_probs=65.0

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.+ |++|+..|||..|+|+.|.|++|.+
T Consensus         2 ~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNL-VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEE-CTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             cEEEECCC-CCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            57999999 8899999999999999999999984        679999999999 9999999999999999999999987


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus        80 ~~   81 (90)
T 2ki2_A           80 KK   81 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.1e-16  Score=106.07  Aligned_cols=68  Identities=24%  Similarity=0.418  Sum_probs=63.9

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ++|||+|| |..+++++|+++|++||+|..+.++        +|+|||+|.+.++|++|+..++ ..|+|+.|.|++|
T Consensus         1 ~~l~v~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESC-CSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            47999999 8999999999999999999999884        5799999999999999999999 9999999999987

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=1e-17  Score=120.21  Aligned_cols=78  Identities=18%  Similarity=0.281  Sum_probs=70.7

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE--------EEEe--------CCeEEEEecCHHHHHHHHHhcCCCcc
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH--------VRIR--------RNFAFVQFETQEEATKALESTDRSKL  125 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~--------~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~  125 (240)
                      ..+.++|||+|| |..+++++|+++|.+||.|..        |.|+        +|||||+|.+.++|++||..|||..|
T Consensus         4 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            4 NSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            346789999999 899999999999999999988        6663        58999999999999999999999999


Q ss_pred             cCcEEEEEEeecCCC
Q 026341          126 VDRVISVEYALKDDS  140 (240)
Q Consensus       126 ~g~~l~v~~a~~~~~  140 (240)
                      .|+.|.|+++.+...
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999987653

>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=99.65  E-value=7.9e-16  Score=105.08  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=60.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcc--cCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKL--VDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |+.+++++|+++|++||.|..|.|+   +|||||+|.+.++|++    |++..+  .|+.|.|.+|
T Consensus         7 ~~~~~~~l~V~~L-p~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            7 HHHHGSKVFVGRC-TEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             ----CCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            3456899999999 9999999999999999999999995   7999999999999983    456554  5899999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      .++.
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            8754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=4.5e-16  Score=110.25  Aligned_cols=72  Identities=21%  Similarity=0.319  Sum_probs=66.0

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ...+|||+|| |+.+++++|+++|.+| .|..|.|+       +|||||+|.+.++|++|| .||+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nL-p~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGM-PFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECC-CSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3579999999 9999999999999999 89999884       789999999999999999 699999999999998886


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            53

>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=99.64  E-value=2.3e-16  Score=126.41  Aligned_cols=74  Identities=18%  Similarity=0.310  Sum_probs=67.8

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC--CeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG--NVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G--~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ..++|||+|| ++.+++++|+++|.+||  .|..|.|+        +|||||+|.+.++|++||+.||+..|+|+.|.|.
T Consensus        67 ~~~~lfVgnL-~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESC-CTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CccEEEEeCC-CCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            4678999999 99999999999999999  99999983        5799999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ++...
T Consensus       146 ~a~~~  150 (229)
T 3q2s_C          146 PVNKQ  150 (229)
T ss_dssp             ECCHH
T ss_pred             ECCCC
Confidence            98753

>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=99.64  E-value=2.1e-16  Score=111.70  Aligned_cols=76  Identities=17%  Similarity=0.196  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCC---eEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGN---VLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~---i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      .....++|||+|| |+.+++++|+++|..||.   |..|.|.       +|||||+|.+.++|++||. ||+..|+|+.|
T Consensus         7 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGL-PWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECC-CSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCC-CCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999 999999999999999988   8888884       6899999999999999999 99999999999


Q ss_pred             EEEEeecC
Q 026341          131 SVEYALKD  138 (240)
Q Consensus       131 ~v~~a~~~  138 (240)
                      .|.++...
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998754

>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=99.64  E-value=6.7e-16  Score=104.76  Aligned_cols=70  Identities=29%  Similarity=0.519  Sum_probs=65.2

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccC----C-------CeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPY----G-------NVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRV  129 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~----G-------~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~  129 (240)
                      .+.++|||+|| |..+++++|+++|.+|    |       .|..+.+.  +|||||+|.+.++|++|+ .|||..|.|+.
T Consensus         4 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESC-CTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            35789999999 8999999999999999    8       89999986  799999999999999999 99999999999


Q ss_pred             EEEEE
Q 026341          130 ISVEY  134 (240)
Q Consensus       130 l~v~~  134 (240)
                      |.|+.
T Consensus        82 l~V~r   86 (87)
T 2hzc_A           82 LKIRR   86 (87)
T ss_dssp             CEEEC
T ss_pred             EEEeC
Confidence            99863

>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=99.63  E-value=5.7e-16  Score=105.50  Aligned_cols=75  Identities=23%  Similarity=0.334  Sum_probs=63.5

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.|.   +|||||+|.+.++|++|+..  ...+.|..|.|.++.++.
T Consensus         3 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            3 SGSSGVFVGRC-TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCCEEEEESC-CSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            35789999999 9999999999999999999999995   79999999999999764321  234589999999988764


Q ss_pred             C
Q 026341          140 S  140 (240)
Q Consensus       140 ~  140 (240)
                      .
T Consensus        80 ~   80 (88)
T 1wf0_A           80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.60  E-value=4.3e-16  Score=102.75  Aligned_cols=67  Identities=24%  Similarity=0.419  Sum_probs=62.3

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +|||+|| |..+++++|+++|++||+|..|.++        +|||||+|.+.++|++|++. ++..|.|+.|.|.+|
T Consensus         1 ~l~v~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGL-SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCC-CSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            5899999 8999999999999999999999884        68999999999999999985 899999999999875

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.59  E-value=1.8e-15  Score=121.07  Aligned_cols=76  Identities=28%  Similarity=0.353  Sum_probs=69.1

Q ss_pred             CCCCCEEEEeccCCCCC---------CHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcc-----
Q 026341           62 QRPTKTLFVINFDPIRT---------RERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKL-----  125 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~---------~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~-----  125 (240)
                      .....+|||+|| +..+         ++++|+++|++||+|..|.|.  +|||||+|.+.++|+.|++.|+|..|     
T Consensus       131 ~~~~rtLfVgnL-~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGI-DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECT-TGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCC-ChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            456899999999 7777         799999999999999999985  79999999999999999999999999     


Q ss_pred             -------cCcEEEEEEeecC
Q 026341          126 -------VDRVISVEYALKD  138 (240)
Q Consensus       126 -------~g~~l~v~~a~~~  138 (240)
                             .|+.|.|.||...
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC--
T ss_pred             ccccccCCCCEEEEEEccCC
Confidence                   8999999999864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.59  E-value=3.7e-15  Score=118.08  Aligned_cols=76  Identities=21%  Similarity=0.466  Sum_probs=68.6

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ..|.++|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.+.++|++||..||+..+.|+.|.|.
T Consensus        12 ~~p~~tlfVgnL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           12 SYPMASLYVGDL-HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ---CCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            456789999999 8999999999999999999999984        4799999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ++...
T Consensus        91 ~~~~~   95 (213)
T 4f02_A           91 WSQRD   95 (213)
T ss_dssp             ECCCC
T ss_pred             ccccc
Confidence            98654

>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=99.59  E-value=6e-15  Score=111.96  Aligned_cols=75  Identities=21%  Similarity=0.412  Sum_probs=69.8

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +.++|||+|| |..+++++|+++|++||+|..|.+.        +|||||+|.+.++|++|++.|+|..|.|+.|.|.++
T Consensus         2 ~~~~l~v~nl-p~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~   80 (168)
T 1b7f_A            2 SNTNLIVNYL-PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA   80 (168)
T ss_dssp             CCSEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CccEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEec
Confidence            4789999999 8899999999999999999999883        489999999999999999999999999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      .+..
T Consensus        81 ~~~~   84 (168)
T 1b7f_A           81 RPGG   84 (168)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            8654

>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=99.59  E-value=1e-14  Score=103.84  Aligned_cols=78  Identities=17%  Similarity=0.215  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEeccCCCCCC-----------HHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcc
Q 026341           61 NQRPTKTLFVINFDPIRTR-----------ERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKL  125 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~-----------~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~  125 (240)
                      ...+..+|+|.|| .....           +++|+++|.+||.|..|.|.    +|||||+|.+.++|++|+..|||..|
T Consensus        11 ~~~~s~~l~l~Nl-~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           11 RMRHERVVIIKNM-FHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CCCSCCEEEEESS-CCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCCCceEEEEEcC-CCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            4567899999999 43322           57999999999999999874    79999999999999999999999999


Q ss_pred             cCcEEEEEEeecCC
Q 026341          126 VDRVISVEYALKDD  139 (240)
Q Consensus       126 ~g~~l~v~~a~~~~  139 (240)
                      +|++|.|.++.+..
T Consensus        90 ~gr~l~v~~a~~~~  103 (112)
T 2dit_A           90 GGRQITAQAWDGTT  103 (112)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCcEEEEEEeCCCC
Confidence            99999999997653

>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=99.58  E-value=3.6e-15  Score=108.08  Aligned_cols=75  Identities=23%  Similarity=0.344  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeE--EEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL--HVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~--~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ......+|||+|| |+.+++++|+++|++| .|.  .|.|+       +|||||+|.+.++|++||+. ++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnL-p~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGL-PFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECC-CTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            3345789999999 9999999999999999 676  78874       79999999999999999984 78999999999


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      |..+..+
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.3e-15  Score=110.12  Aligned_cols=74  Identities=18%  Similarity=0.189  Sum_probs=65.5

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCe----EEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNV----LHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i----~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ....+|||+|| |+.+++++|+++|++||.|    ..|.|+       +|||||+|.+.++|++||+. |+..|.|+.|.
T Consensus        21 ~~~~~v~V~nL-p~~~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 ENQVIVRMRGL-PFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSC-CTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            34689999999 9999999999999999975    466663       68999999999999999986 99999999999


Q ss_pred             EEEeecC
Q 026341          132 VEYALKD  138 (240)
Q Consensus       132 v~~a~~~  138 (240)
                      |..+...
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988643

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.58  E-value=1.3e-15  Score=106.51  Aligned_cols=75  Identities=24%  Similarity=0.463  Sum_probs=68.2

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.|+       +|||||+|.+.++|++|+.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGI-DVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            34689999999 8999999999999999999999984       5899999999999999998  999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      .....
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            87543

>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=99.57  E-value=9.3e-15  Score=110.60  Aligned_cols=74  Identities=20%  Similarity=0.413  Sum_probs=68.8

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |..+++++|+++|+.||.|..+.+.        +|+|||+|.+.++|+.|++.|||..+.|+.|.|.++.
T Consensus         2 ~~~l~v~nl-p~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            2 KTNLIVNYL-PQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cceEEEcCC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            579999999 8899999999999999999999884        3799999999999999999999999999999999987


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.57  E-value=1.1e-14  Score=102.29  Aligned_cols=76  Identities=26%  Similarity=0.268  Sum_probs=66.3

Q ss_pred             CCCCCEEEEeccCC-C---CCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCc
Q 026341           62 QRPTKTLFVINFDP-I---RTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDR  128 (240)
Q Consensus        62 ~~~~~~l~v~nl~~-~---~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~  128 (240)
                      ..++.+|+|.||.. .   ..++++|+++|++||.|..|.|+         +|+|||+|.+.++|++|++.|||..|+|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            35688999999921 1   23689999999999999999884         57999999999999999999999999999


Q ss_pred             EEEEEEeec
Q 026341          129 VISVEYALK  137 (240)
Q Consensus       129 ~l~v~~a~~  137 (240)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999865

>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=99.56  E-value=6.3e-15  Score=118.03  Aligned_cols=78  Identities=23%  Similarity=0.320  Sum_probs=72.4

Q ss_pred             CCCCCCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..++.++|||+|| |. .+++++|+++|++||.|..|.|.   +|||||+|.+.++|++|++.|||..|.|+.|.|.++.
T Consensus        30 ~~~~~~~l~V~nL-p~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           30 AGAGNSVLLVSNL-NPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             GCCCCSEEEEESC-CTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCCCCEEEEeCC-CcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            4567899999999 88 89999999999999999999996   7999999999999999999999999999999999997


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      ...
T Consensus       109 ~~~  111 (229)
T 2adc_A          109 HQN  111 (229)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            653

>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=99.55  E-value=4.7e-14  Score=110.00  Aligned_cols=116  Identities=18%  Similarity=0.302  Sum_probs=82.1

Q ss_pred             ChhHHHHHHHhh--CCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeE
Q 026341           17 DDRDAADAIRGL--DNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL   94 (240)
Q Consensus        17 ~~~~A~~A~~~l--~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~   94 (240)
                      +.+.+..|+...  ....+.  +..+.|....... .+.. ..........++|||+|| |..+++++|+++|++||.|.
T Consensus        63 d~~~I~~Al~~S~~~~lev~--ed~~~vrR~~~~p-~p~~-~~~~~~~~~~~~l~V~nL-p~~~t~~~L~~~F~~~G~v~  137 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEIS--EDKTKIRRSPSKP-LPEV-TDEYKNDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVL  137 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEEC--TTSSEEEECTTSC-CCCC-CHHHHHHHHHTEEEEECC-CTTCCHHHHHHHHTTSCCEE
T ss_pred             CHHHHHHHHhhcccceEEEe--cccceEEecccCC-Cccc-chhhhhccccCEEEecCC-CCcCCHHHHHHHHhcCCCEE
Confidence            667777788766  444443  3334443331111 0000 000001123589999999 89999999999999999999


Q ss_pred             EEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           95 HVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        95 ~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      .|.|+       +|||||+|++.++|++|+..+ +..|+|+.|.|.++..-
T Consensus       138 ~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          138 NIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             EEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             EEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            99885       689999999999999999865 45999999999997654

>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=99.54  E-value=3.1e-14  Score=117.24  Aligned_cols=78  Identities=28%  Similarity=0.546  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHH----HhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIK----RHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~----~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...+.++|||+|| |..+++++|+    ++|.+||.|..|.+.     +|||||+|.+.++|++||+.|||..|.|+.|.
T Consensus         5 ~~~~~~~l~V~nl-p~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            5 ETRPNHTIYINNL-NEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            4567899999999 8999999966    899999999999985     48999999999999999999999999999999


Q ss_pred             EEEeecCC
Q 026341          132 VEYALKDD  139 (240)
Q Consensus       132 v~~a~~~~  139 (240)
                      |.|+....
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99997654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.54  E-value=2.2e-14  Score=108.44  Aligned_cols=73  Identities=22%  Similarity=0.476  Sum_probs=68.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ++|||+|| |..+++++|+++|++||.|..|.+.       +|||||+|.+.++|++|+..|||..|.|+.|.|.++...
T Consensus         1 R~l~V~nl-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNL-DKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEE-ETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCC-CCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            47999999 8999999999999999999999984       579999999999999999999999999999999998765


Q ss_pred             C
Q 026341          139 D  139 (240)
Q Consensus       139 ~  139 (240)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=7.2e-14  Score=99.71  Aligned_cols=69  Identities=16%  Similarity=0.343  Sum_probs=57.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ...++|||+|| |+.+++++|+++|++||.|. +.++           +|||||+|.+.++|++||+.|+  .++|+.|.
T Consensus         6 ~~~~~lfVgnL-p~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            6 SGSRKVFVGGL-PPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SCCCCEEEECC-CTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCEEEEcCC-CCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            45789999999 89999999999999999999 6552           6899999999999999999984  25666665


Q ss_pred             EEEe
Q 026341          132 VEYA  135 (240)
Q Consensus       132 v~~a  135 (240)
                      +..+
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            5543

>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=99.52  E-value=3.4e-14  Score=110.53  Aligned_cols=77  Identities=25%  Similarity=0.499  Sum_probs=68.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||.. ++..|.|+.|.|
T Consensus         9 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            9 EPEQLRKLFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCGGGGEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            4456889999999 8899999999999999999999884        57999999999999999986 999999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      .++....
T Consensus        87 ~~~~~~~   93 (196)
T 1l3k_A           87 KRAVSRE   93 (196)
T ss_dssp             EECCC--
T ss_pred             ecccCcc
Confidence            9987653

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.51  E-value=4.7e-14  Score=115.10  Aligned_cols=76  Identities=33%  Similarity=0.481  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...+.++|||+|| |..+|+++|.++|.+||.|..|.+.  +|||||+|.+.++|+.|+..|||..|.|+.|.|.++.+
T Consensus        18 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           18 TYTQRCRLFVGNL-PTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             SSCGGGEEEEESC-CTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            3455789999999 8999999999999999999999996  79999999999999999999999999999999999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.51  E-value=4.2e-14  Score=111.67  Aligned_cols=74  Identities=27%  Similarity=0.408  Sum_probs=67.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.||+..|.|+.|.|.++
T Consensus        27 ~~~~l~V~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           27 IMSRVYVGSI-YYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHTEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             cCCEEEEECC-CCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            4689999999 8899999999999999999999983        689999999999999999999999999999999887


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      ...
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.51  E-value=1.9e-14  Score=112.35  Aligned_cols=74  Identities=24%  Similarity=0.353  Sum_probs=69.7

Q ss_pred             CCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           65 TKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        65 ~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      .++|||+|| |. .+++++|+++|++||.|..|.+.   +|||||+|.+.++|++|+..|||..|.|+.|.|.++....
T Consensus         3 ~~~l~v~nl-p~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            3 NSVLLVSNL-NPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCEEEEECC-CSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             CcEEEEeCC-CcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            579999999 88 89999999999999999999996   7999999999999999999999999999999999998654

>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=99.47  E-value=1.3e-13  Score=116.02  Aligned_cols=76  Identities=17%  Similarity=0.273  Sum_probs=66.2

Q ss_pred             CCCCCCEEEEeccC-CCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCccc---Cc--EEEE
Q 026341           61 NQRPTKTLFVINFD-PIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLV---DR--VISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~-~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~---g~--~l~v  132 (240)
                      ...|+.+|||+|+. ++.+++++|+++|++||+|..|.+  .+|||||+|.+.++|++||+.|||.++.   |+  +|.|
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            46788999999941 678999999999999999999988  4899999999999999999999999873   44  6777


Q ss_pred             EEee
Q 026341          133 EYAL  136 (240)
Q Consensus       133 ~~a~  136 (240)
                      .|+.
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            7774

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=5.4e-13  Score=92.68  Aligned_cols=63  Identities=22%  Similarity=0.301  Sum_probs=56.2

Q ss_pred             CCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           76 IRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        76 ~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ..+++++|+++|.+||+|..|.|+   +|||||+|++.++|+.||+.+++  +.|++|.|+|+.....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            468999999999999999999994   79999999999999999998554  6799999999987653

>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=99.46  E-value=2.1e-13  Score=95.82  Aligned_cols=75  Identities=25%  Similarity=0.417  Sum_probs=64.8

Q ss_pred             CCCCEEEEeccC-CCCC--------CHHHHHHhhccCCCeEEEEEe----------CCeEEEEecCHHHHHHHHHhcCCC
Q 026341           63 RPTKTLFVINFD-PIRT--------RERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKALESTDRS  123 (240)
Q Consensus        63 ~~~~~l~v~nl~-~~~~--------~~~~l~~~f~~~G~i~~~~~~----------kg~afV~f~~~~~a~~A~~~l~g~  123 (240)
                      .|+.+|.|.|+- +..+        .+++|+++|++||.|..|.|+          +|+|||+|.+.++|++|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            578899999972 2222        237899999999999999984          589999999999999999999999


Q ss_pred             cccCcEEEEEEeec
Q 026341          124 KLVDRVISVEYALK  137 (240)
Q Consensus       124 ~~~g~~l~v~~a~~  137 (240)
                      .++|+.|.|.++..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999854

>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=99.45  E-value=1.7e-13  Score=104.29  Aligned_cols=73  Identities=27%  Similarity=0.484  Sum_probs=66.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccC----C-------CeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPY----G-------NVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~----G-------~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      +.++|||+|| |..+++++|+++|++|    |       .|..+.+.  +|||||+|.+.++|++|+ .|||..|.|+.|
T Consensus         3 ~~~~l~V~nL-p~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i   80 (172)
T 2g4b_A            3 SARRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (172)
T ss_dssp             GGGEEEEESC-CTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             cccEEEEcCC-CcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCcee
Confidence            4689999999 8999999999999999    6       77877774  799999999999999999 899999999999


Q ss_pred             EEEEeecC
Q 026341          131 SVEYALKD  138 (240)
Q Consensus       131 ~v~~a~~~  138 (240)
                      .|.++...
T Consensus        81 ~v~~~~~~   88 (172)
T 2g4b_A           81 KIRRPHDY   88 (172)
T ss_dssp             EEECCSSC
T ss_pred             eecCCccc
Confidence            99987654

>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=99.45  E-value=2.6e-13  Score=103.38  Aligned_cols=75  Identities=25%  Similarity=0.418  Sum_probs=66.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----------CCeEEEEecCHHHHHHHHHhcCCCccc---CcEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKALESTDRSKLV---DRVI  130 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----------kg~afV~f~~~~~a~~A~~~l~g~~~~---g~~l  130 (240)
                      ..++|||+|| |..+++++|+++|.+||+|..|.|.          +|||||+|.+.++|++|++.||+..+.   +..|
T Consensus         2 ~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQV-PRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CceEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            3679999999 8999999999999999999999873          479999999999999999999998876   5788


Q ss_pred             EEEEeecCC
Q 026341          131 SVEYALKDD  139 (240)
Q Consensus       131 ~v~~a~~~~  139 (240)
                      .+.++....
T Consensus        81 ~~~~~~~~~   89 (175)
T 3nmr_A           81 QMKPADSEK   89 (175)
T ss_dssp             EEEECGGGC
T ss_pred             EEccccccc
Confidence            888876554

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.44  E-value=2.2e-13  Score=106.07  Aligned_cols=74  Identities=27%  Similarity=0.469  Sum_probs=66.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccC----C-------CeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPY----G-------NVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~----G-------~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      ..++|||+|| |..+++++|+++|.+|    |       .|..+.+.  +|||||+|.+.++|++|| .|||..|.|+.|
T Consensus         3 ~~~~l~V~nL-p~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i   80 (198)
T 2yh0_A            3 MARRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   80 (198)
T ss_dssp             -CCEEEEESC-CTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEE
T ss_pred             ceeEEEEcCC-CCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceE
Confidence            4689999999 8999999999999999    5       67777764  799999999999999999 899999999999


Q ss_pred             EEEEeecCC
Q 026341          131 SVEYALKDD  139 (240)
Q Consensus       131 ~v~~a~~~~  139 (240)
                      .|.++....
T Consensus        81 ~v~~~~~~~   89 (198)
T 2yh0_A           81 KIRRPHDYQ   89 (198)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999987653

>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=99.43  E-value=7.9e-14  Score=99.67  Aligned_cols=71  Identities=20%  Similarity=0.341  Sum_probs=39.6

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHH
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRER   81 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~   81 (240)
                      ..++|||||+|.+.++|++||+.|||..|  +|++|.|.++.........   .........+|||+|| |..+|++
T Consensus        42 ~~~kg~afV~f~~~~~A~~Ai~~l~~~~~--~g~~i~V~~a~~~~~~~~~---~~~~~~~~~~lyv~Nl-~~~~T~~  112 (115)
T 4f25_A           42 NGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSRKEREAE---LGARAKEFTNVYIKNF-GPGSTRA  112 (115)
T ss_dssp             TEEEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEESSCCCC-------------------------------
T ss_pred             CCCCceEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCccccccc---cccccCCCCceEeCCC-CCCcccc
Confidence            34689999999999999999999999999  6999999999865543221   1122334567999999 7777765

>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=99.42  E-value=2.6e-13  Score=102.79  Aligned_cols=71  Identities=24%  Similarity=0.466  Sum_probs=64.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      +.++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|+..  +..+.|+.|.|.++
T Consensus         2 ~~~~l~v~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            2 ESCKMFIGGL-NWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             GGGEEEECSC-CTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCcEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            4689999999 8999999999999999999999984        58999999999999999984  57889999999887


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      .+
T Consensus        79 ~~   80 (167)
T 2cjk_A           79 IP   80 (167)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.42  E-value=8.5e-13  Score=93.89  Aligned_cols=76  Identities=14%  Similarity=0.214  Sum_probs=64.3

Q ss_pred             CCCCCEEEEeccCCC-CC--------CHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcccCc
Q 026341           62 QRPTKTLFVINFDPI-RT--------RERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLVDR  128 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~-~~--------~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~g~  128 (240)
                      ..++.+|.|.|+-.. ..        -+++|++.|++||.|..|.|.    +|+|||+|.+.++|++|+..|||..|+|+
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~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            346888999998221 10        135789999999999999994    69999999999999999999999999999


Q ss_pred             EEEEEEeec
Q 026341          129 VISVEYALK  137 (240)
Q Consensus       129 ~l~v~~a~~  137 (240)
                      .|.|+|+..
T Consensus        84 ~i~v~~~~~   92 (114)
T 3s6e_A           84 MITAAYVPL   92 (114)
T ss_dssp             ECEEEEECH
T ss_pred             EEEEEEEcH
Confidence            999999863

>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=99.42  E-value=6.5e-14  Score=107.09  Aligned_cols=77  Identities=23%  Similarity=0.304  Sum_probs=66.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.++|||+|| |..+++++|+++|..||.+..+.+       .+|||||+|.+.++|++|++ |||..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECC-CTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            4456899999999 899999999999999986544222       47999999999999999995 99999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++....
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.42  E-value=2.4e-13  Score=97.28  Aligned_cols=71  Identities=14%  Similarity=0.231  Sum_probs=61.2

Q ss_pred             CEEEEecc---CCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecC----HHH----HHHHHH--hcCCCc
Q 026341           66 KTLFVINF---DPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFET----QEE----ATKALE--STDRSK  124 (240)
Q Consensus        66 ~~l~v~nl---~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~----~~~----a~~A~~--~l~g~~  124 (240)
                      ..|||+||   .++.+++++|+++|+.||+|..|.+        ++|||||+|.+    +++    |.+|+.  .|||..
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   2358999999999999999999998        47999999996    333    888988  789999


Q ss_pred             ccCcEEEEEEee
Q 026341          125 LVDRVISVEYAL  136 (240)
Q Consensus       125 ~~g~~l~v~~a~  136 (240)
                      |+|+.|.|.+..
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            999999999864

>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=99.41  E-value=7.2e-13  Score=94.88  Aligned_cols=75  Identities=19%  Similarity=0.230  Sum_probs=64.4

Q ss_pred             CCCCEEEEeccCC-C---CCCHHHHHHhhccCCCeEEEEEe------------CCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           63 RPTKTLFVINFDP-I---RTRERDIKRHFEPYGNVLHVRIR------------RNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        63 ~~~~~l~v~nl~~-~---~~~~~~l~~~f~~~G~i~~~~~~------------kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      +|+.+|+|.|+-. .   .--+++|++.|++||+|..|.|+            +|++||+|.+.++|++|+..|||..|+
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3688999999821 1   12368999999999999999884            279999999999999999999999999


Q ss_pred             CcEEEEEEeec
Q 026341          127 DRVISVEYALK  137 (240)
Q Consensus       127 g~~l~v~~a~~  137 (240)
                      |+.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999864

>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=99.38  E-value=1.1e-13  Score=97.12  Aligned_cols=65  Identities=20%  Similarity=0.360  Sum_probs=56.2

Q ss_pred             EeccCCCCCCHHHHHHhh------------ccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           70 VINFDPIRTRERDIKRHF------------EPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        70 v~nl~~~~~~~~~l~~~f------------~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      +.|| ++.+++++|+++|            ++||.|..|.|+       +|||||+|.+.++|++|+..|||..++|++|
T Consensus        20 ~~~l-~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGL-RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCc-ccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            4566 5666777666665            999999999995       6899999999999999999999999999999


Q ss_pred             EEEEe
Q 026341          131 SVEYA  135 (240)
Q Consensus       131 ~v~~a  135 (240)
                      .|+|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=4.5e-12  Score=90.44  Aligned_cols=77  Identities=14%  Similarity=0.137  Sum_probs=69.0

Q ss_pred             CCCCCCEEEEeccCCCC-CCHHHHHHhhccCCCeEEEEEeCC--eEEEEecC-HHHHHHHHHhcC--CCcccCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIR-TRERDIKRHFEPYGNVLHVRIRRN--FAFVQFET-QEEATKALESTD--RSKLVDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~-~~~~~l~~~f~~~G~i~~~~~~kg--~afV~f~~-~~~a~~A~~~l~--g~~~~g~~l~v~~  134 (240)
                      ..++++.|+|+|| +.. ++.++|+++|++||+|.+|.+..+  .|||.|.+ +++|+.|+..||  +..|+|..+++++
T Consensus        14 ~~~~G~il~v~~l-~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           14 EEKIGCLLKFSGD-LDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             SCCCCCEEEEEES-CCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cccCCeEEEEecC-CCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            5677999999999 777 999999999999999999999754  89999999 899999999994  7789999999988


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      ....
T Consensus        93 L~Ge   96 (121)
T 1owx_A           93 LEGE   96 (121)
T ss_dssp             CCHH
T ss_pred             CCCH
Confidence            7643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=2.9e-12  Score=85.97  Aligned_cols=77  Identities=17%  Similarity=0.294  Sum_probs=65.5

Q ss_pred             CCCCCCEEEEeccCC---CCCCH----HHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDP---IRTRE----RDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~---~~~~~----~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ..+|..+|+|..++.   ...-.    .+|.+.|.+||+|..+++..+.+||+|.+.++|.+||. |||..++|+.|+|+
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSSEEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCCEEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            356788888887721   12223    67899999999999999999999999999999999998 99999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ++.+.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            98753

>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=99.15  E-value=3.2e-11  Score=83.65  Aligned_cols=43  Identities=28%  Similarity=0.556  Sum_probs=40.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++.++|||||+|.++++|++|++.|||..|  +|++|.|+||.+
T Consensus        56 ~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~V~~AkP   98 (99)
T 4fxv_A           56 VAGHSLGYGFVNYVTAKDAERAINTLNGLRL--QSKTIKVSYARP   98 (99)
T ss_dssp             SSCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCB
T ss_pred             CCCcccccEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEeeC
Confidence            4678899999999999999999999999999  699999999975

>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=99.15  E-value=3.7e-10  Score=98.43  Aligned_cols=45  Identities=33%  Similarity=0.497  Sum_probs=40.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|++++|||||+|.++++|++||..|||+.|  +|++|.|+|+.+..
T Consensus       139 ~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i--~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          139 RSGKPRGYAFIEYEHERDMHSAYKHADGKKI--DGRRVLVDVERGRT  183 (437)
T ss_pred             CCCCccceEEEeeccHHHHHHHHHHcCCCEE--CCEEEEEEEeCCCC
Confidence            3678899999999999999999999999999  69999999998543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.15  E-value=3.8e-11  Score=83.45  Aligned_cols=64  Identities=41%  Similarity=0.518  Sum_probs=51.0

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEecc
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINF   73 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl   73 (240)
                      ++|||||+|.+.++|++|++.|||..|  +|+.|.|+++.........+. .........+|||+||
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~~~~~~-~~~~~~~~~~ifvg~L   99 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVI--CGSRVRVELSTGMPRRSRFDR-PPARRKLLEVLFNGPL   99 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCS--SSCCCEEEESSSCCCSSCCCS-CCCSCCCCSCCCSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeE--CCcEEEEEEccCCCCcccCCC-CCccccCCCceecCCC
Confidence            689999999999999999999999998  699999999997664432211 2223344678999999

>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=99.14  E-value=8.2e-12  Score=88.96  Aligned_cols=68  Identities=26%  Similarity=0.337  Sum_probs=57.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      +++.++|||||+|.+.++|++|+..|||..|  +|+.|.|.|+.+....                   .++ +...++++
T Consensus        42 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~~-------------------~~~-~~~~~~~~   99 (115)
T 3lqv_A           42 NTPETRGTAYVVYEDIFDAKNAVDHLSGFNV--SNRYLVVLYYNANRAF-------------------QKM-DTKKKEEQ   99 (115)
T ss_dssp             CSTTTTTCEEEEESSHHHHHHHHHHHTTCBS--SSCBCEEEECCHHHHT-------------------TTS-CHHHHHHH
T ss_pred             eCCCCCcEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEecCChhh-------------------hhh-hHhHhHHH
Confidence            3456799999999999999999999999999  6999999999865432                   355 55678899


Q ss_pred             HHHhhccCCC
Q 026341           83 IKRHFEPYGN   92 (240)
Q Consensus        83 l~~~f~~~G~   92 (240)
                      |.++|++||.
T Consensus       100 l~~~~~~~g~  109 (115)
T 3lqv_A          100 LKLLKEKYGI  109 (115)
T ss_dssp             HHHHHHHHCC
T ss_pred             HHHHHHHhCC
Confidence            9999999983

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=5.8e-11  Score=80.01  Aligned_cols=73  Identities=19%  Similarity=0.273  Sum_probs=63.3

Q ss_pred             CCCCCCEEEEeccCCCC-----CCH----HHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEE
Q 026341           61 NQRPTKTLFVINFDPIR-----TRE----RDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVIS  131 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~-----~~~----~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  131 (240)
                      ..+|..+|+|..+ +..     +-+    .+|.+.|.+||+|..+++...-+||+|.+.++|.+||. |||.+++|+.|+
T Consensus        11 ~GPpD~Tv~V~~~-~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           11 QGPLDATVVVNLQ-SPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CCCTTCEEEEEES-SCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             cCCCCCeEEEEec-CCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCcEEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            5678899999988 421     212    56899999999999999999999999999999999998 999999999999


Q ss_pred             EEEe
Q 026341          132 VEYA  135 (240)
Q Consensus       132 v~~a  135 (240)
                      |++-
T Consensus        89 V~~k   92 (95)
T 1ufw_A           89 ISGP   92 (95)
T ss_dssp             EECC
T ss_pred             Eecc
Confidence            9874

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.11  E-value=8.3e-11  Score=80.24  Aligned_cols=47  Identities=21%  Similarity=0.269  Sum_probs=40.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhC-CCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLD-NIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~-g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .|+.++|||||+|.++++|++||+.|+ +..|  +|++|.|+|+.++.+.
T Consensus        39 ~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~--~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           39 SSGQSRGFAFVEFSHLQDATRWMEANQHSLNI--LGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             SSCCCSSEEEEECSSHHHHHHHHHTTTTEEEE--TTEEEEEECCCSCCCC
T ss_pred             CCCCcCceEEEEecCHHHHHHHHHhcCCCeEE--CCEEEEEEEcCCCCCC
Confidence            468889999999999999999999875 4566  7999999999876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.09  E-value=1e-10  Score=80.44  Aligned_cols=45  Identities=24%  Similarity=0.465  Sum_probs=39.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCc--ccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIP--FGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~--~~~~g~~l~v~~a~~   47 (240)
                      .|++++|||||+|.+.++|++|++.|||..  +.++|++|.|+||+.
T Consensus        48 ~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           48 QTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             SSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            468899999999999999999999999974  222799999999974

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.06  E-value=1.3e-10  Score=77.81  Aligned_cols=39  Identities=18%  Similarity=0.218  Sum_probs=36.4

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++|||||+|.++++|++|++.||+..|  .|++|.|++|.
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l--~gr~I~V~~A~   79 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVL--ANTTIFAESPS   79 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEECCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEE--CCcEEEEEECC
Confidence            4799999999999999999999999999  69999999884

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.06  E-value=1.5e-10  Score=83.84  Aligned_cols=45  Identities=18%  Similarity=0.400  Sum_probs=41.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++++++|||||+|.+.++|++|+..|||..|  .|++|.|+|+....
T Consensus        67 ~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l--~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           67 LSDDNSGKAYIVFATQESAQAFVEAFQGYPF--QGNPLVITFSETPQ  111 (127)
T ss_dssp             CCCSSCCCEEEEESSHHHHHHHHHHSTTCCC--TTSCCEEEECCCCC
T ss_pred             cCCCcCCEEEEEECCHHHHHHHHHHHCCCEe--CCCEEEEEEccCcc
Confidence            4678899999999999999999999999999  69999999998654

>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=99.05  E-value=7.4e-11  Score=80.22  Aligned_cols=46  Identities=13%  Similarity=0.061  Sum_probs=37.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+++++|||||+|.+.++|++|++.|||..|  +|+.|.|.++.+...
T Consensus        40 ~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~--~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           40 ANGQSKGFALVGVGSEASSKKLMDLLPKREL--HGQNPVVTPSNKLEH   85 (90)
T ss_dssp             TTCCEEEEEEECC-CHHHHHHHHHHGGGSCS--SSCCCEECCC-----
T ss_pred             CCCccCcEEEEEECCHHHHHHHHHHcCCCee--CCEEEEEEECCCCcc
Confidence            3788899999999999999999999999999  699999999987553

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.04  E-value=2e-10  Score=81.13  Aligned_cols=45  Identities=16%  Similarity=0.186  Sum_probs=40.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|++++|||||+|.+.++|++||+.|||..|  +|+.|.|+++....
T Consensus        43 ~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~--~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           43 RTRKHLGLARVLFTSTRGAKETVKNLHLTSV--MGNIIHAQLDIKGQ   87 (110)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSTTH
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCc
Confidence            3688999999999999999999999999999  69999999997543

>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=99.04  E-value=2.8e-10  Score=75.94  Aligned_cols=45  Identities=24%  Similarity=0.476  Sum_probs=41.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|++|.|+|+.++.
T Consensus        38 ~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~a~~~~   82 (83)
T 3md1_A           38 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWAAKLE   82 (83)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEECCCCC
T ss_pred             CCCCccceEEEEECCHHHHHHHHHHhcCCee--CCcEEEEEecCcCC
Confidence            3677899999999999999999999999999  69999999998653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=3.7e-10  Score=78.42  Aligned_cols=47  Identities=23%  Similarity=0.476  Sum_probs=42.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++.++|||||+|.++++|++||+.||+..|  +|+.|.|+|+.++...
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           49 ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEI--DGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCCCCSS
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEEecCCCCC
Confidence            3677899999999999999999999999999  6999999999976653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.02  E-value=4.8e-10  Score=76.96  Aligned_cols=47  Identities=19%  Similarity=0.304  Sum_probs=42.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++.++|||||+|.++++|++|++.|||..|  +|++|.|+|+.+....
T Consensus        43 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           43 DTGNSKGYAFINFASFDASDAAIEAMNGQYL--CNRPITVSYAFKKDSK   89 (96)
T ss_dssp             TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE--TTEECEEEESCCCCCC
T ss_pred             CCCCcCeEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEecccCCC
Confidence            4677899999999999999999999999999  6999999999876543

>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=99.01  E-value=7.5e-10  Score=76.43  Aligned_cols=46  Identities=28%  Similarity=0.265  Sum_probs=42.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|++|.|+++......
T Consensus        46 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           46 TKKPKGFAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             TCCCCSEEEEEESSHHHHHHHHHHTTTEES--SSCEEEEEECCCCSTT
T ss_pred             CCCcCeEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcCCCccc
Confidence            677899999999999999999999999999  6999999999987654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.01  E-value=8.6e-10  Score=78.34  Aligned_cols=47  Identities=23%  Similarity=0.399  Sum_probs=42.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH   52 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~   52 (240)
                      ++.++|||||+|.+.++|++||+.|||..|  +|+.|.|+|+.......
T Consensus        53 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           53 TGKSKGYGFVSFFNKWDAENAIQQMGGQWL--GGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECEEEESSCCCCCS
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEccCCCCCC
Confidence            677899999999999999999999999998  69999999999766543

>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=99.01  E-value=3.4e-10  Score=76.19  Aligned_cols=43  Identities=26%  Similarity=0.468  Sum_probs=38.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.|.|+|+.++
T Consensus        44 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~k   86 (87)
T 3bs9_A           44 TGKSKGYGFVSFFNKWDAENAIQQMGGQWL--GGRQIRTNWATRK   86 (87)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEEC--
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEecCCC
Confidence            677899999999999999999999999998  6999999999854

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=5.6e-10  Score=77.53  Aligned_cols=47  Identities=34%  Similarity=0.392  Sum_probs=42.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++.++|||||+|.+.++|++|++.||+..|  +|+.|.|+|+.+....
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           49 ETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             SSCCCSSEEEECCSSHHHHHHHHHHHTTEEE--TTEEEEEEECCCCCCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEeCCCCCCC
Confidence            3567899999999999999999999999999  6999999999976654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=9.2e-10  Score=75.34  Aligned_cols=46  Identities=20%  Similarity=0.320  Sum_probs=41.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++|++.|||..|  +|++|.|+++..+...
T Consensus        43 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           43 TGRSKGYGFITFSDSECARRALEQLNGFEL--AGRPMRVGHVTERLDG   88 (95)
T ss_dssp             SCCCCSEEEEEESCHHHHHHHHHHHTTCCS--SSSCCEEEESSCCCCC
T ss_pred             CCceeeEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEEcccccCC
Confidence            577899999999999999999999999999  6999999999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.99  E-value=6.1e-10  Score=77.49  Aligned_cols=46  Identities=43%  Similarity=0.556  Sum_probs=41.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      |+.++|||||+|.+.++|++|++.|||..|  +|+.|.|+++......
T Consensus        51 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   96 (103)
T 2dnm_A           51 TKAPRGFAFVRFHDRRDAQDAEAAMDGAEL--DGRELRVQVARYGRRD   96 (103)
T ss_dssp             SCSBCSCEEEEESSSSHHHHHHHHHSSCCB--TTBCCEEEECSSCCSC
T ss_pred             CCCCCeEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEECCcCCCC
Confidence            577899999999999999999999999998  6999999999976543

>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=98.98  E-value=8.6e-10  Score=76.99  Aligned_cols=46  Identities=26%  Similarity=0.341  Sum_probs=42.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|++.||+..|  +|++|.|+++.+....
T Consensus        53 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           53 TGQHQGYGFVEFLSEEDADYAIKIMDMIKL--YGKPIRVNKASAHNKN   98 (105)
T ss_dssp             SCSBCSCEEEEESSHHHHHHHHHHSSSCBC--SSCBCEEEETTTTSCC
T ss_pred             CCcCCcEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEECCCCCcC
Confidence            677899999999999999999999999998  6999999999976643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=6.8e-10  Score=77.26  Aligned_cols=46  Identities=37%  Similarity=0.629  Sum_probs=41.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.|||..|  +|+.|.|+|+.+....
T Consensus        53 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           53 TGQSKGFAFISFHRREDAARAIAGVSGFGY--DHLILNVEWAKPSTNS   98 (103)
T ss_dssp             SCSEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECEEEESSCCCCS
T ss_pred             CCceeeEEEEEECCHHHHHHHHHHcCCCee--CCcEEEEEECCCCCCC
Confidence            677899999999999999999999999999  6999999999976543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.98  E-value=6.8e-10  Score=76.85  Aligned_cols=45  Identities=18%  Similarity=0.352  Sum_probs=40.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +++++|||||+|.+.++|++|++.|||..|  +|+.|.|+|+.+...
T Consensus        54 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           54 AGKPKGLAYVEYENESQASQAVMKMDGMTI--KENIIKVAISNSGPS   98 (100)
T ss_dssp             TSCEEEEEEEEESSHHHHHHHHHHHTTEES--SSCEEEEEECCCCSC
T ss_pred             CCCEEeEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCCCC
Confidence            577899999999999999999999999998  699999999987543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=8.1e-10  Score=78.21  Aligned_cols=47  Identities=28%  Similarity=0.246  Sum_probs=42.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .+++++|||||+|.+.++|++||+.|||..|  .|+.|.|+++......
T Consensus        60 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           60 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDF--QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE--TTEECEEECSSCCCCS
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHcCCCcc--CCCEEEEEECCCCCCC
Confidence            4677899999999999999999999999999  6999999999976544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.98  E-value=4.1e-10  Score=78.11  Aligned_cols=43  Identities=23%  Similarity=0.248  Sum_probs=39.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCC-ceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDR-RRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g-~~l~v~~a~~~   48 (240)
                      |++++|||||+|.+.++|++||+.|||..|  +| +.|.|.++.+.
T Consensus        50 tg~~kG~afV~f~~~~~A~~Ai~~lng~~~--~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           50 TGKTKGFLFVECGSMNDAKKIIKSFHGKRL--DLKHRLFLYTMKDV   93 (100)
T ss_dssp             TTEECSEEEEEESSHHHHHHHHHHHTTCBS--SSSCBCEEEESHHH
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCccc--CCCeEEEEEECchh
Confidence            678899999999999999999999999999  57 99999999753

>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=98.98  E-value=7.1e-10  Score=76.16  Aligned_cols=45  Identities=24%  Similarity=0.399  Sum_probs=41.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.|.|.++.+...
T Consensus        40 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           40 TGRSKGYAFIEFRDLESSASAVRNLNGYQL--GSRFLKCGYSSNSDI   84 (96)
T ss_dssp             TCCBCSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSCSSG
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEEcCCCCC
Confidence            577899999999999999999999999999  699999999997653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=7.6e-10  Score=76.72  Aligned_cols=46  Identities=20%  Similarity=0.312  Sum_probs=41.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+++++|||||+|.++++|++||..||+..|  +|+.|.|+|+.+...
T Consensus        48 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           48 QNGKSKGYAFIEFASFEDAKEALNSCNKREI--EGRAIRLELQGPRGS   93 (101)
T ss_dssp             SSSCBCSEEEEECSSHHHHHHHHHHTSSEEE--TTEEEEEEECSSCCC
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHHhCCCEe--CCeEEEEEEcCCCCC
Confidence            3677899999999999999999999999999  699999999987654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=9.2e-10  Score=76.59  Aligned_cols=46  Identities=24%  Similarity=0.374  Sum_probs=41.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.||+..|  +|+.|.|.|+.++...
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIV--ATKPLYVALAQRKEER   96 (103)
T ss_dssp             SSSEEEEEEEEESSHHHHHHHHHHHTTCBS--SSSBCEEEECSSCCCC
T ss_pred             CCCcCEEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEEecccccC
Confidence            567799999999999999999999999999  6999999999976654

>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=98.97  E-value=1.3e-09  Score=77.65  Aligned_cols=46  Identities=26%  Similarity=0.439  Sum_probs=41.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++|++.|||..|  +|+.|.|+++......
T Consensus        44 ~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           44 TSKSRGFAFITFENPADAKNAAKDMNGKSL--HGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             TTTCCCEEEEECSSHHHHHHHHHHCSSCBC--SSSBCEEEECCCSSCS
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCCCCC
Confidence            677899999999999999999999999999  6999999999976543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=9.7e-10  Score=76.30  Aligned_cols=46  Identities=30%  Similarity=0.471  Sum_probs=41.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.++++|++|++.||+..|  +|++|.|+|+......
T Consensus        50 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   95 (102)
T 1x5s_A           50 TQRSRGFGFVTFENIDDAKDAMMAMNGKSV--DGRQIRVDQAGKSSDN   95 (102)
T ss_dssp             SCSCCSEEEEECSSHHHHHHHHHHHTTCCT--TSCCCEEEEEECCCCC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCCCC
Confidence            567899999999999999999999999998  6999999999976543

>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=98.97  E-value=5.9e-10  Score=78.79  Aligned_cols=42  Identities=24%  Similarity=0.299  Sum_probs=38.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++|||||+|.++++|++||+.|||..|  +|++|.|+|+.++.
T Consensus        61 ~~~G~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           61 GPSASAYVTYIRSEDALRAIQCVNNVVV--DGRTLKASLGTTKY  102 (111)
T ss_dssp             CCCEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEESCCCCS
T ss_pred             CCCeEEEEEECcHHHHHHHHHHhCCCEE--CCEEEEEEeccccc
Confidence            4579999999999999999999999999  69999999999765

>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=98.97  E-value=5.3e-10  Score=74.90  Aligned_cols=42  Identities=36%  Similarity=0.444  Sum_probs=38.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|++|.|+|++
T Consensus        44 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~ak   85 (85)
T 3mdf_A           44 ETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAK   85 (85)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             CCCccccEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcC
Confidence            4667899999999999999999999999999  69999999984

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=8.1e-10  Score=77.71  Aligned_cols=47  Identities=47%  Similarity=0.638  Sum_probs=41.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .+..++|||||+|.+.++|++||+.||+..|  +|++|.|+|+......
T Consensus        56 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~~  102 (109)
T 1x4a_A           56 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEFPRSGRGT  102 (109)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEECCCCCCCC
T ss_pred             ECCCCCcEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEcccCCCC
Confidence            4556799999999999999999999999999  6999999999876543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=7.1e-10  Score=77.55  Aligned_cols=44  Identities=23%  Similarity=0.425  Sum_probs=40.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.|.|+|+.++.
T Consensus        61 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~  104 (106)
T 1p27_B           61 TGYLKGYTLVEYETYKEAQAAMEGLNGQDL--MGQPISVDWCFVRG  104 (106)
T ss_dssp             TSSEEEEEEEEESCHHHHHHHHHHHTTCBS--SSSBCEEEESEESS
T ss_pred             CCceeeEEEEEECCHHHHHHHHHHhcCCEE--CCcEEEEEeecCCC
Confidence            577899999999999999999999999998  69999999998653

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=9.2e-10  Score=78.14  Aligned_cols=46  Identities=20%  Similarity=0.324  Sum_probs=42.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++||+.|||..|  +|+.|.|+|+......
T Consensus        63 ~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~v~~a~~~~~~  108 (115)
T 2cpx_A           63 TGRMRGQAFITFPNKEIAWQALHLVNGYKL--YGKILVIEFGKNKKQR  108 (115)
T ss_dssp             CSSSCSEEEEECSSHHHHHHHHHHSTTCBC--SSCBCEEEECCCCSCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEEccCCCCC
Confidence            677899999999999999999999999999  6999999999976654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.96  E-value=5.2e-10  Score=77.27  Aligned_cols=44  Identities=18%  Similarity=0.135  Sum_probs=38.7

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +.||||||+|++.++|.+|++.||+..+.+.|++|.|+|++.+.
T Consensus        55 ~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            46899999999999999999999998744479999999998653

>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=98.95  E-value=8.5e-10  Score=76.02  Aligned_cols=44  Identities=25%  Similarity=0.347  Sum_probs=39.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+++++|||||+|.++++|++||+.|||..|  +|+.|.|+++...
T Consensus        52 ~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~a~~~   95 (98)
T 2cqp_A           52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKLVLGSGP   95 (98)
T ss_dssp             SSSCEEEEEEEEESCHHHHHHHHHHTTTCEE--TTEECEEEESSCS
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCCee--CCeEEEEEEcCCC
Confidence            3667899999999999999999999999999  6999999998753

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.95  E-value=1.3e-09  Score=76.21  Aligned_cols=46  Identities=35%  Similarity=0.491  Sum_probs=41.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhh-CCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGL-DNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l-~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.| |+..|  .|+.|.|+|+.+....
T Consensus        54 ~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--~g~~l~v~~a~~~~~~  100 (107)
T 2cph_A           54 TGAHRGFGFVDFITKQDAKKAFNALCHSTHL--YGRRLVLEWADSEVTV  100 (107)
T ss_dssp             SCSSCSEEEEEESSHHHHHHHHHHHHTCCBS--SSCBCEEEECCCCCCC
T ss_pred             CCCcCceEEEEECCHHHHHHHHHHhccCCeE--CCCEEEEEeCCCCCCC
Confidence            6778999999999999999999999 99999  6999999999976543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.95  E-value=7e-10  Score=76.67  Aligned_cols=42  Identities=29%  Similarity=0.309  Sum_probs=38.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|+.|.|++|.
T Consensus        58 ~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~A~   99 (99)
T 2la6_A           58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEF--SGNPIKVSFAT   99 (99)
T ss_dssp             TTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS--SSSBCEEEECC
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEecC
Confidence            3677899999999999999999999999999  69999999974

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.95  E-value=1.6e-09  Score=74.83  Aligned_cols=45  Identities=20%  Similarity=0.395  Sum_probs=40.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+ ||+..|  +|+.|.|.++.++...
T Consensus        48 ~~~~~g~afV~f~~~~~a~~A~~-~~~~~~--~g~~l~V~~a~~~~~~   92 (99)
T 2dgs_A           48 KQRPRGFGFITFEDEQSVDQAVN-MHFHDI--MGKKVEVKRAEPRDSK   92 (99)
T ss_dssp             TCSCCSEEEEEESSHHHHHHHHH-HCCCBS--SSCBCEEEECCCCCCC
T ss_pred             CCCCCceEEEEECCHHHHHHHHH-hCCCEE--CCeEEEEEECCCCccc
Confidence            67789999999999999999999 999998  6999999999976554

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.95  E-value=8.1e-10  Score=75.46  Aligned_cols=41  Identities=24%  Similarity=0.351  Sum_probs=38.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      ++.++|||||+|.+.++|++|++.||+..|  +|++|.|+||+
T Consensus        54 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~ak   94 (94)
T 2e5h_A           54 TRKSKGVAFILFLDKDSAQNCTRAINNKQL--FGRVIKASIAI   94 (94)
T ss_dssp             SCCCTTCEEEEESCHHHHHHHHHHTTTEEE--TTEEEEEEECC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHcCCCee--CCcEEEEEecC
Confidence            567899999999999999999999999999  69999999984

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.95  E-value=7.6e-10  Score=77.41  Aligned_cols=44  Identities=18%  Similarity=0.317  Sum_probs=40.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCc-eEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRR-RLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~-~l~v~~a~~~   48 (240)
                      .++.++|||||+|.+.++|++|+..|||..|  +|+ +|.|+++...
T Consensus        56 ~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~--~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           56 EDGKTKGYIFLEYASPAHAVDAVKNADGYKL--DKQHTFRVNLFTDF  100 (105)
T ss_dssp             BTTBSCCEEEEEECSSSHHHHHHHHCSSEEC--STTCEEEEECSCCC
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCccc--CCCceEEEEEcchH
Confidence            4678899999999999999999999999999  698 9999999754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.95  E-value=7e-10  Score=76.92  Aligned_cols=45  Identities=22%  Similarity=0.359  Sum_probs=40.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++||+ |||..|  .|+.|.|.++.+...
T Consensus        53 ~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~--~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           53 RTGTNRKFGYVDFESAEDLEKALE-LTGLKV--FGNEIKLEKPKGRDG   97 (101)
T ss_dssp             EEETTTTEEEEEESSHHHHHHHHH-GGGCCB--TTBCCEEECCSCCCC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHh-cCCcEE--CCcEEEEEEcCCCCC
Confidence            357789999999999999999999 999999  699999999987554

>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=98.94  E-value=2.2e-09  Score=75.35  Aligned_cols=46  Identities=37%  Similarity=0.525  Sum_probs=40.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhC--CCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLD--NIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~--g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|+..||  +..|  +|+.|.|+|+.+....
T Consensus        48 ~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~--~g~~l~V~~a~~~~~~   95 (109)
T 2dis_A           48 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQL--WGHQIAVDWAEPEIDV   95 (109)
T ss_dssp             TTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB--TTBCCEEEESCSSCST
T ss_pred             CCCcCcEEEEEecCHHHHHHHHHHhhCCCcee--cCCeEEEEEcCCCCCc
Confidence            56789999999999999999999996  4777  6999999999976653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.94  E-value=8.3e-10  Score=76.05  Aligned_cols=46  Identities=24%  Similarity=0.379  Sum_probs=41.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      |+.++|||||+|.+.++|++|++.|||..|  +|+.|.|+++......
T Consensus        46 t~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   91 (98)
T 2cpf_A           46 VLLSMGFGFVEYKKPEQAQKALKQLQGHTV--DGHKLEVRISERATKP   91 (98)
T ss_dssp             CEEEEEEEEEEESSHHHHHHHHHHSTTCEE--TTEECEEECSSCSSCC
T ss_pred             CcCcccEEEEEECCHHHHHHHHHHhCCCee--CCeEEEEEEccCCCCC
Confidence            347799999999999999999999999999  6999999999876543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=98.94  E-value=4.5e-10  Score=77.23  Aligned_cols=45  Identities=29%  Similarity=0.592  Sum_probs=40.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +++.++|||||+|.+.++|++|+..|||..|  +|+.|.|+|+.+..
T Consensus        46 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           46 RSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPMRIQYAKTDS   90 (97)
T ss_dssp             HHHHHTTCEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSSCC
T ss_pred             cCCCcCcEEEEEeCCHHHHHHHHHHhCCCEE--CCcEEEEEEccCCC
Confidence            3456789999999999999999999999999  69999999998754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.94  E-value=7.4e-10  Score=76.03  Aligned_cols=46  Identities=20%  Similarity=0.352  Sum_probs=41.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++|+..|||..|  +|+.|.|+++.+...
T Consensus        48 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTGEKGG   93 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEE--TTEEEEEEECSSSCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEEcCCCCC
Confidence            4667899999999999999999999999999  699999999986543

>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=98.94  E-value=1.1e-09  Score=77.22  Aligned_cols=45  Identities=20%  Similarity=0.335  Sum_probs=41.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++.++|||||+|.+.++|++|+..|||..|  +|+.|.|.|+.++.
T Consensus        63 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           63 RTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQVDWCFVKG  107 (110)
T ss_dssp             TTSSBCSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEESEESS
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEEcccCC
Confidence            3677899999999999999999999999999  69999999998654

>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=98.94  E-value=9.6e-10  Score=79.89  Aligned_cols=45  Identities=38%  Similarity=0.618  Sum_probs=41.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++.++|||||+|.+.++|++||+.|||..|  +|++|.|+|+.+++
T Consensus        83 ~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i--~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           83 QSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIRVDFSITKR  127 (129)
T ss_dssp             SSSCCCCEEEEEESCHHHHHHHHHHHTTCCS--SSSCCEESCCSSSS
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEecCCC
Confidence            3577899999999999999999999999999  69999999998754

>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=98.93  E-value=9.7e-10  Score=78.09  Aligned_cols=46  Identities=22%  Similarity=0.392  Sum_probs=41.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.||+..|  +|+.|.|+|+.++...
T Consensus        63 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           63 TNLSKCFGFVSYDNPVSAQAAIQSMNGFQI--GMKRLKVQLKRSKNDS  108 (115)
T ss_dssp             SCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEECCCCSCCC
T ss_pred             CCCcCccEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEcCCCCcC
Confidence            677899999999999999999999999999  6999999999976543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=9.4e-10  Score=75.72  Aligned_cols=43  Identities=26%  Similarity=0.319  Sum_probs=39.4

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +.++|||||+|.+.++|++|++.|||..|  +|+.|.|+++.++.
T Consensus        53 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           53 QGPRRRAFLHYPDSAAAQQAVSCLQGLRL--GTDTLRVALARQQR   95 (97)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCCS--SSSCCEEEECCCCC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcCCCC
Confidence            46799999999999999999999999999  69999999998754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.93  E-value=1.3e-09  Score=75.83  Aligned_cols=45  Identities=24%  Similarity=0.484  Sum_probs=40.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++|| .||+..|  +|+.|.|+++.+....
T Consensus        52 ~g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           52 TDKFKGFCYVEFDEVDSLKEAL-TYDGALL--GDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             SCSEEEEEEEEESSHHHHHHHG-GGTTCEE--TTEECEEEECCCCCCC
T ss_pred             CCccceEEEEEECCHHHHHHHH-hhCCCeE--CCeEEEEEEecCCCCC
Confidence            6778999999999999999999 8999999  6999999999976543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=1e-09  Score=75.11  Aligned_cols=42  Identities=38%  Similarity=0.574  Sum_probs=38.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|++|.|+|+..
T Consensus        53 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~   94 (95)
T 2cqc_A           53 SRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIRVSGPSS   94 (95)
T ss_dssp             SSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEECCSC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEecCC
Confidence            567899999999999999999999999999  699999999873

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=2e-09  Score=74.85  Aligned_cols=44  Identities=25%  Similarity=0.459  Sum_probs=39.8

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++|||||+|.+.++|++|+..||+..|  .|+.|.|+|+.+....
T Consensus        53 ~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   96 (103)
T 2cqi_A           53 SNDPYCFVEFYEHRDAAAALAAMNGRKI--LGKEVKVNWATTPSSQ   96 (103)
T ss_dssp             SSCCEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCCTTCC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCCc--CCCeEEEEECCCCccc
Confidence            3689999999999999999999999999  6999999999976543

>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=98.92  E-value=1.6e-09  Score=75.65  Aligned_cols=46  Identities=26%  Similarity=0.309  Sum_probs=41.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCC---ceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDR---RRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g---~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.|||..|.  |   ++|.|+|+......
T Consensus        52 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           52 DGSSKGCAFVKFSSHTEAQAAIHALHGSQTM--PGASSSLVVKFADTDKES  100 (105)
T ss_dssp             SSCEEEEEEEEESSHHHHHHHHHHHSSCCCC--TTCSSCCEEEESCSSCCC
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHHcCCccC--CCCCccEEEEECccCccc
Confidence            5677999999999999999999999999984  5   99999999976654

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.92  E-value=8.8e-10  Score=77.01  Aligned_cols=40  Identities=28%  Similarity=0.431  Sum_probs=37.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ++.++|||||+|.++++|++|+..|||..|  +|++|.|+|+
T Consensus        64 ~~~~~G~~fV~f~~~~~A~~A~~~lng~~~--~Gr~i~v~~s  103 (104)
T 1jmt_A           64 GDHLVGNVYVKFRREEDAEKAVIDLNNRWF--NGQPIHAELS  103 (104)
T ss_dssp             SSSSEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECCEEEC
T ss_pred             CCCccEEEEEEECCHHHHHHHHHHHCCCEE--CCEEEEEEEc
Confidence            456799999999999999999999999999  6999999986

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=1.1e-09  Score=74.33  Aligned_cols=44  Identities=16%  Similarity=0.286  Sum_probs=40.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+++++|||||+|.+.++|++|+. ||+..|  +|+.|.|.++....
T Consensus        45 ~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~--~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           45 AHGNKTGYIFVDFSNEEEVKQALK-CNREYM--GGRYIEVFREKSGP   88 (91)
T ss_dssp             TTSCEEEEEEEECSSHHHHHHHHH-SCSEEE--TTEEEEEEEESSCC
T ss_pred             CCCCCceEEEEEECCHHHHHHHHH-hCCcee--CCcEEEEEECCcCC
Confidence            367789999999999999999999 999999  69999999998654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.92  E-value=1.2e-09  Score=76.38  Aligned_cols=41  Identities=22%  Similarity=0.125  Sum_probs=38.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +.++|||||+|.++++|++|+..|||..|  +|+.|.|.++..
T Consensus        53 ~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~--~Gr~i~v~~a~~   93 (105)
T 2pe8_A           53 DDEAVRIFLEFERVESAIKAVVDLNGRYF--GGRVVKACFYNL   93 (105)
T ss_dssp             TTTSEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCH
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHHCCCEE--CCcEEEEEEcCH
Confidence            57799999999999999999999999999  699999999974

>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=98.91  E-value=1.1e-09  Score=75.01  Aligned_cols=42  Identities=24%  Similarity=0.304  Sum_probs=38.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++.++|||||+|.++++|++||+.||+..|  +|++|.|+++.
T Consensus        52 ~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~gr~l~v~~a~   93 (95)
T 2ek1_A           52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKLSGPS   93 (95)
T ss_dssp             TTSCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEECCC
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHHhCCCeE--CCcEEEEEecc
Confidence            3567899999999999999999999999999  69999999886

>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=98.91  E-value=1.1e-09  Score=76.94  Aligned_cols=43  Identities=21%  Similarity=0.376  Sum_probs=39.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|++|.|+++.++
T Consensus        64 ~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i--~g~~l~V~~a~~k  106 (108)
T 2jrs_A           64 TGRSKGYGFITFSDSECAKKALEQLNGFEL--AGRPMKVGHVTER  106 (108)
T ss_dssp             TTEEEEEEEEEESCHHHHHHHHHHHTTCCS--SSSCCEEECSCSS
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEcccC
Confidence            567799999999999999999999999998  6999999999865

>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=98.91  E-value=1.6e-09  Score=78.17  Aligned_cols=46  Identities=22%  Similarity=0.388  Sum_probs=41.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.|||..|  +|+.|.|+|+......
T Consensus        60 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           60 TGYLKGYTLVEYETYKEAQAAMEGLNGQDL--MGQPISVDWCFVRGPP  105 (126)
T ss_dssp             TSSBCSCEEEEESSHHHHHHHHHHHTTCBS--SSSBCEEEESEESSSC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCee--CCeEEEEEEecCCCCC
Confidence            677899999999999999999999999999  6999999999865543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.91  E-value=1.2e-09  Score=74.31  Aligned_cols=46  Identities=24%  Similarity=0.311  Sum_probs=41.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++|++.||+..|  +|+.|.|+++.+...
T Consensus        43 ~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~a~~~~~   88 (92)
T 2dgv_A           43 ENGKSKGCGVVKFESPEVAERACRMMNGMKL--SGREIDVRIDRNASG   88 (92)
T ss_dssp             SSSCEEEEEEEEESSHHHHHHHHHHHTTCCB--TTBCCCCEECSCCSS
T ss_pred             cCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcCCCCC
Confidence            3667899999999999999999999999999  699999999987553

>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=98.90  E-value=2.9e-09  Score=75.00  Aligned_cols=46  Identities=24%  Similarity=0.358  Sum_probs=41.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhC------CCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLD------NIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~------g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||+.||      +..|  +|+.|.|.|+.+....
T Consensus        53 ~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~--~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           53 TEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--DGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--SSCEEEEECCCCCCCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE--cCEEEEEEECCCCccC
Confidence            56789999999999999999999999      9888  6999999999976543

>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=98.90  E-value=2.3e-09  Score=74.70  Aligned_cols=44  Identities=23%  Similarity=0.420  Sum_probs=40.4

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +.++|||||+|.+.++|++|| .||+..|  +|+.|.|+++.++...
T Consensus        54 g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           54 ERLKGFGYAEFEDLDSLLSAL-SLNEESL--GNKRIRVDVADQAQDK   97 (104)
T ss_dssp             TSBCSCEEEEESSHHHHHHHH-GGGTCEE--TTEECEEEECCCCCCC
T ss_pred             CCcCeEEEEEECCHHHHHHHH-hcCCCEe--CCcEEEEEEccCCCCC
Confidence            778999999999999999999 8999999  6999999999976654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.90  E-value=1.5e-09  Score=76.71  Aligned_cols=41  Identities=22%  Similarity=0.370  Sum_probs=37.7

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +++|||||+|.+.++|++||+.|||..|  +|+.|.|+++...
T Consensus        65 ~~rGfaFV~F~~~e~A~~Ai~~lng~~l--~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           65 DFDGTGALEFPSEEILVEALERLNNIEF--RGSVITVERDDNP  105 (111)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHTTTEEE--TTEEEEEEESCC-
T ss_pred             CCCCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEECCCC
Confidence            5799999999999999999999999999  6999999999754

>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=98.89  E-value=1.3e-09  Score=75.83  Aligned_cols=45  Identities=29%  Similarity=0.480  Sum_probs=41.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.|.|+|+.....
T Consensus        46 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~   90 (104)
T 1p1t_A           46 TGKPKGYGFCEYQDQETALSAMRNLNGREF--SGRALRVDNAASEKN   90 (104)
T ss_dssp             TTEEEEEEEEECSCHHHHHHHHHHSSSBSC--SSSCBEEEETTCTTH
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEeCCCccc
Confidence            667799999999999999999999999999  699999999987553

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.89  E-value=1.8e-09  Score=75.21  Aligned_cols=46  Identities=17%  Similarity=0.273  Sum_probs=41.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCc-ccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIP-FGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~-~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|++.||+.. |  +|++|.|.++.+....
T Consensus        47 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--~g~~l~v~~a~~~~~~   93 (104)
T 2dhg_A           47 TGVSKGYGFVKFTDELEQKRALTECQGAVGL--GSKPVRLSVAIPKASR   93 (104)
T ss_dssp             TCCEEEEEEEEESCHHHHHHHHHHTTTCCSS--SSSCCCCCBCCCCCSC
T ss_pred             CCCccceEEEEECCHHHHHHHHHHccCCccc--CCEeEEEEEccCCCcC
Confidence            67789999999999999999999999998 8  6999999999866543

>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=98.89  E-value=1.3e-09  Score=75.57  Aligned_cols=42  Identities=26%  Similarity=0.425  Sum_probs=39.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +++++|||||+|.+.++|++|+ .|||..|  +|+.|.|+++.+.
T Consensus        57 ~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~--~g~~l~V~~a~~~   98 (100)
T 2j76_E           57 PERLKGFGYAEFEDLDSLLSAL-SLNEESL--GNRRIRVDVADQA   98 (100)
T ss_dssp             TCCCCSCEEEEECCHHHHHHHH-HTTTCCB--TTBCCCCEECCCS
T ss_pred             CCccCeEEEEEECCHHHHHHHH-hcCCCEE--CCeEEEEEeccCC
Confidence            6788999999999999999999 8999999  6999999999864

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=98.89  E-value=1.6e-09  Score=75.86  Aligned_cols=41  Identities=29%  Similarity=0.428  Sum_probs=38.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      +++++|||||+|.+.++|++|++.|||..|  +|+.|.|+++.
T Consensus        66 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~  106 (107)
T 3ulh_A           66 SGRSLGTADVHFERKADALKAMKQYNGVPL--DGRPMNIQLVT  106 (107)
T ss_dssp             TSCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEEC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEEeC
Confidence            677899999999999999999999999999  69999999986

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=3.3e-09  Score=73.69  Aligned_cols=44  Identities=30%  Similarity=0.381  Sum_probs=40.0

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++|||||+|.+.++|++||..||+..|  +|+.|.|+++.+....
T Consensus        53 ~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   96 (103)
T 2cq3_A           53 GSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVNNATARVMT   96 (103)
T ss_dssp             TTCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEECCSSCCC
T ss_pred             CCcEEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcccCCCC
Confidence            3699999999999999999999999999  6999999999976544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.88  E-value=5.1e-09  Score=74.11  Aligned_cols=45  Identities=20%  Similarity=0.172  Sum_probs=40.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +++++|||||+|.+.++|++||+.||+..|  +|+.|.|+++.....
T Consensus        52 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~   96 (114)
T 2do0_A           52 DGKSRGIGTVTFEQSIEAVQAISMFNGQLL--FDRPMHVKMDERALP   96 (114)
T ss_dssp             TCSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSCCCC
T ss_pred             CCCeeeEEEEEECCHHHHHHHHHHhCCCEe--CCCEEEEEEcccCCC
Confidence            567799999999999999999999999999  699999999986543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=2.3e-09  Score=75.52  Aligned_cols=42  Identities=31%  Similarity=0.427  Sum_probs=38.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +.++|||||+|.+.++|++|++.|||..|  +|+.|.|+++.++
T Consensus        66 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~  107 (109)
T 2err_A           66 RGSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVNNATAR  107 (109)
T ss_dssp             TBCTTEEEEECCCSHHHHHHHHHHTTCEE--TTEECEEEECCCS
T ss_pred             CCCceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCC
Confidence            34699999999999999999999999999  6999999999864

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=98.87  E-value=1.4e-09  Score=80.28  Aligned_cols=46  Identities=22%  Similarity=0.333  Sum_probs=42.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++||..|||..|  +|+.|.|+|+.....
T Consensus        87 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~V~~a~~~~~  132 (143)
T 3egn_A           87 KEGRMKGQAFIGLPNEKAAAKALKEANGYVL--FGKPMVVQFARSARP  132 (143)
T ss_dssp             EETTTEEEEEEECSSHHHHHHHHHHHTTBEE--TTEECEEEECCCSCC
T ss_pred             cCCCcccEEEEEeCCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCCC
Confidence            5788899999999999999999999999999  699999999986543

>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=98.87  E-value=2.2e-09  Score=72.27  Aligned_cols=41  Identities=22%  Similarity=0.394  Sum_probs=38.2

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++|||||+|.+.++|++|++.|||..|  +|+.|.|+++.+..
T Consensus        46 ~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           46 SKGYAYVEFENPDEAEKALKHMDGGQI--DGQEITATAVLAPW   86 (88)
T ss_dssp             ECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEECCCC
T ss_pred             CCcEEEEEEecHHHHHHHHHHcCCCeE--CCeEEEEEECCCCC
Confidence            799999999999999999999999999  69999999997643

>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=98.87  E-value=2.4e-09  Score=72.31  Aligned_cols=43  Identities=33%  Similarity=0.495  Sum_probs=39.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++|+ .|||..|  +|+.|.|+++.+..
T Consensus        44 ~~~~~g~afV~f~~~~~a~~a~-~~~g~~~--~g~~l~V~~a~~~~   86 (89)
T 3ucg_A           44 SGHPKGFAYIEFSDKESVRTSL-ALDESLF--RGRQIKVIPKRTNR   86 (89)
T ss_dssp             SSSCCEEEEEEESSTHHHHHHG-GGTTCEE--TTEECEEEETTTTS
T ss_pred             CCCcceEEEEEECCHHHHHHHH-hcCCCEE--CCcEEEEEEccCCC
Confidence            6788999999999999999999 8999999  69999999998643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.87  E-value=1.7e-09  Score=81.18  Aligned_cols=43  Identities=14%  Similarity=0.134  Sum_probs=40.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|++++|||||+|.+.++|++||+.|||..|  +|+.|.|.++..
T Consensus        94 ~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~--~Gr~l~V~~a~~  136 (156)
T 3n9u_C           94 ANGQSKGYAEVVVASENSVHKLLELLPGKVL--NGEKVDVRPATR  136 (156)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHHHSTTCEE--TTEECEEEECCH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCEE--CCeEeEEEEcCC
Confidence            4788899999999999999999999999999  699999999974

>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=98.87  E-value=2.8e-09  Score=73.22  Aligned_cols=40  Identities=25%  Similarity=0.299  Sum_probs=37.5

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +|||||+|.+.++|++|++.|||..|  +|++|.|+++.+..
T Consensus        52 rg~afV~f~~~~~A~~Ai~~l~g~~~--~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           52 QLKAVVQMENLQDAIGAVNSLHRYKI--GSKKILVSLATGAS   91 (96)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCCSS
T ss_pred             CeEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEEcCCCC
Confidence            89999999999999999999999999  69999999998654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.87  E-value=3.1e-09  Score=78.04  Aligned_cols=46  Identities=30%  Similarity=0.490  Sum_probs=41.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++||+.|||..|  +|+.|.|+++......
T Consensus        80 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           80 TRQSRGYGFVKFQSGSSAQQAIAGLNGFNI--LNKRLKVALAASGHQR  125 (139)
T ss_dssp             TTEEEEEEEEEESSHHHHHHHHHHTTTEEC--SSCEEEEEESSCCCCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCCCC
Confidence            567799999999999999999999999998  6999999999976554

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=3e-09  Score=73.14  Aligned_cols=44  Identities=25%  Similarity=0.271  Sum_probs=39.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++|||||+|.+.++|++||..|||..|  +|++|.|+|+.+....
T Consensus        47 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           47 PPRNCAFVTYEKMESADQAVAELNGTQV--ESVQLKVNIARKQPML   90 (97)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHTTTEEE--TTEEEEEECCSSCCCC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEECCCCCCC
Confidence            5699999999999999999999999999  6999999999876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.86  E-value=1.6e-09  Score=74.71  Aligned_cols=44  Identities=20%  Similarity=0.332  Sum_probs=40.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCce----EEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRR----LSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~----l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.    |.|+|+.+..
T Consensus        48 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~~~~~l~v~~a~~~~   95 (99)
T 2div_A           48 TGIPAGYCFVEFADLATAEKCLHKINGKPL--PGATPAKRFKLNYATYSG   95 (99)
T ss_dssp             SCCEEEEEEEECSCHHHHHHHHHTTTTSEE--SSCSSCEECCEEETTCCS
T ss_pred             CCCcCCEEEEEeCCHHHHHHHHHHHcCCcc--CCCCcceeEEEeecCCCC
Confidence            677899999999999999999999999999  6888    9999998654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=98.86  E-value=2e-09  Score=73.68  Aligned_cols=42  Identities=24%  Similarity=0.278  Sum_probs=38.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ++.++|||||+|.++++|++|++.||+..|  +|++|.|+|+..
T Consensus        53 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~   94 (95)
T 2ywk_A           53 EGKPKSFGFVCFKHPESVSYAIALLNGIRL--YGRPINVSGPSS   94 (95)
T ss_dssp             TSCEEEEEEEEESSTHHHHHHHHHHTTCEE--TTEECEEECCCC
T ss_pred             CCCCceEEEEEECCHHHHHHHHHHhCCCEE--CCCEEEEEEcCC
Confidence            466799999999999999999999999999  699999999863

>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=98.86  E-value=3.9e-09  Score=73.71  Aligned_cols=48  Identities=21%  Similarity=0.113  Sum_probs=41.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCccc-CCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFG-YDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~-~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++|++.||+..++ ..|++|.|.++..+...
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~   99 (106)
T 2dgp_A           51 TGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG   99 (106)
T ss_dssp             SCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccccc
Confidence            6778999999999999999999999998752 13799999999976543

>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=98.86  E-value=4.2e-09  Score=79.00  Aligned_cols=46  Identities=43%  Similarity=0.614  Sum_probs=42.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|+..|||..|  +|++|.|.|+.+....
T Consensus       108 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A          108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMARYGRPP  153 (158)
T ss_dssp             CTTSCCEEEEEESBHHHHHHHHHHSTTEES--SSSEEEEEEECCSSCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCCCC
Confidence            788999999999999999999999999998  6999999999976543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.86  E-value=4.2e-09  Score=75.81  Aligned_cols=46  Identities=26%  Similarity=0.340  Sum_probs=41.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|+.|.|+++......
T Consensus        72 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~~  117 (124)
T 2kt5_A           72 SGRSLGTADVHFERRADALKAMKQYKGVPL--DGRPMDIQLVASQIDL  117 (124)
T ss_dssp             SSSCCSEEEEEESSHHHHHHHHHHHTTEES--SSCEEEEEEECCTTCC
T ss_pred             CCCEeeEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEEeCCCCCC
Confidence            677899999999999999999999999998  6999999999875543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.86  E-value=1e-09  Score=72.93  Aligned_cols=38  Identities=21%  Similarity=0.419  Sum_probs=34.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCc-eEEE
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRR-RLSV   42 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~-~l~v   42 (240)
                      .+++++|||||+|.+.++|++|++.|||..|  +|+ +|.|
T Consensus        42 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~--~g~~~l~V   80 (81)
T 2krb_A           42 EDGKTKGYIFLEYASPAHAVDAVKNADGYKL--DKQHTFRV   80 (81)
T ss_dssp             BTTBCCCEEEEEESSHHHHHHHHTTSSSCCC--SSSSCCCC
T ss_pred             CCCcEeEEEEEEECCHHHHHHHHHHhcCccc--CCceeEEe
Confidence            4778899999999999999999999999999  588 8876

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.85  E-value=2.8e-09  Score=74.53  Aligned_cols=40  Identities=25%  Similarity=0.345  Sum_probs=37.4

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++|||||+|.++++|++|+..|||..|  +|++|.|.|+..
T Consensus        57 ~~~G~~fV~f~~~~~A~~Ai~~lnG~~f--~GR~i~v~~~~~   96 (105)
T 3v4m_A           57 PGCGKIFVEFTSVFDCQKAMQGLTGRKF--ANRVVVTKYCDP   96 (105)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEECH
T ss_pred             CCcEEEEEEECCHHHHHHHHHHhCCCEe--CCCEEEEEEeCH
Confidence            5799999999999999999999999999  799999999864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.85  E-value=2e-09  Score=70.24  Aligned_cols=39  Identities=18%  Similarity=0.280  Sum_probs=36.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ++.++|||||+|.++++|++|++ ||+..|  +|++|.|++|
T Consensus        37 ~~~~~g~afV~f~~~~~a~~a~~-~~~~~~--~g~~l~v~~A   75 (75)
T 2mss_A           37 TNRHRGFGFVTFESEDIVEKVCE-IHFHEI--NNKMVECKKA   75 (75)
T ss_dssp             STTSCBEEEEECSCHHHHHHHHS-SSCCCS--SSCCCEEECC
T ss_pred             CCCcCcEEEEEECCHHHHHHHHH-CCCCEE--CCEEEEEEeC
Confidence            67789999999999999999998 999999  6999999986

>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=98.85  E-value=3.4e-09  Score=79.43  Aligned_cols=45  Identities=27%  Similarity=0.523  Sum_probs=41.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++||+.||+..|  +|++|.|+|+.+...
T Consensus        77 ~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           77 KKTACGFCFVEYYSRADAENAMRYINGTRL--DDRIIRTDWDAGFKE  121 (156)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHTTTSEE--TTEECEEEEESCCCT
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCCC
Confidence            577899999999999999999999999999  699999999987554

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=2.8e-09  Score=72.08  Aligned_cols=42  Identities=19%  Similarity=0.207  Sum_probs=38.5

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .|||||+|.+.++|++|++.|||..|  .|++|.|.||+.....
T Consensus        46 gG~AfV~F~~~esA~~A~~~l~G~~l--~gr~i~v~~A~~~sd~   87 (96)
T 2diu_A           46 GCSAILRFINQDSAERAQKRMENEDV--FGNRIIVSFTPKNREL   87 (96)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCCS--SSSCCEEESSCCSCCC
T ss_pred             cCEEEEEECCHHHHHHHHHHhcCCcc--CCceEEEEecCCCcce
Confidence            39999999999999999999999999  4999999999976654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=5.2e-09  Score=70.88  Aligned_cols=42  Identities=29%  Similarity=0.448  Sum_probs=38.7

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +|||||+|.+.++|++|++.||+..|  +|++|.|+|+.+....
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKL--HGVNINVEASKNKSKA   83 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBC--SSCBCEEECSSCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCcc--CCcEEEEEECCCCCCC
Confidence            79999999999999999999999998  6999999999976653

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=3.7e-09  Score=72.03  Aligned_cols=44  Identities=25%  Similarity=0.434  Sum_probs=39.4

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCC-CcccCCCceEEEEeccCCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDN-IPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g-~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++|||||+|.+.++|++|++.||| ..|  +|++|.|+|+.++...
T Consensus        42 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~--~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           42 LKSGYAFVDYPDQNWAIRAIETLSGKVEL--HGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEE--TTEECEEEECCCCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHccCCeeE--CCEEEEEEEccCcccc
Confidence            3589999999999999999999999 888  6999999999876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=98.84  E-value=2.5e-09  Score=72.25  Aligned_cols=41  Identities=22%  Similarity=0.295  Sum_probs=37.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +++|||||+|.++++|++|++.|||..|  +|++|.|+|+...
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~a~~~   78 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSF--RGKDLIVQLQPTD   78 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEE--TTEEEEEEECCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeE--CCcEEEEEEcCCC
Confidence            5689999999999999999999999999  6999999999753

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.84  E-value=2e-09  Score=76.71  Aligned_cols=42  Identities=24%  Similarity=0.414  Sum_probs=38.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .+++++|||||+|.+.++|++|++.|||..|  +|+.|.|+|++
T Consensus        77 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~ak  118 (118)
T 2khc_A           77 QTSLSKCFGFVSFDNPDSAQVAIKAMNGFQV--GTKRLKVQLKK  118 (118)
T ss_dssp             SSSCCCCEEEEEEESSHHHHHHHHHCCCCEE--TTEECCEEEC-
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEecC
Confidence            3677899999999999999999999999999  69999999974

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.83  E-value=4.9e-09  Score=73.15  Aligned_cols=45  Identities=16%  Similarity=0.227  Sum_probs=37.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .||||||+|++.++|++|++.|++..+.+.|++|.|+|+..+...
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            489999999999999999999987643237999999999876543

>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=98.83  E-value=2.2e-09  Score=72.69  Aligned_cols=44  Identities=30%  Similarity=0.464  Sum_probs=37.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.+ |++|+..|||..|  +|++|.|++|.+...
T Consensus        39 ~~~~~g~afV~f~~~~-a~~a~~~l~g~~~--~g~~l~V~~a~~~~~   82 (90)
T 2ki2_A           39 TKKPKGFGFVEMQEES-VSEAIAKLDNTDF--MGRTIRVTEANPKKS   82 (90)
T ss_dssp             SCCCCEEEEEEECTTH-HHHHHHTSCSSCC--SSSSCSEEEC-----
T ss_pred             CCCcceEEEEEECCHH-HHHHHHHhCCCEE--CCeEEEEEEcCCCCC
Confidence            5778999999999999 9999999999999  699999999986543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.83  E-value=2.9e-09  Score=77.94  Aligned_cols=46  Identities=43%  Similarity=0.614  Sum_probs=41.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +++++|||||+|.+.++|++||+.|||..|  +|++|.|+|+.+....
T Consensus        85 ~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i--~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           85 TKESRGFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMARYGRPP  130 (135)
T ss_dssp             SSSCCSCCEEECSCHHHHHHHHTTTTTCCS--SSSCCEEEECCCCCCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCCCC
Confidence            678899999999999999999999999998  6999999999976543

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.82  E-value=3.2e-09  Score=73.73  Aligned_cols=45  Identities=16%  Similarity=0.118  Sum_probs=37.3

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ..+|||||+|+++++|++||+.||+..+.+.|++|.|+|+.....
T Consensus        50 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           50 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   94 (102)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCC
Confidence            457999999999999999999998754212799999999996543

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.81  E-value=3.3e-09  Score=74.89  Aligned_cols=45  Identities=16%  Similarity=0.189  Sum_probs=37.1

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++|||||+|++.++|++||+.||+..+.+.|++|.|+|+.....
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            468999999999999999999887543222799999999986554

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=98.81  E-value=1.2e-08  Score=70.96  Aligned_cols=44  Identities=14%  Similarity=0.412  Sum_probs=39.6

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRH   52 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~   52 (240)
                      .+|||||+|.+.++|++||+.||+..|  +|+.|.|+|+.+.....
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDL--EGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCCCCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCcc--CCCEEEEEEcCCCcccc
Confidence            378999999999999999999999998  69999999999766543

>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=98.81  E-value=2.6e-09  Score=76.96  Aligned_cols=43  Identities=19%  Similarity=0.147  Sum_probs=39.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+++++|||||+|.+.++|++||+ ||+..|  +|+.|.|.++..+
T Consensus        62 ~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~--~gr~i~V~~a~~~  104 (124)
T 1wel_A           62 PNGKATGEGFVEFRNEADYKAALC-RHKQYM--GNRFIQVHPITKK  104 (124)
T ss_dssp             TTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS--TTSCBEEEEECHH
T ss_pred             CCCCCCeEEEEEECCHHHHHHHHH-hCCCeE--CCcEEEEEECCHH
Confidence            467889999999999999999999 999999  6999999998753

>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=98.81  E-value=3.1e-08  Score=78.48  Aligned_cols=73  Identities=19%  Similarity=0.224  Sum_probs=60.3

Q ss_pred             CCEEEEeccCC----CCCCHHHHHHhhccCCCeEEEEEe------------CCeEEEEecCHHHHHHHHHhcCCCcccCc
Q 026341           65 TKTLFVINFDP----IRTRERDIKRHFEPYGNVLHVRIR------------RNFAFVQFETQEEATKALESTDRSKLVDR  128 (240)
Q Consensus        65 ~~~l~v~nl~~----~~~~~~~l~~~f~~~G~i~~~~~~------------kg~afV~f~~~~~a~~A~~~l~g~~~~g~  128 (240)
                      ...+.+.|+-.    ....+++|.+.|.+||.|..+.|+            +|++||+|.+.++|++|+..|||..++|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            44555555411    233468899999999999999984            47999999999999999999999999999


Q ss_pred             EEEEEEeec
Q 026341          129 VISVEYALK  137 (240)
Q Consensus       129 ~l~v~~a~~  137 (240)
                      .|.|.+...
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999753

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.80  E-value=3.7e-09  Score=75.44  Aligned_cols=41  Identities=22%  Similarity=0.189  Sum_probs=37.8

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +.++|||||+|.++++|.+|+..|||..|  +|+.|.|.|+..
T Consensus        68 ~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f--~GR~i~v~~~~~  108 (118)
T 3ue2_A           68 AEIIVKIFVEFSIASETHKAIQALNGRWF--AGRKVVAEVYDQ  108 (118)
T ss_dssp             CEEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEECH
T ss_pred             CcceEEEEEEECCHHHHHHHHHHHCCCEE--CCcEEEEEEcCh
Confidence            45689999999999999999999999999  799999999864

>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=98.80  E-value=4.1e-09  Score=74.69  Aligned_cols=43  Identities=26%  Similarity=0.281  Sum_probs=39.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++|| .|||..|  +|+.|.|+++....
T Consensus        63 ~g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           63 SRRSKGIAYVEFCEIQSVPLAI-GLTGQRL--LGVPIIVQASQAEK  105 (114)
T ss_dssp             SSSCCCCEEEEESCGGGHHHHH-HHTTEEE--TTEEEEEEEHHHHH
T ss_pred             CCccCcEEEEEeCcHHHHHHHH-HcCCCEe--CCeEEEEEecCCCc
Confidence            5778999999999999999999 8999999  69999999998544

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.80  E-value=5.5e-09  Score=72.07  Aligned_cols=43  Identities=30%  Similarity=0.424  Sum_probs=39.0

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +.+|||||+|.+.++|++|++.|||..|  +|++|.|.|+.++..
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFACHSAS   91 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCB--TTBCCEEEESSCCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEe--CCceEEEEEcCCCCC
Confidence            3589999999999999999999999998  699999999987553

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=8e-09  Score=73.03  Aligned_cols=43  Identities=30%  Similarity=0.374  Sum_probs=39.1

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++|||||+|.+.++|++|+..|||..|  +|++|.|+|+.+...
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWF--GGRQITAQAWDGTTD  104 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEE--TTEECEEEECCSCCC
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEEeCCCCC
Confidence            3699999999999999999999999999  699999999987543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=1.1e-08  Score=72.68  Aligned_cols=44  Identities=23%  Similarity=0.249  Sum_probs=39.2

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +++++|||||+|.+.++|++||+.|++ .|  .|+.|.|+|+.....
T Consensus        55 ~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~--~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           55 TGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKANVNLAYLGAK   98 (116)
T ss_dssp             SCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECEEEESTTTCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHhCCC-cC--CCEEEEEEEcccCCC
Confidence            677899999999999999999999998 66  699999999986543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=6.7e-09  Score=71.64  Aligned_cols=42  Identities=26%  Similarity=0.438  Sum_probs=38.7

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+|||||+|.+.++|++|+..|||..|  +|+.|.|+|+.+...
T Consensus        50 ~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           50 IRDYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAKPVDK   91 (99)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHSSEEE--TTEEEEEECCCCCCC
T ss_pred             eCCeEEEEeCCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCCC
Confidence            489999999999999999999999999  699999999987654

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.79  E-value=6.6e-09  Score=71.39  Aligned_cols=40  Identities=28%  Similarity=0.518  Sum_probs=37.4

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCC--CceEEEEeccCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYD--RRRLSVEWARGER   49 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~--g~~l~v~~a~~~~   49 (240)
                      +|||||+|.+.++|++|++.||+..|  .  |+.|.|+|+.++.
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~--~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPL--GGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBC--SSSSCBCEEEECCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEe--CCCCcEEEEEECCCCC
Confidence            89999999999999999999999998  5  8999999998754

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=98.79  E-value=4.6e-09  Score=79.51  Aligned_cols=46  Identities=20%  Similarity=0.316  Sum_probs=41.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++||..|||..|  .|++|.|.|+.....
T Consensus       109 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A          109 RTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQVDWCFVKGP  154 (165)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEESEECC-
T ss_pred             CCCcEeeEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEecCCCC
Confidence            3677899999999999999999999999999  699999999986554

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=98.78  E-value=8.2e-09  Score=77.51  Aligned_cols=44  Identities=16%  Similarity=0.110  Sum_probs=38.8

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..+|||||+|.+.++|++|++.|||..|+.+++.|.|+|+++..
T Consensus        82 ~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           82 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            35789999999999999999999999996335999999999764

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=98.78  E-value=6.9e-09  Score=71.43  Aligned_cols=40  Identities=20%  Similarity=0.291  Sum_probs=37.1

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ++|||||+|.+.++|++|+..|||..|  +|+.|.|+++...
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMN--FGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEE--TTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEecCCC
Confidence            489999999999999999999999999  6999999999854

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.78  E-value=1e-08  Score=73.71  Aligned_cols=45  Identities=24%  Similarity=0.387  Sum_probs=40.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++|+ .|||..|  +|+.|.|+++.....
T Consensus        73 ~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~~a~~~~~  117 (124)
T 2jwn_A           73 FSGHPKGYAYIEFAERNSVDAAV-AMDETVF--RGRTIKVLPKRTNMP  117 (124)
T ss_dssp             TTSSCEEEEEEEESSHHHHHHHH-TTTTCEE--TTEECEEEESSCCCS
T ss_pred             CCCCcccEEEEEECCHHHHHHHH-hcCCCeE--CCeEEEEEECCCCCC
Confidence            36788999999999999999999 7999999  699999999986543

>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=98.78  E-value=4.3e-09  Score=73.17  Aligned_cols=44  Identities=20%  Similarity=0.140  Sum_probs=39.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++++++|||||+|.++++|++||+ +|+..|  +|+.|.|.++....
T Consensus        50 ~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~--~gr~i~V~~~~~~~   93 (102)
T 1wez_A           50 PDGRVTGEADVEFATHEDAVAAMA-KDKANM--QHRYVELFLNSTAG   93 (102)
T ss_dssp             SSSCEEEEEEEECSSSHHHHHHHT-TSSCCS--SSSCCEEEEECCCC
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHH-hCCCeE--CCcEEEEEECCCCC
Confidence            377889999999999999999995 899988  69999999988654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.78  E-value=2.6e-09  Score=77.71  Aligned_cols=44  Identities=27%  Similarity=0.519  Sum_probs=40.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCC----cccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNI----PFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~----~~~~~g~~l~v~~a~~~~~   50 (240)
                      |++++|||||+|.+. +|++|+..|||.    .|  +|+.|.|+++.+...
T Consensus        63 tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~--~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           63 TQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI--DGKTINVEFAKGSKR  110 (131)
T ss_dssp             SSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG--GGCCCCCEECCCSCC
T ss_pred             CCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC--CCEEEEEEECCCCCC
Confidence            788999999999999 999999999999    87  699999999987654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.77  E-value=5.2e-09  Score=72.92  Aligned_cols=43  Identities=7%  Similarity=0.128  Sum_probs=37.3

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCC--CcccCCCceEEEEeccCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDN--IPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g--~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .||||||+|+++++|++||+.|++  ..|  .|++|.|+|+..+...
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l--~Gr~l~V~~A~~~~~~   95 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIYIQFSNHKELK   95 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEE--TTEECCBCCCSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceE--CCEEEEEEEcCCCCCC
Confidence            489999999999999999998875  566  6999999999876544

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.77  E-value=1.1e-08  Score=71.87  Aligned_cols=42  Identities=21%  Similarity=0.463  Sum_probs=38.7

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +|||||+|.+.++|++|+..|||..|  +|+.|.|.|+......
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTI--EGHVVKCYWGKESPDM  102 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEECCCCCCSS
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEecCCCCCC
Confidence            89999999999999999999999999  6999999999976543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=5.2e-09  Score=72.96  Aligned_cols=46  Identities=17%  Similarity=0.239  Sum_probs=40.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++.++|||||+|.++++|++||+. |+..|  +|+.|.|.++.++...
T Consensus        53 ~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~--~g~~l~V~~a~~~~~~   98 (105)
T 2dh8_A           53 TTNQSRGFGFVKFKDPNCVGTVLAS-RPHTL--DGRNIDPKPCTPRGMQ   98 (105)
T ss_dssp             SSCCEEEEEEEEESSTTHHHHHHHH-CSEEE--TTEEEBCCCSCCSSCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHh-CCCeE--CCEEEEEEEccCCCCC
Confidence            3677899999999999999999998 99988  6999999999976654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=8.2e-09  Score=72.63  Aligned_cols=42  Identities=19%  Similarity=0.150  Sum_probs=37.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ++++++|||||+|.++++|++|| .||+..|  +|+.|.|..+..
T Consensus        51 ~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~--~gr~i~V~~a~~   92 (109)
T 2dnn_A           51 HVGRNNGNGLVKFLSPQDTFEAL-KRNRMLM--IQRYVEVSPATE   92 (109)
T ss_dssp             TTCCCCSEEEEECSSHHHHHHHH-HTTTEEE--TTEEEEEEECCH
T ss_pred             CCCCCCeEEEEEECCHHHHHHHH-hcCCCeE--CCeEEEEEECCc
Confidence            35778999999999999999999 5999998  799999988763

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.76  E-value=6.4e-09  Score=73.06  Aligned_cols=41  Identities=34%  Similarity=0.522  Sum_probs=37.7

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +|||||+|.+.++|++|++.|||..|  +|+.|.|+|+.....
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~  105 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSF--ANQPLEVVYSKLPAK  105 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEESCSCCC-
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEecCCCC
Confidence            89999999999999999999999999  699999999987553

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.76  E-value=5.6e-09  Score=68.41  Aligned_cols=39  Identities=21%  Similarity=0.328  Sum_probs=35.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ++.++|||||+|.+.++|++|++.++ ..|  +|++|.|++|
T Consensus        38 ~~~~~g~afV~f~~~~~a~~a~~~~~-~~~--~g~~l~v~~a   76 (77)
T 1uaw_A           38 TKRSRGFGFVTFMDQAGVDKVLAQSR-HEL--DSKTIDPKVA   76 (77)
T ss_dssp             SSSCSSEEEECCCCTTHHHHHHHTTT-CCC--SSCCCEEEEC
T ss_pred             CCCcCceEEEEEcCHHHHHHHHHhCC-Ccc--CCEEEEEEec
Confidence            67789999999999999999999999 777  6999999987

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=1.3e-08  Score=68.94  Aligned_cols=42  Identities=29%  Similarity=0.457  Sum_probs=38.4

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      +|||||+|.+.++|++|++.|||..|  +|+.|.|+++.+....
T Consensus        43 ~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~   84 (90)
T 2dnp_A           43 KDYAFVHMEKEADAKAAIAQLNGKEV--KGKRINVELSTKGQKK   84 (90)
T ss_dssp             SSCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEESCCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEECCCCCCC
Confidence            78999999999999999999999999  6999999999876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.76  E-value=1.6e-08  Score=68.76  Aligned_cols=42  Identities=38%  Similarity=0.627  Sum_probs=38.4

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++||||+|.+.++|++|+..||+..|  .|+.|.|+++.+....
T Consensus        44 ~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   85 (92)
T 2dgt_A           44 KDYAFVHMERAEDAVEAIRGLDNTEF--QGKRMHVQLSTSRLRT   85 (92)
T ss_dssp             SSEEEEEESCHHHHHHHHHHHTTEEE--TTEEEEEEESSCCCSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEEccCCCCC
Confidence            78999999999999999999999999  6999999999876543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.76  E-value=3.9e-09  Score=73.08  Aligned_cols=40  Identities=30%  Similarity=0.601  Sum_probs=37.3

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++|||||+|.+.++|++|+..|||..|  +|+.|.|.|+.+
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~  100 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPF--QGRNLRTGWGKE  100 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEE--TTEECCCCBCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEeccC
Confidence            4689999999999999999999999999  699999999875

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.75  E-value=6.9e-09  Score=71.20  Aligned_cols=42  Identities=19%  Similarity=0.255  Sum_probs=38.4

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++|||||+|.+.++|++|++.|||..|  .|++|.|+++.....
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMN--FGKKLILEVSSSNAR   85 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSC--BTTTBCEEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCee--CCcEEEEEEcCcCCC
Confidence            389999999999999999999999999  599999999986554

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.75  E-value=7.6e-09  Score=71.78  Aligned_cols=43  Identities=7%  Similarity=0.131  Sum_probs=36.8

Q ss_pred             ccceEEEEeCChhHHHHHHHhhC--CCcccCCCceEEEEeccCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLD--NIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~--g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .+|||||+|++.++|++|++.|+  +..|  .|++|.|+|+......
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~--~Gr~l~V~~a~~~~~~   94 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHL--RNQPIYIQYSNHKELK   94 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEECSCSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceE--CCcEEEEEEcCcccCc
Confidence            48999999999999999999875  5566  6999999999976543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.75  E-value=1.1e-08  Score=71.91  Aligned_cols=44  Identities=20%  Similarity=0.302  Sum_probs=38.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++|+..+ +..|  +|+.|.|.++.+...
T Consensus        63 tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l--~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           63 TKRSRGFGFVTFMDQAGVDKVLAQS-RHEL--DSKTIDPKVAFPRRA  106 (109)
T ss_dssp             TCCCTTCEEEEESSHHHHHHHHHSS-CEEE--TTEEEEEEECCCCCC
T ss_pred             CCCcCcEEEEEECCHHHHHHHHHHC-CCcC--CCEEEEEEEccCCCC
Confidence            5788999999999999999999976 4666  799999999987654

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=98.75  E-value=8.6e-09  Score=72.53  Aligned_cols=42  Identities=24%  Similarity=0.423  Sum_probs=38.3

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++|||||+|.+.++|++|++.||+..|  +|+.|.|+|+.....
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~~  102 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVL--AGQTLDINMAGEPKP  102 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEE--TTEECCEEESCCCCS
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEECCCCCC
Confidence            589999999999999999999999999  699999999986543

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.74  E-value=9.6e-09  Score=72.52  Aligned_cols=42  Identities=29%  Similarity=0.247  Sum_probs=38.3

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++|||||+|.+.++|++||..|||..|  +|+.|.|+|+....
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~   85 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKF--HHVPLYLEWAPIGV   85 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBS--SSSBCEEEEEETTT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCc
Confidence            4689999999999999999999999999  69999999998543

>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=98.74  E-value=5.4e-09  Score=83.42  Aligned_cols=43  Identities=14%  Similarity=0.087  Sum_probs=39.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|++++|||||+|.+.++|++||+.||++.|  +|+.|.|.++..
T Consensus       107 ~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~--~Gr~l~V~~a~~  149 (229)
T 3q2s_C          107 ANGQSKGFALVGVGSEASSKKLMDLLPKREL--HGQNPVVTPVNK  149 (229)
T ss_dssp             TTCCEEEEEEEEESCTTHHHHHHTTSTTSCB--TTBCCEEEECCH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCeE--CCEEeEEEECCC
Confidence            3788999999999999999999999999999  699999999874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=1.2e-08  Score=72.52  Aligned_cols=46  Identities=22%  Similarity=0.263  Sum_probs=40.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .++.++|||||+|.+.++|++||+. ++..|  +|+.|.|+++.++...
T Consensus        64 ~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~--~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           64 ASKRSRGFGFVTFSSMAEVDAAMAA-RPHSI--DGRVVEPKRAVAREES  109 (116)
T ss_dssp             TTSSCCSEEEEECSSHHHHHHHHTS-CSEEE--TTEEEEEECCSSCCCC
T ss_pred             CCCCcCceEEEEeCCHHHHHHHHHh-CCcEE--CCEEEEEEECCCCccC
Confidence            3677899999999999999999997 99888  6999999999976653

>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=98.74  E-value=1.6e-08  Score=70.40  Aligned_cols=44  Identities=18%  Similarity=0.197  Sum_probs=39.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+++++|||||+|.++++|++||.. |+..|  +|+.|.|.++....
T Consensus        52 ~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~--~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           52 FQGRSTGEAFVQFASQEIAEKALKK-HKERI--GHRYIEIFKSSRAE   95 (104)
T ss_dssp             SSSCBCSEEEEEESSHHHHHHHHTT-TTCCS--SSSCCEEEEECTTT
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHh-Ccchh--CCcEEEEEECCHHH
Confidence            3678899999999999999999996 99888  69999999987544

>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=98.73  E-value=7.5e-09  Score=73.41  Aligned_cols=44  Identities=23%  Similarity=0.158  Sum_probs=39.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++++++|||||+|.+.++|++||+. |+..|  +|+.|.|.++..+.
T Consensus        52 ~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~--~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           52 NNGQGLGQALVQFKNEDDARKSERL-HRKKL--NGREAFVHVVTLED   95 (114)
T ss_dssp             TTSSCSSCEEEECSSHHHHHHHGGG-CSEEE--TTEEEEEEEECHHH
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHh-CCCcc--CCeEEEEEECCHHH
Confidence            3678899999999999999999986 99988  69999999998543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.20  E-value=1.2e-09  Score=77.71  Aligned_cols=46  Identities=26%  Similarity=0.271  Sum_probs=41.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++|++.|||..|  +|++|.|+++.++...
T Consensus        53 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           53 TGKLKGEATVSFDDPPSAKAAIDWFDGKEF--SGNPIKVSFATRRADF   98 (116)
Confidence            567899999999999999999999999999  6999999999976544

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.73  E-value=1.6e-08  Score=72.06  Aligned_cols=44  Identities=7%  Similarity=0.123  Sum_probs=37.8

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCC--CcccCCCceEEEEeccCCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDN--IPFGYDRRRLSVEWARGERGRH   52 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g--~~~~~~g~~l~v~~a~~~~~~~   52 (240)
                      .+|||||+|++.++|++|++.|++  ..|  .|++|.|+|+..+....
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l--~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCB--TTBCCEEEECSSSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceE--CCeEEEEEEccCCCCCc
Confidence            489999999999999999999885  466  69999999998766543

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=1.4e-08  Score=71.79  Aligned_cols=45  Identities=13%  Similarity=0.126  Sum_probs=38.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccC------CCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGY------DRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~------~g~~l~v~~a~~~   48 (240)
                      ++.++|||||+|.+.++|++|++.|||..|..      .+++|.|.|+.+.
T Consensus        62 ~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           62 SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            66789999999999999999999999998821      2778999999853

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=2.3e-09  Score=71.79  Aligned_cols=42  Identities=17%  Similarity=0.237  Sum_probs=37.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|+.|+|.++.
T Consensus        42 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~~~~~~~~   83 (85)
T 1x4e_A           42 TTNKCKGYGFVDFDSPSAAQKAVTALKASGV--QAQMAKQSGPS   83 (85)
T ss_dssp             SSCSCCSEEEEEESCHHHHHHHHHHHHHHTC--CEESCCSSCCC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHhcCCeE--eeEEEeecCCC
Confidence            3677899999999999999999999999998  69988877654

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.72  E-value=9.2e-09  Score=68.75  Aligned_cols=38  Identities=29%  Similarity=0.492  Sum_probs=35.2

Q ss_pred             ccceEEEEeCChhHHHHHHHhh-CCCcccCCCceEEEEecc
Q 026341            7 YAGFAFVYFEDDRDAADAIRGL-DNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l-~g~~~~~~g~~l~v~~a~   46 (240)
                      .+|||||+|.+.++|++|+..| ++..|  +|++|.|+|++
T Consensus        47 ~kg~afV~f~~~~~A~~a~~~l~~~~~~--~g~~l~v~~ak   85 (85)
T 2ytc_A           47 RQQCAFIQFATRQAAEVAAEKSFNKLIV--NGRRLNVKWGR   85 (85)
T ss_dssp             GGTEEEEEESSHHHHHHHHHTTTTTCEE--TTEECCEEECC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhcCCeeE--CCCEEEEEecC
Confidence            4899999999999999999999 99988  69999999974

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=1.4e-08  Score=71.76  Aligned_cols=43  Identities=9%  Similarity=0.155  Sum_probs=37.0

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcc---cCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPF---GYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~---~~~g~~l~v~~a~~~~   49 (240)
                      .+|||||+|.+.++|++|++.|||..|   +..|.+|+|.|+....
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCc
Confidence            489999999999999999999999876   2248899999998543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.72  E-value=6.9e-09  Score=74.09  Aligned_cols=42  Identities=24%  Similarity=0.246  Sum_probs=38.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .++++|||||+|.++++|++||+ ||+..|  +|+.|.|.++...
T Consensus        57 ~g~~~G~afV~F~~~~~a~~Al~-~~g~~~--~gr~i~V~~a~~~   98 (118)
T 2db1_A           57 EGRQSGEAFVELESEDDVKLALK-KDRESM--GHRYIEVFKSHRT   98 (118)
T ss_dssp             SSCEEEEEEEEBSSHHHHHHHGG-GTTEEE--TTEEEEEEEECHH
T ss_pred             CCCCCeEEEEEECCHHHHHHHHh-cCCCeE--CCeEEEEEECCHH
Confidence            46789999999999999999999 999998  6999999998743

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.71  E-value=1e-08  Score=71.45  Aligned_cols=41  Identities=15%  Similarity=0.258  Sum_probs=37.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+.++|||||+|.++++|++||. +++..|  +|+.|.|.++..
T Consensus        48 ~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~--~gr~l~V~~~~~   88 (103)
T 1s79_A           48 HKAFKGSIFVVFDSIESAKKFVE-TPGQKY--KETDLLILFKDD   88 (103)
T ss_dssp             TTSCCCEEEEEESSHHHHHHHHT-SSCCCC--TTTTCEEEEHHH
T ss_pred             CCCCccEEEEEECCHHHHHHHHH-cCCCEE--CCEEEEEEEchH
Confidence            36789999999999999999999 999998  699999998874

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.70  E-value=1.5e-08  Score=71.08  Aligned_cols=40  Identities=28%  Similarity=0.318  Sum_probs=37.0

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCC-----ceEEEEeccCCCC
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDR-----RRLSVEWARGERG   50 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g-----~~l~v~~a~~~~~   50 (240)
                      |||||+|.+.++|++||+.||++.|  +|     +.|.|+++.+...
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~~~~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKVDGPRSP   95 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEE--ECTTSCEEEEEEEESSCCSC
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCc--cCCcCcceEEEEEeCCCCCC
Confidence            9999999999999999999999999  58     9999999997554

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.69  E-value=1.3e-08  Score=72.18  Aligned_cols=39  Identities=15%  Similarity=0.148  Sum_probs=36.7

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+|||||+|.+.++|++|+..|||..|  +|+.|.|+|+..
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f--~GR~i~v~~~~~   92 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWF--AGKMITAAYVPL   92 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEEECH
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEEcH
Confidence            489999999999999999999999999  799999999873

>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=98.68  E-value=1.8e-08  Score=67.66  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=35.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .++.++|||||+|.+.++|++|++ +++..|  +|+.|.|++|
T Consensus        48 ~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~--~g~~i~v~~A   87 (87)
T 3s7r_A           48 NTGRSRGFGFILFKDAASVEKVLD-QKEHRL--DGRVIDPKKA   87 (87)
T ss_dssp             TTCCEEEEEEEEESSTHHHHHHHH-SSCEEE--TTEEEEEEEC
T ss_pred             CCCccccEEEEEECCHHHHHHHHH-hCCCEE--CCEEEEEEeC
Confidence            367889999999999999999997 577777  7999999986

>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=98.67  E-value=1.2e-08  Score=71.57  Aligned_cols=42  Identities=19%  Similarity=0.222  Sum_probs=37.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .++++|||||+|.+.++|++||. ||+..|  +|+.|.|.++...
T Consensus        51 ~g~~~G~afV~F~~~~~a~~Al~-~~~~~~--~gr~i~V~~a~~~   92 (107)
T 2lmi_A           51 DGKRRGDALIEMESEQDVQKALE-KHRMYM--GQRYVEVYEINNE   92 (107)
T ss_dssp             TSTTCSEEEEEBSSHHHHHHHHT-TTTCCS--SSSCCCCEECCHH
T ss_pred             CCCEeeEEEEEECCHHHHHHHHH-hCccee--CCeEEEEEECCHH
Confidence            46789999999999999999999 999988  6999999998743

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.66  E-value=2.9e-08  Score=71.29  Aligned_cols=42  Identities=31%  Similarity=0.304  Sum_probs=36.2

Q ss_pred             cce-EEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            8 AGF-AFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         8 kG~-aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|| |||+|.+.++|++|++.|||..|+..++.|.|+||++..
T Consensus        61 ~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            386 999999999999999999999995222699999998764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.66  E-value=2.3e-08  Score=72.25  Aligned_cols=43  Identities=19%  Similarity=0.210  Sum_probs=37.6

Q ss_pred             ccce-EEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGF-AFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~-aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+|| |||+|.+.++|++|++.|||..|+.+++.|.|+|++...
T Consensus        64 ~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           64 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            4688 999999999999999999999996223899999999764

>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=98.66  E-value=1.3e-08  Score=74.57  Aligned_cols=41  Identities=22%  Similarity=0.225  Sum_probs=37.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++++|||||+|.++++|++||+ ||+..|  +|+.|.|.++..
T Consensus        84 ~g~srG~aFV~F~~~e~a~~Al~-~~g~~l--~gr~i~V~~a~~  124 (136)
T 2hgl_A           84 EGRQSGEAFVELGSEDDVKMALK-KDRESM--GHRYIEVFKSHR  124 (136)
T ss_dssp             SSCEEEEEEEECSSHHHHHHHHT-TTEEES--SSSEEEEEECCH
T ss_pred             CCCCCeEEEEEECCHHHHHHHHh-cCCCEE--CCEEEEEEECCh
Confidence            47789999999999999999999 999998  699999998864

>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=98.65  E-value=1.5e-08  Score=65.94  Aligned_cols=39  Identities=13%  Similarity=0.273  Sum_probs=35.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ++.++|||||+|.++++|++|++ +++..|  +|+.|.|.+|
T Consensus        37 ~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~--~g~~l~v~~a   75 (75)
T 1iqt_A           37 TNKRRGFCFITFKEEEPVKKIME-KKYHNV--GLSKCEIKVA   75 (75)
T ss_dssp             CSSSCCCEEEECSSSHHHHHHHT-TSSCCB--TTBCCCEEEC
T ss_pred             CCCcCCEEEEEECCHHHHHHHHH-hCCCeE--CCEEEEEEEC
Confidence            57789999999999999999999 588888  6999999875

>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=98.63  E-value=4.4e-08  Score=67.93  Aligned_cols=44  Identities=18%  Similarity=0.327  Sum_probs=38.0

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|++||.  ++..|  +|+.|.|.++.++...
T Consensus        53 ~g~~~g~afV~f~~~~~a~~A~~--~~~~~--~g~~l~v~~a~~~~~~   96 (103)
T 2cqg_A           53 TGHSKGFGFVRFTEYETQVKVMS--QRHMI--DGRWCDCKLPNSKQSQ   96 (103)
T ss_dssp             SCSEEEEEEEEESSHHHHHHHHH--SCEEE--TTEEEEEECCCTTCCC
T ss_pred             CCCccceEEEEECCHHHHHHHHH--cCCee--CCeEEEEEecCCCCcC
Confidence            67889999999999999999998  46666  6999999999976543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.63  E-value=4e-08  Score=67.94  Aligned_cols=42  Identities=21%  Similarity=0.293  Sum_probs=35.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++++|||||+|.+.++|++||+.+++  +  .|++|.|+|+.....
T Consensus        51 ~~~rGfaFVeF~~~~~A~~Ai~~~~~--~--~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           51 SKKPGTAVVEFATVKAAELAVQNEVG--L--VDNPLKISWLEGQPQ   92 (100)
T ss_dssp             SSSSSEEEEEESCHHHHHHHHHTCCB--C--SSSBCEEECSSCCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHhcCC--C--CCCeEEEEEccCCCC
Confidence            36799999999999999999998655  3  489999999986653

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.61  E-value=3.2e-08  Score=66.32  Aligned_cols=36  Identities=25%  Similarity=0.478  Sum_probs=33.1

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEe
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEW   44 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~   44 (240)
                      ..+|||||+|.++++|++|+ .|||..|  +|+.|.|+.
T Consensus        51 ~~kg~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~r   86 (87)
T 2hzc_A           51 QDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQSLKIRR   86 (87)
T ss_dssp             SSSSEEEEEESSHHHHHHHG-GGTTCEE--TTEECEEEC
T ss_pred             CCCcEEEEEcCCHHHHHHHH-hcCCCEE--CCeEEEEeC
Confidence            44899999999999999999 9999999  699999974

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.58  E-value=1.9e-07  Score=64.14  Aligned_cols=70  Identities=14%  Similarity=0.122  Sum_probs=64.0

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccC-----CCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPY-----GNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~-----G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...+|-|-|| |..+++..|+.+++++     |.|..+.+.  -+-|+|+|.+...|.+|.-+|+|.+|.|++|.|.-
T Consensus        20 ~~rtiaL~~i-pDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPL-SDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECC-CTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecC-CCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            3678999999 8899999999999999     999999885  47899999999999999999999999999998854

>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=98.58  E-value=1.5e-08  Score=74.47  Aligned_cols=44  Identities=18%  Similarity=0.135  Sum_probs=39.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++++++|||||+|.++++|++|| .||+..|  +|+.|.|.++....
T Consensus        81 ~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l--~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           81 PDGRVTGEADVEFATHEEAVAAM-SKDRANM--QHRYIELFLNSTTG  124 (139)
T ss_dssp             SSSCSSCCCEEECSHHHHHHHHT-TCCSCSS--SSCCCCCEECCCSC
T ss_pred             CCCCCceEEEEEeCCHHHHHHHH-hhCCCEE--CCEEEEEEECCCCC
Confidence            35778999999999999999999 7999988  69999999988654

>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=98.55  E-value=4e-08  Score=70.82  Aligned_cols=41  Identities=22%  Similarity=0.173  Sum_probs=36.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++++|||||+|.++++|++||+ +++..|  +|+.|.|.++..
T Consensus        80 ~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l--~gR~I~V~~a~~  120 (126)
T 2hgm_A           80 EGKITGEAFVQFASQELAEKALG-KHKERI--GHRYIEVFKSSQ  120 (126)
T ss_dssp             SSSSCSEEEEEESSTTHHHHHHT-TTTCCB--TTBCCCCEEECH
T ss_pred             CCCCceEEEEEECCHHHHHHHHH-HCCCEE--CCEEEEEEECCH
Confidence            47789999999999999999998 577777  799999988864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.52  E-value=3.2e-08  Score=71.12  Aligned_cols=42  Identities=21%  Similarity=0.218  Sum_probs=36.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+++++|||||+|.++++|++||+. |+..|  +|+.|.|..+..
T Consensus        63 ~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l--~gR~i~V~~a~~  104 (123)
T 2dha_A           63 PDGRPTGDAFVLFACEEYAQNALRK-HKDLL--GKRYIELFRSTA  104 (123)
T ss_dssp             TTSCEEEEEEECCSSHHHHHHHHTT-TTEES--SSCEECCEEECH
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHh-CCCee--CCeEEEEEECCH
Confidence            4678899999999999999999995 88887  699999988763

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=98.48  E-value=1.3e-07  Score=67.04  Aligned_cols=38  Identities=29%  Similarity=0.380  Sum_probs=32.5

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCCce-----EEEEeccCC
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-----LSVEWARGE   48 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~-----l~v~~a~~~   48 (240)
                      |||||+|.++++|++||+.|||..|  +|++     |.|..+.+.
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~--~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBC--CCTTSCCCBCEEEECC--
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEE--CCcEeeeEEEEeccCCCC
Confidence            9999999999999999999999999  6888     666666543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.46  E-value=3.3e-07  Score=62.49  Aligned_cols=39  Identities=18%  Similarity=0.307  Sum_probs=36.1

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .|.|||+|.+.++|++|+..|||..|  +|++|.|+++.++
T Consensus        54 ~~~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~a~~~   92 (96)
T 2e44_A           54 TAVVNVTYSSKDQARQALDKLNGFQL--ENFTLKVAYIPDE   92 (96)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCBC--SSCBCEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcCcc
Confidence            45699999999999999999999999  6999999999876

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.44  E-value=7.2e-08  Score=66.69  Aligned_cols=43  Identities=23%  Similarity=0.380  Sum_probs=37.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++|+.  ++..|  +|+.|.|.++..+..
T Consensus        46 ~g~~~g~afV~f~~~~~a~~Ai~--~~~~~--~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           46 TGVSKGYGFVSFYNDVDVQKIVE--SQINF--HGKKLKLGPAIRKQN   88 (102)
T ss_dssp             TSCEEEEEEEEESSCCCHHHHTT--CCCEE--TTEECEEEEEEECC-
T ss_pred             CCCccceEEEEECCHHHHHHHHh--CCCeE--CCEEEEEEECCcCcc
Confidence            67789999999999999999998  88888  699999999986543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=2.2e-07  Score=63.25  Aligned_cols=38  Identities=18%  Similarity=0.144  Sum_probs=34.9

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ||||+|.+.++|++|++ |||..|  +|+.|.|+++.....
T Consensus        47 ~afV~f~~~~~a~~ai~-l~g~~~--~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           47 FAIVEMGDVGAREAVLS-QSQHSL--GGHRLRVRPREQKEF   84 (94)
T ss_dssp             EEEEEESSHHHHHHHHT-CSCCEE--TTEECCCBCSCCSCC
T ss_pred             EEEEEECCHHHHHHHHh-cCCeEE--CCEEEEEEECCcCCC
Confidence            99999999999999999 999999  699999999876544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.33  E-value=4.9e-07  Score=63.85  Aligned_cols=38  Identities=16%  Similarity=0.229  Sum_probs=31.3

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      ++++|||||+|.++++|++||+.|++  +  +|+.|.+..+.
T Consensus        49 g~~~G~aFV~f~~~~~a~~Ai~~~~~--~--~G~~~~~~~~~   86 (114)
T 2dnl_A           49 FPPKGYAFLLFQEESSVQALIDACLE--E--DGKLYLCVSSP   86 (114)
T ss_dssp             SCTTSEEEECCSSHHHHHHHHHHSEE--E--TTEEEEEECCS
T ss_pred             CCcccEEEEEECCHHHHHHHHHhhhh--c--CCcEEEeccCC
Confidence            68899999999999999999998854  4  57777776544

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.27  E-value=4.9e-07  Score=64.72  Aligned_cols=43  Identities=14%  Similarity=0.017  Sum_probs=35.5

Q ss_pred             ccCCccceEEEEeCC----hhH----HHHHHH--hhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFED----DRD----AADAIR--GLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~----~~~----A~~A~~--~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|+.++|||||+|.+    +++    |.+|+.  .|||..|  +|++|.|++...
T Consensus        43 ~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I--~Gr~irV~ln~~   95 (136)
T 2j8a_A           43 NSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFI--MGFKFEVILNKH   95 (136)
T ss_dssp             TTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEE--TTEEEEEEECCT
T ss_pred             CCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCee--cCcEEEEEECcc
Confidence            488999999999996    444    788988  7899999  799999997763

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=98.26  E-value=8.7e-07  Score=59.71  Aligned_cols=40  Identities=25%  Similarity=0.306  Sum_probs=31.0

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++|||||+|.++++|++    |++..+.+.|+.|.|.++.++.
T Consensus        46 ~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~   85 (89)
T 3d2w_A           46 PFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKH   85 (89)
T ss_dssp             SCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC---
T ss_pred             CCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCC
Confidence            369999999999999883    5676664579999999998654

>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=98.20  E-value=2.3e-06  Score=71.84  Aligned_cols=40  Identities=10%  Similarity=0.159  Sum_probs=33.8

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCccc-CCCc--eEEEEecc
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFG-YDRR--RLSVEWAR   46 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~-~~g~--~l~v~~a~   46 (240)
                      +||||||+|.+.++|++||+.|||..+. ..|+  .|+|.|+.
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            6899999999999999999999999873 1245  68888875

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.14  E-value=1.7e-06  Score=57.87  Aligned_cols=38  Identities=13%  Similarity=0.231  Sum_probs=34.1

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+.|||+|.+.++|.+|++ |||..|  .|+.|+|+++.+.
T Consensus        49 ~d~~fVtF~d~~sAlaAi~-mnG~~v--~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           49 EDKMWVTFLEGSSALNVLS-LNGKEL--LNRTITIALKSPS   86 (91)
T ss_dssp             SSSEEEEESSHHHHHHGGG-GTTCEE--TTEEEEEEECCCS
T ss_pred             cCCEEEEECChHHHHHHHh-cCCeEe--CCeEEEEEeCCCC
Confidence            3569999999999999998 999999  6999999998853

>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=97.97  E-value=6.6e-06  Score=55.00  Aligned_cols=41  Identities=22%  Similarity=0.250  Sum_probs=32.3

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++|||||+|.+.++|++|    ++..+.+.|..|.|.++.++...
T Consensus        41 ~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~~~   81 (88)
T 1wf0_A           41 FRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCCCC
Confidence            689999999999999754    44444447999999999876543

>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=97.90  E-value=1.4e-05  Score=54.65  Aligned_cols=73  Identities=10%  Similarity=0.113  Sum_probs=60.9

Q ss_pred             CCEEEEeccCCCCC-C----HHHHHHhhccCCCeEEEEEeCC--eEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           65 TKTLFVINFDPIRT-R----ERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        65 ~~~l~v~nl~~~~~-~----~~~l~~~f~~~G~i~~~~~~kg--~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      .++|+|.|| +..+ .    .+.++++|..|+++....+.+.  -..|.|.+.++|.+|-..||+..+.|..|+|-++.+
T Consensus         5 pntLiitnl-~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVA-NDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECC-CGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecC-CHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            467999999 5322 2    2678999999998887777654  478999999999999999999999999999999884


Q ss_pred             C
Q 026341          138 D  138 (240)
Q Consensus       138 ~  138 (240)
                      .
T Consensus        84 ~   84 (104)
T 1wey_A           84 L   84 (104)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.84  E-value=0.0003  Score=47.87  Aligned_cols=75  Identities=17%  Similarity=0.137  Sum_probs=62.0

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhcc---C--CCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEP---Y--GNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~---~--G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ....+|.|.|| |..+.++.|.-.|+.   -  |+|..+....+-|+|+|.+.+.|+..|+. ....|++..|.|.-..+
T Consensus         6 ~~~~~I~V~~l-Pp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            6 SGGVAVEVRGL-PPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCCCEEEEESC-CTTSCHHHHHHHHHCTTTTCCCCEEEEEEETTEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             cCccEEEEECC-CCCCChhHheEEEeCCCcCCCceeeEEEEcCCcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            34689999999 778999999999986   2  58999998889999999999999999873 36788899999866544


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus        84 ~~   85 (104)
T 2dhx_A           84 RA   85 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=97.84  E-value=8.6e-05  Score=49.94  Aligned_cols=55  Identities=25%  Similarity=0.443  Sum_probs=48.6

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD  121 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~  121 (240)
                      .++++| ++ |..+...||.++|+.||.|.--+|.-..|||.|.+.+.|..|+..+.
T Consensus        16 ~HVf~l-~F-P~ewKt~DI~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-EC-CTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eC-ChhhhhHHHHHHhhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            456667 99 88999999999999999887777889999999999999999999763

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.82  E-value=1.6e-05  Score=53.50  Aligned_cols=34  Identities=18%  Similarity=0.311  Sum_probs=31.2

Q ss_pred             eEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341           10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus        10 ~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      -+||+|.+.++|.+||+ |||..|  .|+.|+|++..
T Consensus        60 ~~fVtF~d~~sAl~AI~-ldG~~v--~Gr~L~V~~k~   93 (95)
T 1ufw_A           60 QMLVTFADSHSALSVLD-VDGMKV--KGRAVKISGPS   93 (95)
T ss_dssp             EEEEECSCSHHHHHHHH-GGGSEE--TTEEEEEECCC
T ss_pred             cEEEEEcChHHHHHHHh-cCCeee--CCeEEEEeccC
Confidence            39999999999999999 999999  69999998754

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.68  E-value=6.3e-05  Score=50.76  Aligned_cols=54  Identities=26%  Similarity=0.452  Sum_probs=47.4

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD  121 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~  121 (240)
                      .+++| ++ |..+...||.++|+.||.|.--+|.-..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~F-P~ewKt~Di~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-EC-CTTCCHHHHHHHTTTSEEEEEEEEETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eC-ChhhhhHHHHHHHhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            45666 89 88999999999999999777777788999999999999999999764

>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=97.58  E-value=0.00046  Score=46.27  Aligned_cols=70  Identities=17%  Similarity=0.253  Sum_probs=56.3

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----------CCeEEEEecCHHHHHHHHHhcCCCcccC-----cEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKALESTDRSKLVD-----RVI  130 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----------kg~afV~f~~~~~a~~A~~~l~g~~~~g-----~~l  130 (240)
                      +.|.|.+| |..+|++++.+.+.....+....+.          -.-|||.|.+.+++....+.++|..+.+     .+.
T Consensus         2 ~KvVIRrL-PP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a   80 (91)
T 1uw4_A            2 SKVVIRRL-PPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             cEEEEeCC-CCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeee
Confidence            47899999 7799999999999998877666553          2469999999999999999999987753     233


Q ss_pred             EEEEee
Q 026341          131 SVEYAL  136 (240)
Q Consensus       131 ~v~~a~  136 (240)
                      .|++|-
T Consensus        81 ~VE~AP   86 (91)
T 1uw4_A           81 IVEFAP   86 (91)
T ss_dssp             EEEECS
T ss_pred             EEEEcC
Confidence            566654

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=97.53  E-value=5.8e-05  Score=60.16  Aligned_cols=29  Identities=21%  Similarity=0.190  Sum_probs=26.7

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCccc
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFG   34 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~   34 (240)
                      .++|||||+|.+.++|+.|++.|+|..|+
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            46999999999999999999999999883

>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=97.53  E-value=0.00035  Score=49.04  Aligned_cols=68  Identities=25%  Similarity=0.399  Sum_probs=56.2

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccC-cEEEEEEe
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVD-RVISVEYA  135 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g-~~l~v~~a  135 (240)
                      ..-|.|.++ |.. ....|...|.+||+|.....+  ..+..|.|++..+|++||. .||..|.| ..|-|...
T Consensus        24 ~~wVtVFGF-p~~-~~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGF-PQA-SASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECC-CGG-GHHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCEEEEECC-CHH-HHHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            567888899 543 467889999999999998884  4699999999999999998 49999985 55666664

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.01  E-value=0.00095  Score=47.53  Aligned_cols=69  Identities=14%  Similarity=0.321  Sum_probs=53.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEE-EEE---------------------eCCeEEEEecCHHHHHHHHHhcCC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRI---------------------RRNFAFVQFETQEEATKALESTDR  122 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~-~~~---------------------~kg~afV~f~~~~~a~~A~~~l~g  122 (240)
                      ..-|.|.++ |. .....|.+.|++||.|.. +.+                     -..+..|+|++..+|++||. .||
T Consensus         7 e~~VtVFGF-p~-~~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            7 ELAILVFGY-PE-TMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             -CEEEEECC-CG-GGHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             ceEEEEEec-CH-HHHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            456778888 64 446778889999999876 211                     14688999999999999998 599


Q ss_pred             CcccCcEEEEEEee
Q 026341          123 SKLVDRVISVEYAL  136 (240)
Q Consensus       123 ~~~~g~~l~v~~a~  136 (240)
                      ..|.|.-|-|....
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999877787764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.88  E-value=0.0028  Score=42.70  Aligned_cols=71  Identities=13%  Similarity=0.199  Sum_probs=53.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----------CCeEEEEecCHHHHHHHHHhcCCCcccC-----cE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKALESTDRSKLVD-----RV  129 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----------kg~afV~f~~~~~a~~A~~~l~g~~~~g-----~~  129 (240)
                      ...|.|..| |..+|++++.+.+..+-++....+.          -.-|||.|.+.++.....+.++|..+.+     .+
T Consensus         9 ~~KvVIRrL-PP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            9 SHMVVIRRL-PPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCEEEECC-CSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             ceeEEEeCC-CCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            457899999 7799999999888876554333321          2469999999999999999999987643     34


Q ss_pred             EEEEEee
Q 026341          130 ISVEYAL  136 (240)
Q Consensus       130 l~v~~a~  136 (240)
                      ..|++|-
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            5566664

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=96.59  E-value=0.0022  Score=44.07  Aligned_cols=35  Identities=20%  Similarity=0.194  Sum_probs=31.1

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEe
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEW   44 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~   44 (240)
                      -|=|+|+|.|...|-+|.-.|+|..|  +|++|.|.-
T Consensus        62 H~GAivef~d~~~AgKasLaL~G~ef--~gr~Lr~gT   96 (117)
T 2l9w_A           62 FNGAIIIFRDSKFAAKMLMILNGSQF--QGKVIRSGT   96 (117)
T ss_dssp             TTEEEEECSCHHHHHHHHHHHSSEEE--TTEEEEEEC
T ss_pred             CCceEEEEccchhhHHHHhhcCCeee--cCeEEEecC
Confidence            35599999999999999999999999  799998863

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.08  E-value=0.011  Score=41.76  Aligned_cols=37  Identities=14%  Similarity=0.311  Sum_probs=29.8

Q ss_pred             cceEEEEeCC-hhHHHHHHHhhC--CCcccCCCceEEEEecc
Q 026341            8 AGFAFVYFED-DRDAADAIRGLD--NIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         8 kG~aFV~F~~-~~~A~~A~~~l~--g~~~~~~g~~l~v~~a~   46 (240)
                      .-.|||+|.+ +++|.+|+..||  +..|  .|..++++...
T Consensus        55 ~~tgfVrf~~~~~~A~~av~~ln~~~~~i--~g~~~~~evL~   94 (121)
T 1owx_A           55 AKEGIILFKEKAKEALGKAKDANNGNLQL--RNKEVTWEVLE   94 (121)
T ss_dssp             CSEEEEEESSCHHHHHHHHHHTTTSCBCT--TSSSEEEEECC
T ss_pred             CCEEEEEECCChHHHHHHHHHhhcCCcEE--eCcEEEEEECC
Confidence            3479999999 799999999996  4455  68888887665

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.62  E-value=0.0054  Score=53.30  Aligned_cols=53  Identities=15%  Similarity=0.269  Sum_probs=39.5

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHh
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALES  119 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~  119 (240)
                      .+.|+|. + +..+++.+|.+.|++||+|..+.+-   .-||+|||.+.+++..++..
T Consensus        53 ~rsv~v~-~-~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-C-PEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-E-CCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-c-CCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            4789997 6 6689999999999999999999884   34999999999999877653

>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=95.53  E-value=0.0023  Score=46.84  Aligned_cols=38  Identities=11%  Similarity=0.014  Sum_probs=34.5

Q ss_pred             eCCeEEEEecCHHHHHHHHHhc-CCCcccCcEEEEEEeec
Q 026341           99 RRNFAFVQFETQEEATKALEST-DRSKLVDRVISVEYALK  137 (240)
Q Consensus        99 ~kg~afV~f~~~~~a~~A~~~l-~g~~~~g~~l~v~~a~~  137 (240)
                      .+|+++|+|.+.++|++|++.| ||..++| .|.+.++..
T Consensus        12 l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            3689999999999999999999 9999999 999987754

>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=95.12  E-value=0.022  Score=38.85  Aligned_cols=36  Identities=22%  Similarity=0.249  Sum_probs=32.7

Q ss_pred             EEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341           11 AFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus        11 aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      ..|.|.++++|.+|...|++..|  .|+.|+|-|+.+.
T Consensus        49 irv~F~~~~~A~~AR~~Lh~~~f--~g~~~r~YFgq~~   84 (104)
T 1wey_A           49 VRINFSNPLSAADARLRLHKTEF--LGKEMKLYFAQTL   84 (104)
T ss_dssp             EEEECSSTTHHHHHHHTSTTSEE--TTEECEEECCCCS
T ss_pred             EEEEeCChHHHHHHHHHhcccee--cCceeEEEecCCC
Confidence            47899999999999999999999  5999999999843

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.38  E-value=0.21  Score=44.03  Aligned_cols=56  Identities=25%  Similarity=0.418  Sum_probs=47.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR  122 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g  122 (240)
                      ...++|+ + |..+...+|.++|+.||.|.-.+|....|||.|.+.+.|..++..+..
T Consensus       440 ~~vl~v~-f-~~~~~~~~i~~~fs~fg~v~V~widdt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-F-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-C-CTTCCHHHHHHHGGGGCCCEEEECSSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-C-CCCCCHHHHHHHHHhcCCEEEEEEcCCeEEEEECCHHHHHHHHHHHHh
Confidence            3567776 6 667889999999999998777777889999999999999999998853

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=93.05  E-value=1  Score=29.49  Aligned_cols=57  Identities=16%  Similarity=0.242  Sum_probs=48.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhc
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALEST  120 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l  120 (240)
                      ..++.|.|-|+ |..+-..++.-.....|---+|....|.|+|.|.+.++..-|++.|
T Consensus        10 kqnclikiini-pqgtlkaevvlavrhlgyefycdyidgqamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A           10 KQNCLIKIINI-PQGTLKAEVVLAVRHLGYEFYCDYIDGQAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             CCSCEEEEECC-CTTCCHHHHHHHHHTTCCCEEEEECSSCEEEEESSHHHHHHHHHHH
T ss_pred             hhCcEEEEEec-CCCceeeeeEEeehhcCeeEeeeeecCeeEEEecCChHHHHHHHHH
Confidence            34788899999 8788788877777778877889999999999999999999999876

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=92.28  E-value=0.33  Score=30.79  Aligned_cols=60  Identities=13%  Similarity=0.190  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHhhccCC-----CeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           76 IRTRERDIKRHFEPYG-----NVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        76 ~~~~~~~l~~~f~~~G-----~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+...+|..++..-+     .|-.+.+...|.||+... +.|..++..|++..+.|+.+.|+.++
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECSSCEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeCCcEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            3566777777776543     567788889999999875 45778899999999999999988764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.20  E-value=0.22  Score=33.76  Aligned_cols=51  Identities=18%  Similarity=0.194  Sum_probs=35.3

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCC
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRT   78 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~   78 (240)
                      +-|+|+|.+.+.|+..++ .....|  .+..|.|....+.               ...+|++.+| +..+
T Consensus        48 ~~AvItF~d~~va~rVL~-k~~H~L--~~~~LsV~P~~~~---------------~~~r~ll~gl-~~~t   98 (104)
T 2dhx_A           48 CGGVLTFREPADAERVLA-QADHEL--HGAQLSLRPAPPR---------------APARLLLQGL-PPGT   98 (104)
T ss_dssp             TEEEEEESSHHHHHHHHT-CSCCBS--SSSBCEEEECCCC---------------CCCCCCCCSC-CCCC
T ss_pred             CcEEEEEcChHHHHHHhc-CCccee--cCeEEEEEcCCCC---------------CcceEeeecC-CCCC
Confidence            679999999999998886 224455  5778888654432               2456777888 4444

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=83.71  E-value=1.2  Score=31.47  Aligned_cols=36  Identities=17%  Similarity=0.192  Sum_probs=29.8

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++--|+|.+..+|.+|+. .||.+|  +|..|-|.+..
T Consensus        62 ~NWikItYds~~~A~rAL~-~NG~ii--~G~mIGV~Py~   97 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALL-ENGAVF--NGVLLGVIPYT   97 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHT-TTTCEE--TTEECEEEECC
T ss_pred             CcEEEEEcCCHHHHHHHHH-hCCeEe--CcEEEEEEECC
Confidence            4677999999999999998 899998  57766666554

---

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	240
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-04
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-04
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.001
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-04
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	0.002
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	0.002
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.003
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.002
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.002
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-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	2e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	0.002
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.003
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.004
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	0.001
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-05
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:) 6e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.001
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.002
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	0.002

>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 = 69.1 bits (169), Expect = 5e-16
 Identities = 17/81 (20%), Positives = 38/81 (46%)

Query: 62  QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD 121
           +     +F+ N + +  ++ D++  F  YG ++   + + FAFVQ+  +  A  A+   D
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGED 71

Query: 122 RSKLVDRVISVEYALKDDSER 142
              +  +V+ +  A +    R
Sbjct: 72  GRMIAGQVLDINLAAEPKVNR 92

>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 = 39.9 bits (93), Expect = 2e-05
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 6  HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           + GFAFV + ++R+A  A+ G D        + L +  A   +      S
Sbjct: 48 VHKGFAFVQYVNERNARAAVAGEDGRMI--AGQVLDINLAAEPKVNRSGPS 96

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.2 bits (143), Expect = 2e-12
 Identities = 21/92 (22%), Positives = 43/92 (46%), Gaps = 11/92 (11%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN---------FAFVQFET 109
           +  ++ T  + V N    +  +R+I+  F  +G +  VR+ +          F FV F T
Sbjct: 2   VPKKQTTSKILVRNIPF-QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 110 QEEATKALESTDRSKLVD-RVISVEYALKDDS 140
           +++A KA  +   S  +  R + +E+A  + +
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 92

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE 48
          GF FV F   +DA  A   L +       RRL +EWA  E
Sbjct: 52 GFGFVDFITKQDAKKAFNALCH-STHLYGRRLVLEWADSE 90

>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 = 57.6 bits (139), Expect = 6e-12
 Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 9/80 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKALE 118
           +L+V +  P    E  +   F P G +L +R+ R         +A+V F+   +A +AL+
Sbjct: 2   SLYVGDLHP-DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 119 STDRSKLVDRVISVEYALKD 138
           + +   +  + + + ++ +D
Sbjct: 61  TMNFDVIKGKPVRIMWSQRD 80

>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 = 37.2 bits (86), Expect = 1e-04
 Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
            I+    G+A+V F+   DA  A+  ++        + + + W++
Sbjct: 35 DMITRRSLGYAYVNFQQPADAERALDTMNFDVI--KGKPVRIMWSQ 78

>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 = 57.3 bits (138), Expect = 2e-11
 Identities = 17/109 (15%), Positives = 36/109 (33%), Gaps = 6/109 (5%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVL-----HVRIRRNFAFVQFETQEEATKAL 117
              + L++ N    +    ++   F  YG +      +    R  A+V +E   +A  A 
Sbjct: 5   EVNRILYIRNLPY-KITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAC 63

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPYGRSPSP 166
           +      + +R + V Y   + + +                 YG +  P
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 112

>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 = 3e-06
 Identities = 19/91 (20%), Positives = 29/91 (31%), Gaps = 22/91 (24%)

Query: 1   MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMA 60
           +  +    G A+V +ED  DA +A   L         R L V +    R   +  +K   
Sbjct: 39  VGNTPETRGTAYVVYEDIFDAKNACDHLSGFNV--CNRYLVVLYYNANRAFQKMDTKK-- 94

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYG 91
                             +E  +K   E YG
Sbjct: 95  ------------------KEEQLKLLKEKYG 107

>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 = 55.3 bits (133), Expect = 5e-11
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 11/79 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKALE 118
            L+V N       +  +   F  YG+++   I R          AFV++  +EEA +A+ 
Sbjct: 8   NLYVTNLPR-TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 119 STDRSKL--VDRVISVEYA 135
           + +        + +SV  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.4 bits (102), Expect = 9e-07
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
            ++    G AFV +    +A +AI  L+N+      + LSV  A
Sbjct: 41 DKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 55.4 bits (133), Expect = 7e-11
 Identities = 14/77 (18%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALE 118
           +     T++          ++ +++ F P+G ++ +R+     ++FV+F T E A  A+ 
Sbjct: 14  SSPKNCTVYCGGIAS-GLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIV 72

Query: 119 STDRSKLVDRVISVEYA 135
           S + + +   V+   + 
Sbjct: 73  SVNGTTIEGHVVKCYWG 89

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 120
           L V N D     + DI+  F  +G +    +  +        A V FE + +A KA++  
Sbjct: 3   LLVSNLDF-GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 121 DRSKLVDRVISVEYA 135
           +   L  R ++++  
Sbjct: 62  NGVPLDGRPMNIQLV 76

>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 = 35.3 bits (81), Expect = 8e-04
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 2/45 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
             S    G A V+FE   DA  A++  + +P   D R ++++  
Sbjct: 34 YDRSGRSLGTADVHFERKADALKAMKQYNGVPL--DGRPMNIQLV 76

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------FAFVQFETQEE 112
           M +    +TL+V N       E  I + F   G     ++         + FV+F    +
Sbjct: 2   MEDDGQPRTLYVGNLSR-DVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRD 60

Query: 113 ATKALESTDRSKLVDRVISVEYALKDDSER 142
           A  AL + +  K++ + + V +A    S++
Sbjct: 61  AAAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 53.1 bits (127), Expect = 3e-10
 Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 11/89 (12%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIR-----RNFAFVQFETQEEA 113
           RP  T+++ N +  + ++ ++K+     F  +G +L + +      R  AFV F+    A
Sbjct: 1   RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59

Query: 114 TKALESTDRSKLVDRVISVEYALKDDSER 142
           T AL S       D+ + ++YA K DS+ 
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYA-KTDSDI 87

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          +  SL   G AFV F++   A +A+R +   PF    + + +++A+
Sbjct: 39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPMRIQYAK 82

>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 = 52.7 bits (126), Expect = 4e-10
 Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEE 112
           G K+   +     LFV N  P    E ++++ FE YG    V I   + F F++ ET+  
Sbjct: 1   GEKTFTQRS---RLFVGNLPP-DITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTL 56

Query: 113 ATKALESTDRSKLVDRVISVEYA 135
           A  A    D   L  + + V +A
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFA 79

>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 = 4e-04
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 2/46 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
                  GF F+  E    A  A   LDN+P     ++L V +A 
Sbjct: 37 EVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFAC 80

>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 = 52.6 bits (126), Expect = 5e-10
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 9/88 (10%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEAT 114
           + + TL+V N     T E  I   F   G++  + +  +        F FV++ ++ +A 
Sbjct: 5   KKSCTLYVGNLSF-YTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 115 KALESTDRSKLVDRVISVEYALKDDSER 142
            A+   + ++L DR+I  ++       R
Sbjct: 64  NAMRYINGTRLDDRIIRTDWDAGFKEGR 91

>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 = 38.0 bits (88), Expect = 1e-04
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 6  HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHR 53
             GF FV +    DA +A+R ++      D R +  +W  G +   +
Sbjct: 47 TACGFCFVEYYSRADAENAMRYINGTRL--DDRIIRTDWDAGFKEGRQ 92

>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 = 52.3 bits (125), Expect = 7e-10
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDR 122
            K L+V N     T E  I++ F         R++  R++AFV F  +E+A +A+++ + 
Sbjct: 8   VKILYVRNLML-STSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 123 SKLVDRVISVEYA 135
             L    I V  A
Sbjct: 67  KVLDGSPIEVTLA 79

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALES 119
           R  +TL   N       E ++K  FE    +  V      +  A+++F+++ +A K LE 
Sbjct: 14  RAARTLLAKNLSF-NITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 120 TDRSKLVDRVISVEYALKDDSER 142
              +++  R +S+ Y  +    R
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 35.8 bits (82), Expect = 6e-04
 Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 2/51 (3%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
          +       G A++ F+ + DA   +          D R +S+ +   + G 
Sbjct: 46 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTGEKGGT 94

>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 = 50.4 bits (120), Expect = 4e-09
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 9/89 (10%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQ 110
           ++ +    T++V   D  +  E  +   F   G V++  +         + + FV+F ++
Sbjct: 3   ISERNQDATVYVGGLDE-KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 111 EEATKALESTDRSKLVDRVISVEYALKDD 139
           E+A  A++  D  KL  + I V  A   +
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHN 90

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.0 bits (119), Expect = 4e-09
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 12/79 (15%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLH-----------VRIRRNFAFVQFETQEEATKA 116
           LF+ N +   T E  +K  F   G +             V +   F FV+++  E+A KA
Sbjct: 1   LFIKNLNF-STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

Query: 117 LESTDRSKLVDRVISVEYA 135
           L+      +    + V  +
Sbjct: 60  LKQLQGHTVDGHKLEVRIS 78

>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 = 34.2 bits (78), Expect = 0.002
 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 2/46 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
              L   GF FV ++    A  A++ L       D  +L V  + 
Sbjct: 36 KAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV--DGHKLEVRISE 79

>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 = 50.1 bits (119), Expect = 5e-09
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 11/101 (10%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFD-PIRTRERDIKRHFEPYGNVLHVRIR--RN 101
           A+    RH            T++L V N           +    E  G V  + +   + 
Sbjct: 1   AKHTLLRHEGIE---TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP 57

Query: 102 FAFVQFETQEEATKALESTDRSKLVDR-----VISVEYALK 137
           ++F ++ T EE+ +A  + +  ++VD       + + +  K
Sbjct: 58  YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 50.2 bits (119), Expect = 5e-09
 Identities = 7/79 (8%), Positives = 20/79 (25%), Gaps = 6/79 (7%)

Query: 63  RPTKTLFVINFDP----IRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKA 116
             +  L     +             +  F  Y      +         + F     A  A
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADA 62

Query: 117 LESTDRSKLVDRVISVEYA 135
                +++ + + + + +A
Sbjct: 63  RLRLHKTEFLGKEMKLYFA 81

>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 = 34.8 bits (79), Expect = 0.002
 Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 6/66 (9%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMA 60
                      + F +   AADA   L      +  + + + +A+        GS  +A
Sbjct: 39 TFQYFKSFKRVRINFSNPLSAADARLRLHKTE--FLGKEMKLYFAQ----TLHIGSSHLA 92

Query: 61 NQRPTK 66
             P K
Sbjct: 93 PPNPDK 98

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 1e-08
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 10/82 (12%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEEATKALE 118
           +F+ N DP    E+ +   F  +G +L              + +AF+ F + + +  A+E
Sbjct: 1   IFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 59

Query: 119 STDRSKLVDRVISVEYALKDDS 140
           + +   L +R I+V YA K DS
Sbjct: 60  AMNGQYLCNRPITVSYAFKKDS 81

>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 = 34.0 bits (77), Expect = 0.002
 Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 4/52 (7%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA--RGERG 50
             + +  G+AF+ F     +  AI  ++        R ++V +A  +  +G
Sbjct: 34 DPDTGNSKGYAFINFASFDASDAAIEAMNGQYL--CNRPITVSYAFKKDSKG 83

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALEST 120
           R   TL+V   D        ++  F P+GN++ + +   RN AFV +E  E A +A+   
Sbjct: 3   RKGNTLYVYGED---MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 59

Query: 121 DRSKLVDRVISVEYA 135
           + +++    + V  A
Sbjct: 60  NGTQVESVQLKVNIA 74

>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 = 2e-08
 Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 9/83 (10%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFET 109
           + AN  P   L V       T ERD++  F  YG +  V I  +         AFV FE 
Sbjct: 2   NRANPDPNCCLGVFGLSL-YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 110 QEEATKALESTDRSKLVDRVISV 132
            ++A +A E  +  +L  R I V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 14/79 (17%), Positives = 37/79 (46%), Gaps = 4/79 (5%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALE 118
                + + +++F   +     + +  EP+G + +  I  + N AF++  T E+A  A++
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 63

Query: 119 --STDRSKLVDRVISVEYA 135
             +T  + +  + + V  +
Sbjct: 64  YYTTTPALVFGKPVRVHLS 82

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 11/85 (12%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQ 110
           MA  +  + L+V         ++ +   F P+G++  ++I  ++        AFV+FE  
Sbjct: 1   MATTK--RVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 57

Query: 111 EEATKALESTDRSKLVDRVISVEYA 135
           E+A  A+++ + S+L  R I V  A
Sbjct: 58  EDAAAAIDNMNESELFGRTIRVNLA 82

>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 = 33.9 bits (77), Expect = 0.003
 Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
             +  + GFAFV FE   DAA AI  ++        R + V  A+  R +
Sbjct: 40 DYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAKPMRIK 88

>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 = 47.7 bits (113), Expect = 3e-08
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 118
            L V         +R++   F   G +   RI           +AFV F ++ ++ +A++
Sbjct: 4   NLIVNYLPQ-DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 119 STDRSKLVDRVISVEYA 135
             +   + ++ + V YA
Sbjct: 63  VLNGITVRNKRLKVSYA 79

>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 = 47.3 bits (112), Expect = 3e-08
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 10/76 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           +FV    P  T E  I+ +F  +G V  + +  +        F F+ F+ +E   K +E 
Sbjct: 2   IFVGGLSP-DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 120 TDRSKLVDRVISVEYA 135
                +      ++ A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>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 = 47.3 bits (112), Expect = 3e-08
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 10/76 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           +F+      +T +  ++ +F  +G V    + R+        F FV F  Q    K L  
Sbjct: 3   MFIGGLSW-QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 120 TDRSKLVDRVISVEYA 135
             R +L  + I  + A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (112), Expect = 7e-08
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 14/90 (15%)

Query: 60  ANQRPTKTLFVIN-FDP---------IRTRERDIKRHFEPYGNVLHVRIRRN----FAFV 105
           +  R  + + + N F P         +     D++     +G +  + +        A V
Sbjct: 3   SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASV 62

Query: 106 QFETQEEATKALESTDRSKLVDRVISVEYA 135
            F   EEA   +++ D      R I+ +  
Sbjct: 63  SFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 9e-05
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG 47
          +    H  G A V F D  +A   I+ LD   F    R+++ +   G
Sbjct: 50 LLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF--GGRQITAQAWDG 94

>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 = 46.5 bits (110), Expect = 7e-08
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 9/76 (11%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALES 119
           LF+         +  +K     +G +    +         + +AF ++       +A+  
Sbjct: 4   LFIGGLPN-YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 120 TDRSKLVDRVISVEYA 135
            +  +L D+ + V+ A
Sbjct: 63  LNGMQLGDKKLLVQRA 78

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)

Query: 10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
          +AF  + D      AI GL+ +      ++L V+ A 
Sbjct: 45 YAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRAS 79

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 1e-07
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFET 109
           S +  ++   K L V N    R R+ D+++ F  +G +L V I       + F FV FE 
Sbjct: 2   SGNSESKSTPKRLHVSNIPF-RFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFEN 60

Query: 110 QEEATKALESTDRSKLVDRVISVEYA 135
             +A +A E    + +  R I V  A
Sbjct: 61  SADADRAREKLHGTVVEGRKIEVNNA 86

>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 = 45.5 bits (107), Expect = 1e-07
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALE 118
            L V         + + +  F   G +   ++ R+          FV +   ++A KA+ 
Sbjct: 4   NLIVNYLPQ-NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 119 STDRSKLVDRVISVEYA 135
           + +  +L  + I V YA
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
            I+    G+ FV + D +DA  AI  L+ +      + + V +AR
Sbjct: 37 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYAR 80

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 27/106 (25%), Positives = 42/106 (39%), Gaps = 6/106 (5%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDR 122
             L V N +P R   + +   F  YG+V  V+I    +  A VQ     +A  A+   + 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 62

Query: 123 SKLVDRVISVEYALKDD--SERDDRYDSPRRGGYGRHSPYGRSPSP 166
            KL  + I +  +   +    R+ + D      YG  SP  R   P
Sbjct: 63  HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN-SPLHRFKKP 107

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALES 119
           P+ TL + N  P    E D+K  F   G V+         R  A +Q  + EEA +AL  
Sbjct: 9   PSATLHLSNIPP-SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 120 TDRSKLVD-RVISVEYA 135
                L +   + V ++
Sbjct: 68  LHNHDLGENHHLRVSFS 84

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALE 118
            L+V         ++++++ F  YG ++  RI         R   F++F+ + EA +A++
Sbjct: 8   NLYVSGLPK-TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 119 STDRSKL--VDRVISVEYA 135
             +  K       I+V++A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 6  HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA 45
             G  F+ F+   +A +AI+GL+          ++V++A
Sbjct: 46 VSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 10/92 (10%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR---NFAFVQFETQEEATKALEST 120
            +  +FV         E +++  F  YG+V+ V I +    FAFV F   + A       
Sbjct: 4   GSSGVFVGRCTG-DMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG-- 60

Query: 121 DRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           +   +    + +  A      + +    P  G
Sbjct: 61  EDLIIKGISVHISNA----EPKHNSNSGPSSG 88

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 14/91 (15%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKA 116
            LF+        +  +I          +   I           R FAFV++E+   A  A
Sbjct: 3   RLFIGGIPK-MKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 117 LE--STDRSKLVDRVISVEYALKDDSERDDR 145
                  R +L    I+V++A + + + D+ 
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWA-EPEIDVDED 91

>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 = 2e-06
 Identities = 17/54 (31%), Positives = 23/54 (42%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRD 54
              +   GFAFV +E  R AA A R L          +++V+WA  E     D
Sbjct: 38 AADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 91

>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 = 45.0 bits (106), Expect = 3e-07
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 11/86 (12%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEAT 114
           + T  L V+     +T E+D+K +F  +G VL V+++++        F FV+F   E   
Sbjct: 6   QKTSDLIVLGLPW-KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 115 KALESTDRSKLVDRVISVEYALKDDS 140
           K +    R  +  R    +      S
Sbjct: 65  KVMS--QRHMIDGRWCDCKLPNSKQS 88

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 0.002
 Identities = 8/43 (18%), Positives = 14/43 (32%), Gaps = 4/43 (9%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
          GF FV F +       +     I    D R    +    ++ +
Sbjct: 51 GFGFVRFTEYETQVKVMSQRHMI----DGRWCDCKLPNSKQSQ 89

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 6e-07
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 19/102 (18%)

Query: 64  PTKTLFVIN-FDP--------IRTRERDIKRHFEPYGNVLHVRIRRN----------FAF 104
           PT+ L ++N   P              D++     YG V  + I R             F
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRY 146
           V+F +  +  KA++     K  +RV+  +Y   D   R D +
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW 104

>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 = 44.3 bits (104), Expect = 7e-07
 Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 53  RDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQ 110
             G        PT  L+V    P  T    + R F+ +G++  +   +   FA++Q+E+ 
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGP-NTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESL 63

Query: 111 EEATKALESTDRSKL--VDRVISVEYALKDDS 140
           + A  A        L   DR + V++A    S
Sbjct: 64  DAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 12/50 (24%), Positives = 20/50 (40%)

Query: 1  MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG 50
              +    FA++ +E    A  A   +   P G   RRL V++A+    
Sbjct: 46 TIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 43.9 bits (103), Expect = 7e-07
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 10/80 (12%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKA 116
            + LF+       T +  ++ HFE +G +    +         R F FV + T EE   A
Sbjct: 6   LRKLFIGGLSF-ETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 117 LESTDRSKLVDRVISVEYAL 136
           + +    K+  RV+  + A+
Sbjct: 65  MNARPH-KVDGRVVEPKRAV 83

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN------FAFVQFETQEEATKALE 118
              +F+ N D      + +   F  +GN+L  ++  +      + FV FETQE A +A+E
Sbjct: 8   VGNIFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 66

Query: 119 STDRSKLVDRVISVEYALKDDSER 142
             +   L DR + V    K   ER
Sbjct: 67  KMNGMLLNDRKVFVGRF-KSRKER 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 = 43.9 bits (103), Expect = 1e-06
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 13/103 (12%)

Query: 59  MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEAT 114
           MA Q P   + V N          + + F  +G VL +       +  A +Q+     A 
Sbjct: 1   MAGQSPVLRIIVENLFY-PVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 59

Query: 115 KALESTDRSKLVD--RVISVEYA------LKDDSERDDRYDSP 149
            A  S D   + +    + ++++      +K ++++   Y  P
Sbjct: 60  HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRP 102

>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 = 34.2 bits (78), Expect = 0.003
 Identities = 7/38 (18%), Positives = 14/38 (36%)

Query: 9  GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR 46
            A + + D   A  A   LD          L +++++
Sbjct: 46 FQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 83

>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 = 42.6 bits (100), Expect = 2e-06
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--NFAFVQFETQEEATKALE 118
            + V  F         I   F  YGN+L   +    N+  ++++++ +A KAL 
Sbjct: 6   WVTVFGFPQASASY--ILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS 57

>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 = 2e-06
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 62  QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEA 113
                T+ V N     TRE D++  F P+G++  + + ++        FAF+ F  +E+A
Sbjct: 5   ADDNATIRVTNLSE-DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 114 TKALESTDRSKLVDRVISVEYA 135
            +A+           +++VE+A
Sbjct: 64  ARAIAGVSGFGYDHLILNVEWA 85

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 17/77 (22%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALE 118
            LFV +      +E +I+  F  YG + ++ +  +        +A V++ET ++A  A E
Sbjct: 9   ILFVTSIHE-EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 119 STDRSKLVDRVISVEYA 135
           + + ++++ + I V++ 
Sbjct: 68  ALNGAEIMGQTIQVDWC 84

>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 = 42.3 bits (99), Expect = 2e-06
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALES 119
           +F+       T ++D+K +F  +G V+   ++ +        F FV F+  E   K ++ 
Sbjct: 2   MFIGGLSW-DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 120 TDRSKLVDRVISVEYA 135
            +  KL  +VI  + A
Sbjct: 61  KEH-KLNGKVIDPKRA 75

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 10/76 (13%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALES 119
           +FV       T   D+K +FE +G V    +  +          FV FE+++   K  E 
Sbjct: 2   IFVGGLSV-NTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 120 TDRSKLVDRVISVEYA 135
               ++ ++++  + A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 42.1 bits (98), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 9/77 (11%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKALE 118
           TL++ NF P    +R+I+   +    V       +         A++   ++E+A   +E
Sbjct: 3   TLWMTNFPP-SYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 119 STDRSKLVDRVISVEYA 135
             +  K+    +  + +
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>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 = 42.4 bits (99), Expect = 4e-06
 Identities = 23/97 (23%), Positives = 37/97 (38%), Gaps = 12/97 (12%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
            +  LFV N     + E D+++ F  YG +  +    +        FAFV F   E A K
Sbjct: 7   GSGRLFVRNLSY-TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
           A    D      R++ V  +     +++     P  G
Sbjct: 66  AYAEVDGQVFQGRMLHVLPS---TIKKEASQSGPSSG 99

>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 = 33.5 bits (76), Expect = 0.004
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 10 FAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKS 58
          FAFV F     A  A   +D   F    R L V  +  ++   + G  S
Sbjct: 52 FAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHVLPSTIKKEASQSGPSS 98

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (102), Expect = 4e-06
 Identities = 29/145 (20%), Positives = 48/145 (33%), Gaps = 18/145 (12%)

Query: 1   MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMA 60
              +    GF FV +    +   A+    +   G             +R   R+ S+   
Sbjct: 41  DPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGR--------VVEPKRAVSREDSQRPG 92

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEE 112
                K +FV       T E  ++ +FE YG +  + I        +R FAFV F+  + 
Sbjct: 93  AHLTVKKIFVGGIKE-DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 113 ATKALESTDRSKLVDRVISVEYALK 137
             K +       +      V  AL 
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKALS 175

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (85), Expect = 7e-04
 Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 9/103 (8%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVR--------IRRNFAFVQFETQEEATKAL 117
           + LF+       T +  ++ HFE +G +              R F FV + T EE   A+
Sbjct: 7   RKLFIGGLSF-ETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 118 ESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGYGRHSPY 160
            +         V       ++DS+R   + + ++   G     
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKED 108

>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 = 42.0 bits (98), Expect = 4e-06
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF-----AFVQFETQEEATKAL 117
                ++V N  P   R +DI+  F  YG +  + ++        AFV+FE   +A  A+
Sbjct: 12  NNDCRIYVGNLPP-DIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 70

Query: 118 ESTDRSKLVDRVISVEYA 135
              D        + VE+ 
Sbjct: 71  YGRDGYDYDGYRLRVEFP 88

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 22/46 (47%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 6  HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR 51
              FAFV FED RDA DA+ G D   +  D  RL VE+ R  RG 
Sbjct: 51 GGPPFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEFPRSGRGT 94

>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 = 42.1 bits (98), Expect = 4e-06
 Identities = 15/99 (15%), Positives = 29/99 (29%), Gaps = 5/99 (5%)

Query: 56  SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--AFVQFETQEEA 113
           S S      +  + V         E D+    E +G + +V +      A V+FE  + A
Sbjct: 6   SGSHHKVSVSPVVHVRGLCE-SVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSA 64

Query: 114 TKALESTDRSKLV--DRVISVEYALKDDSERDDRYDSPR 150
            + +       +    +     Y+      R        
Sbjct: 65  KECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 8/55 (14%), Positives = 21/55 (38%)

Query: 2  CISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGS 56
           + + +   A V FE+   A + +    ++P     ++    ++  +R      S
Sbjct: 45 VMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 10/84 (11%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATK 115
             + LF+       T E  ++ ++E +G +    +         R F FV F +  E   
Sbjct: 19  QFRKLFIGGLSF-ETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 116 ALESTDRSKLVDRVISVEYALKDD 139
           A+       +  RV+  + A+  +
Sbjct: 78  AMA-ARPHSIDGRVVEPKRAVARE 100

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 63  RPTKTLFVINFDPIRTRERDIKRHFEPYGNV-LHVRIRRNFAFVQFETQEEATKALESTD 121
             +  + V N  P  +  +++    + Y     +V   +  AFV     E+A  A++   
Sbjct: 3   SGSSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 122 RSKLVDRVISVEYALKD 138
           +     + + V+    D
Sbjct: 62  QYSFRGKDLIVQLQPTD 78

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.5 bits (94), Expect = 1e-05
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 10/79 (12%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKA 116
           + + + N       E  ++  FE +G++  + I             AF+ FE ++ A +A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 117 LESTDRSKLVDRVISVEYA 135
           L+  +RS L +R ISV  A
Sbjct: 65  LQ-MNRSLLGNREISVSLA 82

>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 = 41.4 bits (96), Expect = 1e-05
 Identities = 19/118 (16%), Positives = 43/118 (36%), Gaps = 9/118 (7%)

Query: 45  ARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF-- 102
            + ++ +H   ++        + L V         E  +++ FE YG +  V+I  +   
Sbjct: 22  LQQQQQQHIPPTQMNPEPDVLRNLMVNYIPT-TVDEVQLRQLFERYGPIESVKIVCDRET 80

Query: 103 ------AFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRGGY 154
                  FV+F++   A +A+   +   ++++ + V  A                 GY
Sbjct: 81  RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGY 138

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 16/96 (16%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQ 106
            + S         LF+ +       ++D+ + F P+GNV+  ++         + F FV 
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQ-EFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 66

Query: 107 FETQEEATKALESTDRSKLVDRVISVEYALKDDSER 142
           ++    A  A++S +  ++  + + V+     +  +
Sbjct: 67  YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 10/82 (12%)

Query: 62  QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEA 113
           +R  +T+F +     R R RD++  F   G V  VRI  +         A+V+F   +  
Sbjct: 15  ERDARTVFCMQLAA-RIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 73

Query: 114 TKALESTDRSKLVDRVISVEYA 135
             A+      +L+   I V+ +
Sbjct: 74  PLAIG-LTGQRLLGVPIIVQAS 94

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (93), Expect = 2e-05
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATK 115
           S ++ R    +   N  P  T   +I+  F  +G++  V +      A V+F    EA K
Sbjct: 3   SGSSGRSKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61

Query: 116 ALESTDRSKLVDRVISVEYALKDDSERDDR 145
           A      SK     + +E+A         +
Sbjct: 62  AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQ 91

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

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]

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVL---HVRIRRNFAFVQFETQEEAT 114
           +   Q P + LF+ N  P  T E  +   F  +        V  R + AFV+F T+ ++ 
Sbjct: 1   AQTEQPPNQILFLTNL-PEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSN 59

Query: 115 KALESTDRSKLVD-RVISVEYALK 137
            A E+    K+     + + +A K
Sbjct: 60  AAKEALQGFKITPTHAMKITFAKK 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 = 39.4 bits (91), Expect = 4e-05
 Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 9/94 (9%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQE 111
           A  R  +++FV N       E  +K  F   G V+  R+  +          F +++ QE
Sbjct: 3   AVDRSLRSVFVGNIPY-EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 112 EATKALESTDRSKLVDRVISVEYALKDDSERDDR 145
            A  A+ + +  +   R + V+ A  + ++ + +
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNAASEKNKEELK 95

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 4/64 (6%)

Query: 1   MCISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMA 60
              +    G+ F  ++D   A  A+R L+   F    R L V+ A  E  ++++  KS+ 
Sbjct: 43  DRETGKPKGYGFCEYQDQETALSAMRNLNGREF--SGRALRVDNAASE--KNKEELKSLG 98

Query: 61  NQRP 64
              P
Sbjct: 99  TGAP 102

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.4 bits (91), Expect = 4e-05
 Identities = 18/99 (18%), Positives = 29/99 (29%), Gaps = 6/99 (6%)

Query: 55  GSKSMANQRPTKTLFVINFDPIRTRERDIKRHF-EPYGNVLHVRIRRNFAFVQFETQEEA 113
            S     +R    + V    P     +D+K H  E          +     V++  +E+ 
Sbjct: 5   SSGGPPTRRSDFRVLVSGL-PPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDM 63

Query: 114 TKALESTDRSKLVDRVISVEYALKDDSERDDRYDSPRRG 152
             AL   D +K         Y         +R   P  G
Sbjct: 64  EYALRKLDDTKFRSHEGETSYI----RVYPERSSGPSSG 98

>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 = 38.6 bits (89), Expect = 6e-05
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 67  TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALE 118
            LFV       T E+ +++ F  YG +  V +         R F FV FE  ++A  A+ 
Sbjct: 7   KLFVGGLSF-DTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 119 STDRSKLVDRVISVEYALKDDSER 142
           + +   +  R I V+ A K    R
Sbjct: 66  AMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 38.9 bits (90), Expect = 6e-05
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 80  ERDIKRHFEPYGNVLHVRIRRNF-------AFVQFETQEEATKALESTDRSKLVDRVISV 132
           E       E YG V  + +  N         +V+F  +E+A KA+   +      + I  
Sbjct: 41  EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

Query: 133 EY 134
           E 
Sbjct: 101 EL 102

>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 = 37.8 bits (87), Expect = 1e-04
 Identities = 14/91 (15%), Positives = 23/91 (25%), Gaps = 17/91 (18%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN----------------FAF 104
                  ++V   +       D+   F+  G V   +                     A 
Sbjct: 4   EDSDNSAIYVQGLND-SVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 105 VQFETQEEATKALESTDRSKLVDRVISVEYA 135
           V +E    A  A+E  D        + V  A
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>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 = 37.3 bits (86), Expect = 1e-04
 Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 9/86 (10%)

Query: 58  SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFET 109
           + + +     + V N  P      +I   F  Y  +                 A V FE+
Sbjct: 2   ASSGKPGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 110 QEEATKALESTDRSKLVDRVISVEYA 135
           ++EAT A+   +   +  R + +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 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 = 36.6 bits (84), Expect = 2e-04
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEA 113
           N    +++++  F P      DIK   E  G VL++++R       +   FV F++ E A
Sbjct: 2   NDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 114 TKALESTDRSKLVDRVISVEYA 135
            K +E T   K  +  + + + 
Sbjct: 61  KKFVE-TPGQKYKETDLLILFK 81

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 5e-04
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 10/87 (11%)

Query: 64  PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATK 115
           P K L++ N  P R  ERD+   F  +       I+           AF+ F  +E A +
Sbjct: 17  PNKVLYLKNLSP-RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 116 ALESTDRSKLVDRVISVEYALKDDSER 142
           AL   +  KL  +++ +E+  K+  +R
Sbjct: 76  ALHLVNGYKLYGKILVIEFG-KNKKQR 101

>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 = 35.5 bits (81), Expect = 6e-04
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 10/79 (12%)

Query: 66  KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKAL 117
           K +FV       T E  ++ +FE YG +  + I  +        FAFV F+  +   K +
Sbjct: 3   KKIFVGGIKE-DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 118 ESTDRSKLVDRVISVEYAL 136
                  +      V  AL
Sbjct: 62  I-QKYHTVNGHNCEVRKAL 79

>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 = 35.6 bits (81), Expect = 0.001
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 16/96 (16%)

Query: 60  ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQE 111
           ++    KT+F+ N     + E  +    + +G++ +VR+  +         AF QF TQE
Sbjct: 3   SDVTEGKTVFIRNLSF-DSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 112 EATKALE------STDRSKLVDRVISVEYAL-KDDS 140
            A K L            KL  R + V+ A+ +D++
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 61  NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRRNFAFVQFETQEEATKALE 118
           +  P++ L +       T   ++     P+G V  + +   +N AF++  T+E A   + 
Sbjct: 4   DGAPSRVLHIRKLPGEVTET-EVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 119 --STDRSKLVDRVISVEYA 135
             S     L ++ I ++Y+
Sbjct: 63  YYSAVTPHLRNQPIYIQYS 81

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.1 bits (77), Expect = 0.002
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 68  LFVINFDPIRTRERDIKRHFEPYGNV-LHVRIRRNFAFVQFETQEEATKALESTDRSKLV 126
           + +    P     +++      Y      V   +  AFV     E+A  A+ +  +S+L 
Sbjct: 1   ILIRGL-PGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 127 DRVISVEYALKD 138
           +R +SV+    D
Sbjct: 60  ERELSVQLQPTD 71

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 14/89 (15%), Positives = 32/89 (35%), Gaps = 10/89 (11%)

Query: 65  TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR--------NFAFVQFETQEEATKA 116
              +FV       T +  ++++FE +G++    +           + FV    +  A +A
Sbjct: 10  FTKIFVGGLPY-HTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 117 LESTDRSKLVDRVISVEYALKDDSERDDR 145
            +  +   +  R  +V  A      R  +
Sbjct: 69  CKDPN-PIIDGRKANVNLAYLGAKPRSLQ 96

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	240
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.78
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.78
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.77
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.77
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.76
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.75
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.75
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.74
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.73
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.73
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.73
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.72
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.69
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.69
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.69
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.45
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	99.45
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.38
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.22
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.17
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.14
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.14
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.14
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.14
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.13
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.13
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.13
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.12
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.12
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.11
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.1
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.09
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.09
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.08
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.08
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.07
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.07
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.06
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.05
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.05
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.05
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.03
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.03
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.03
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.03
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.03
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.02
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.02
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.02
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.02
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.02
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.01
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.01
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.0
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.99
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.99
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.99
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.99
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.98
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.96
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.96
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.95
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	98.94
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.91
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.9
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.89
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.89
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.88
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.86
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.86
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.86
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.85
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.85
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.85
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.8
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.78
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.78
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.77
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.75
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.72
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.67
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.59
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.57
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.56
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.53
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.37
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.32
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.06
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.79
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.73
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.63
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.9
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	93.99
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	92.84

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=3.5e-22  Score=153.12  Aligned_cols=126  Identities=23%  Similarity=0.339  Sum_probs=103.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCCCCCCCCCCCCCCCCCEEEEeccCCCCCCHHH
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERD   82 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~~   82 (240)
                      .++.++|||||+|.++++|++|+..++ ..+  .+..+.+.+.........     ........+|||+|| |..+++++
T Consensus        43 ~~~~~~g~afv~f~~~~~a~~a~~~~~-~~~--~~~~~~~~~~~~~~~~~~-----~~~~~~~~~i~V~~l-p~~~te~~  113 (183)
T d1u1qa_          43 NTKRSRGFGFVTYATVEEVDAAMNARP-HKV--DGRVVEPKRAVSREDSQR-----PGAHLTVKKIFVGGI-KEDTEEHH  113 (183)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHTCS-CEE--TTEECEEEECCCTTGGGS-----TTTTCCCSEEEEECC-CTTCCHHH
T ss_pred             cCCCccCceecccCCHHHHHHHHHhcC-Ccc--cccchhhhhhhhcccccc-----cccccccceeEEccC-CCcCCHHH
Confidence            367789999999999999999999544 445  377777776654443221     123455789999999 89999999


Q ss_pred             HHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           83 IKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        83 l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |.++|..||.|..+.|.        +|||||+|.+.++|++||+ +++..|+|+.|.|.+|.++
T Consensus       114 L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             HHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             HhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            99999999999999873        5799999999999999997 7889999999999998654

>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=99.84  E-value=6.2e-21  Score=131.16  Aligned_cols=77  Identities=21%  Similarity=0.481  Sum_probs=70.7

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ...++|||+||++..+++++|+++|.+||.|..|.|.++||||+|++.++|++||+.|||..|.|+.|.|+|+..+.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEeCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            34567999999546788999999999999999999999999999999999999999999999999999999997643

>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=5.8e-20  Score=125.14  Aligned_cols=77  Identities=23%  Similarity=0.413  Sum_probs=70.7

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+++|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.+.++|+.|++.|||..|+|++|.|+
T Consensus         4 ~~~s~tlfV~nl-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~   82 (93)
T d1h2vz_           4 LKKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD   82 (93)
T ss_dssp             TTTCCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCEEEEeCC-CCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999 8899999999999999999999983        5799999999999999999999999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      |+....
T Consensus        83 ~a~~~~   88 (93)
T d1h2vz_          83 WDAGFK   88 (93)
T ss_dssp             EESCCC
T ss_pred             EcCCCC
Confidence            987543

>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=99.81  E-value=6.2e-20  Score=122.10  Aligned_cols=72  Identities=22%  Similarity=0.433  Sum_probs=67.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |..+++++|+++|++||.|..+.|        .+|||||+|.+.++|+.||+.|||..|.|+.|.|+||+
T Consensus         2 ~t~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYL-PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999 889999999999999999999988        36899999999999999999999999999999999997


Q ss_pred             c
Q 026341          137 K  137 (240)
Q Consensus       137 ~  137 (240)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=6.6e-20  Score=123.58  Aligned_cols=76  Identities=22%  Similarity=0.482  Sum_probs=69.8

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ...+.+|||+|| |..+++++|.++|++||+|..|.|.        +|||||+|.+.++|+.|+..|||..|.|+.|.|+
T Consensus         4 s~~~~~l~V~nL-~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           4 SVEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CC-CEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345789999999 8899999999999999999999883        5799999999999999999999999999999999


Q ss_pred             EeecC
Q 026341          134 YALKD  138 (240)
Q Consensus       134 ~a~~~  138 (240)
                      ||.++
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99865

>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=9.9e-20  Score=123.94  Aligned_cols=76  Identities=24%  Similarity=0.337  Sum_probs=70.6

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|++||+.|||..|.|+.|.|.|
T Consensus         7 ~~~~tlfV~nL-p~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           7 NQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CTTTEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCEEEEeCC-CCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44679999999 9999999999999999999999883        68999999999999999999999999999999999


Q ss_pred             eecCC
Q 026341          135 ALKDD  139 (240)
Q Consensus       135 a~~~~  139 (240)
                      |.+..
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            98754

>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=99.80  E-value=1.5e-19  Score=122.39  Aligned_cols=78  Identities=23%  Similarity=0.373  Sum_probs=71.4

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..+.++|||+|| |..+++++|+++|++||+|..|.|.      ++||||+|.+.++|+.|+..|||..|.|+.|.|.||
T Consensus         5 ~~~~~tl~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           5 DGQPRTLYVGNL-SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             SCCCCEEEEESC-CTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345679999999 8899999999999999999999884      579999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            86543

>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=99.80  E-value=2.6e-19  Score=123.36  Aligned_cols=77  Identities=27%  Similarity=0.426  Sum_probs=70.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...++|||+|| |+.+++++|+++|.+||.|..|.|+        +|||||+|.+.++|+.||+.||+..|+|+.|.|.+
T Consensus         6 ~~~~~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_           6 SGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCEEEEECC-CCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34678999999 9999999999999999999999983        68999999999999999999999999999999999


Q ss_pred             eecCCC
Q 026341          135 ALKDDS  140 (240)
Q Consensus       135 a~~~~~  140 (240)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987643

>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=9.3e-20  Score=126.24  Aligned_cols=79  Identities=20%  Similarity=0.441  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..+++++|||+|| |+.+++++|+++|+.||.|..+.+.        +|||||+|.+.++|+.||+.|||..|.|+.|.|
T Consensus        14 ~~p~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V   92 (102)
T d2cpza1          14 EGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   92 (102)
T ss_dssp             CCSTTCCEEEESC-CSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4456789999999 9999999999999999999988873        579999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +|+.++..
T Consensus        93 ~~a~~k~~  100 (102)
T d2cpza1          93 QLKRSKND  100 (102)
T ss_dssp             ECCCCSCC
T ss_pred             EEeCCCCC
Confidence            99988754

>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=99.80  E-value=1e-19  Score=121.08  Aligned_cols=71  Identities=21%  Similarity=0.425  Sum_probs=67.2

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ++|||+|| |..+++++|+++|++||+|..|.+.        +|||||+|.+.++|+.|++.|||..|.|+.|.|+||++
T Consensus         3 t~l~V~nL-p~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYL-PQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            57999999 8999999999999999999999983        57999999999999999999999999999999999975

>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=99.80  E-value=1.6e-19  Score=122.22  Aligned_cols=75  Identities=27%  Similarity=0.517  Sum_probs=69.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .+.++|||+|| |..+++++|.++|++||+|..|.|+        +|||||+|.+.++|++||+.|||..|+|+.|.|+|
T Consensus         6 ~~~~~i~V~nL-p~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           6 DDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             SSSEEEEEESC-CTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35689999999 8999999999999999999999884        57999999999999999999999999999999999


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      |++.
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9864

>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=99.80  E-value=3.7e-19  Score=121.08  Aligned_cols=77  Identities=32%  Similarity=0.536  Sum_probs=71.0

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .....+|||+|| |..+++++|+++|.+||+|..|.+.      +|||||+|.+.++|++||..|||..|.|+.|.|++|
T Consensus         8 ~~~~~~l~v~nL-p~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESC-CTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            344678999999 8999999999999999999999984      689999999999999999999999999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8753

>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=99.80  E-value=3.3e-19  Score=130.46  Aligned_cols=78  Identities=23%  Similarity=0.458  Sum_probs=70.9

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ...++|||+|| |..+++++|+++|++||+|..|.|.        +|||||+|.+.++|+.||+.|||..|+|+.|.|++
T Consensus        40 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          40 DVLRNLMVNYI-PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTSEEEEESC-STTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34578999999 8899999999999999999999883        57999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 026341          135 ALKDDSE  141 (240)
Q Consensus       135 a~~~~~~  141 (240)
                      |.....+
T Consensus       119 a~~~~~~  125 (139)
T d1u6fa1         119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             cCCCCCC
Confidence            9865543

>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=99.79  E-value=2.7e-19  Score=119.22  Aligned_cols=76  Identities=28%  Similarity=0.466  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCccc-CcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLV-DRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~-g~~l~v~~a~  136 (240)
                      ..+|+++|||+|| |..+++++|.++|++||+|..|.+.   +|||||+|.+.++|+.|++.|||..|. |+.|.|+||+
T Consensus         4 ~~pP~~tl~V~nL-p~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNL-PEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESC-CTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4567899999999 8899999999999999999999984   589999999999999999999999885 6899999986


Q ss_pred             c
Q 026341          137 K  137 (240)
Q Consensus       137 ~  137 (240)
                      .
T Consensus        83 k   83 (83)
T d2b0ga1          83 K   83 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=1e-19  Score=122.92  Aligned_cols=75  Identities=29%  Similarity=0.549  Sum_probs=69.9

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.+.++|+.|++.|||..|+|+.|.|++|
T Consensus         4 ~~~tlfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           4 TKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCSCEEEESC-CSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCcEEEEeCC-CCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4679999999 8999999999999999999999883        689999999999999999999999999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      .+..
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.2e-19  Score=121.91  Aligned_cols=77  Identities=26%  Similarity=0.436  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+.++|||+|| |..+++++|+++|.+||.|..+.+.     ++||||+|.+.++|+.||+.|||..|.|++|.|+||
T Consensus        10 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          10 AGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCCSSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            3456789999999 8899999999999999999999884     689999999999999999999999999999999998


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=99.79  E-value=1.2e-19  Score=122.59  Aligned_cols=74  Identities=27%  Similarity=0.480  Sum_probs=69.3

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..+|||+|| |..+++++|+++|++||.|..+.|.      +|||||+|.+.++|++||+.|||..|+|+.|.|++++++
T Consensus         8 ~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESC-CSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            457999999 8899999999999999999999984      689999999999999999999999999999999999875


Q ss_pred             C
Q 026341          139 D  139 (240)
Q Consensus       139 ~  139 (240)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.3e-19  Score=122.74  Aligned_cols=75  Identities=19%  Similarity=0.462  Sum_probs=70.1

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ++.++|||+|| |..+++++|+++|++||.|..|.|.  +|||||+|.+.++|+.|+..|||..|.|+.|.|.|++..
T Consensus        16 ~~~~~l~v~nL-~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          16 PKNCTVYCGGI-ASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SSCCEEEEECC-SSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEcCC-CCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            44678999999 8899999999999999999999995  789999999999999999999999999999999998764

>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=4.6e-19  Score=120.84  Aligned_cols=76  Identities=30%  Similarity=0.590  Sum_probs=70.2

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhc-CCCcccCcEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALEST-DRSKLVDRVISV  132 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l-~g~~~~g~~l~v  132 (240)
                      .+..+|||+|| |..+++++|+++|.+||.|..|.|+         +|||||+|.+.++|++||+.| ||..|+|++|.|
T Consensus         6 ~~~~~l~V~nL-p~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           6 QTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            45678999999 8999999999999999999999983         589999999999999999998 899999999999


Q ss_pred             EEeecCC
Q 026341          133 EYALKDD  139 (240)
Q Consensus       133 ~~a~~~~  139 (240)
                      +||....
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998764

>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=99.78  E-value=3.9e-19  Score=119.26  Aligned_cols=77  Identities=29%  Similarity=0.395  Sum_probs=69.5

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      ...++|||+|| |..+++++|+++|++||.|..+.+  .+|||||+|.+.++|..|+..|||..|.|+.|.|+||++...
T Consensus         6 ~~~k~l~V~nL-p~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1           6 SSVKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             SCCCEEEEESC-CTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             cCCCEEEEcCC-CCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            34689999999 899999999999999997766555  689999999999999999999999999999999999987653

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4e-19  Score=120.25  Aligned_cols=75  Identities=29%  Similarity=0.492  Sum_probs=69.6

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+|||+|| |..+++++|+++|.+||.|..+.+        ++|||||+|.++++|+.||+.|||..|+|+.|.|++|.
T Consensus         5 ~~kifV~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           5 EGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CSEEEEESC-CTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCEEEEECC-CCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            567999999 899999999999999999999887        36899999999999999999999999999999999998


Q ss_pred             cCCC
Q 026341          137 KDDS  140 (240)
Q Consensus       137 ~~~~  140 (240)
                      +...
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.78  E-value=2.5e-19  Score=118.84  Aligned_cols=71  Identities=21%  Similarity=0.322  Sum_probs=66.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ++|||+|| |..+++++|+++|++||.|..+.+        .+|||||+|.+.++|++|++.|||..|.|++|.|++++|
T Consensus         2 ~tl~v~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNF-PPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECC-CTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECC-CCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999 999999999999999999987665        368999999999999999999999999999999999875

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=4e-19  Score=116.89  Aligned_cols=69  Identities=23%  Similarity=0.380  Sum_probs=65.7

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .|||+|| |+.+++++|+++|.+||.|..+.|.       +|||||+|.+.++|+.|++.|||..|.|++|.|++|.
T Consensus         2 rl~V~nL-p~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESC-CTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECC-CCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999 8899999999999999999999983       6799999999999999999999999999999999985

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=8.9e-20  Score=122.66  Aligned_cols=73  Identities=21%  Similarity=0.263  Sum_probs=67.6

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ++|||+|| |..+++++|+++|++||+|..+.+. .|||||+|.+.++|++||..|||..|.|+.|.|.++....
T Consensus         1 nrvfV~nl-p~~~~~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEEC-CSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECC-CCcCCHHHHHHHHhhhcccccccccccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            36999999 8999999999999999999999985 5899999999999999999999999999999998887554

>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=99.78  E-value=5.7e-19  Score=118.84  Aligned_cols=75  Identities=17%  Similarity=0.270  Sum_probs=68.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCC-CeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G-~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ...+|||+|| |..+++++|+++|.+|| .+..+...++||||+|.+.++|++||+.||+..|+|+.|.|+|++...
T Consensus         4 ~s~~i~V~nL-p~~~t~~~l~~lF~~~G~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESC-CSSCCHHHHHHHTCSSCCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCC-CCccChHHHHHHHHhcCceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            3578999999 89999999999999999 566666679999999999999999999999999999999999996543

>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=99.78  E-value=4.9e-19  Score=116.79  Aligned_cols=73  Identities=27%  Similarity=0.473  Sum_probs=67.8

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      ..+++|||+|| +  +|+++|+++|++||.|..|.+.  ++||||+|.+.++|+.|+..|||..|+|+.|.|+|++++
T Consensus         3 ~~~~ti~V~~~-~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGE-D--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECS-S--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECC-C--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            34789999999 5  8999999999999999999994  699999999999999999999999999999999999764

>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=99.78  E-value=4e-19  Score=117.53  Aligned_cols=70  Identities=20%  Similarity=0.460  Sum_probs=66.1

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      +|||+|| |..+++++|.++|++||+|..|.|+        +|||||+|.+.++|+.|++.|||..|.|++|.|+||+.
T Consensus         2 slfV~nL-~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDL-HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCC-CCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6999999 8899999999999999999999984        58999999999999999999999999999999999853

>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=99.78  E-value=5.5e-19  Score=124.85  Aligned_cols=75  Identities=21%  Similarity=0.414  Sum_probs=70.0

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ..+++|||+|| |..+++++|.++|++||.|..|.+.     +|||||+|.+.++|..||+.|||..|+|+.|.|.++..
T Consensus         5 ~~~r~l~V~nL-p~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           5 EVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            34689999999 9999999999999999999999995     68999999999999999999999999999999999865


Q ss_pred             C
Q 026341          138 D  138 (240)
Q Consensus       138 ~  138 (240)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=3.7e-19  Score=119.10  Aligned_cols=70  Identities=26%  Similarity=0.428  Sum_probs=65.6

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      |||+|| |..+++++|+++|++||+|..|.|.           +|||||+|.+.++|+.|++.|||..|+|+.|.|+|+.
T Consensus         1 LfV~nL-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCC-CCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            799999 9999999999999999999999883           5799999999999999999999999999999999986


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      ..
T Consensus        80 ~~   81 (85)
T d2cpfa1          80 RA   81 (85)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.77  E-value=7.9e-19  Score=120.47  Aligned_cols=78  Identities=19%  Similarity=0.282  Sum_probs=71.8

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCCC
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS  140 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  140 (240)
                      .....+|||+|| |+.+++++|+++|.+||+|..+.|. +|||||+|.+.++|++||+.|||..|.|+.|.|.+++....
T Consensus        12 ~~~~~~i~V~Nl-p~~~~~~~L~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          12 RRSDFRVLVSGL-PPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             CSCSCEEEEECC-CSSCCHHHHHHHHTTSSCEEEEEEETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHHhhcccccccccccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            345678999999 9999999999999999999999985 78999999999999999999999999999999999987543

>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=99.77  E-value=7.5e-19  Score=118.35  Aligned_cols=75  Identities=28%  Similarity=0.381  Sum_probs=68.6

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcc-cCcEEEEEEee
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKL-VDRVISVEYAL  136 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~-~g~~l~v~~a~  136 (240)
                      .+|+.+|||+|| |..+++++|+++|.+||.|..+.+.    +++|||+|++.++|.+|+..|||..| +|+.|.|+|++
T Consensus         7 ~pPs~tL~V~NL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           7 FPPSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CCSCSEEEEECC-CTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            467899999999 8999999999999999999877663    68999999999999999999999988 58999999987


Q ss_pred             c
Q 026341          137 K  137 (240)
Q Consensus       137 ~  137 (240)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.77  E-value=7.5e-19  Score=117.72  Aligned_cols=75  Identities=29%  Similarity=0.462  Sum_probs=69.8

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ..++|||+|| |..+++++|.++|++||+|..|.+.  ++||||+|.+.++|+.|++.|||..|+|+.|.|+||....
T Consensus         7 ~~~~l~V~nL-p~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESC-CTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECC-CCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3568999999 8899999999999999999999995  6899999999999999999999999999999999997653

>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=99.77  E-value=8.3e-19  Score=123.31  Aligned_cols=75  Identities=24%  Similarity=0.288  Sum_probs=70.2

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ..++|||+|| |..+++++|+++|.+||+|..|.|.  ++||||+|.+.++|++||+.|||..|.|+.|.|+|+....
T Consensus         9 ~~~~l~V~nL-p~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           9 SKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEECC-CCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            4679999999 8899999999999999999999995  6899999999999999999999999999999999997654

>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=99.77  E-value=6.1e-19  Score=117.92  Aligned_cols=73  Identities=16%  Similarity=0.331  Sum_probs=68.4

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ..|||+|| |..+++++|+++|++||+|..|.|.        +|||||+|.++++|+.|+..|||..|.|+.|.|++|..
T Consensus         2 ~rlfV~nl-p~~~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 HKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETC-CSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            46999999 9999999999999999999999984        68999999999999999999999999999999999986


Q ss_pred             CC
Q 026341          138 DD  139 (240)
Q Consensus       138 ~~  139 (240)
                      ..
T Consensus        81 ~~   82 (85)
T d2u2fa_          81 GA   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=5.4e-19  Score=117.75  Aligned_cols=70  Identities=37%  Similarity=0.555  Sum_probs=65.0

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|+.|+..|||..|+|+.|.|
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 PDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESC-CSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346789999999 8999999999999999999999883        579999999999999999999999999999987

>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=99.77  E-value=6.3e-19  Score=120.64  Aligned_cols=79  Identities=23%  Similarity=0.405  Sum_probs=71.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      ...+..+|||+|| |..+++++|+++|.+||.|..+..   .++||||+|.+.++|++|+..|||..|+|+.|.|.|+.+
T Consensus        12 ~~~~~~~l~V~nL-~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          12 KVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESC-CSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3445789999999 899999999999999999887765   479999999999999999999999999999999999987


Q ss_pred             CCC
Q 026341          138 DDS  140 (240)
Q Consensus       138 ~~~  140 (240)
                      +..
T Consensus        91 k~~   93 (96)
T d1fjca_          91 KGG   93 (96)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1e-18  Score=122.42  Aligned_cols=75  Identities=25%  Similarity=0.395  Sum_probs=68.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      +.+|||+||+|..+++++|.++|+.||+|..|.|.   +|+|||+|++.++|++||+.|||..|+|+.|.|+|++...
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57899999955679999999999999999999985   5899999999999999999999999999999999987543

>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=99.76  E-value=3e-19  Score=118.06  Aligned_cols=74  Identities=20%  Similarity=0.404  Sum_probs=66.6

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCC-cccCcEEEEEEeecCCC
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRS-KLVDRVISVEYALKDDS  140 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~-~~~g~~l~v~~a~~~~~  140 (240)
                      ++|||+|| |..+++++|+++|.+||.|..+.+  .+|||||+|.+.++|+.|++.|||. .|+|++|.|+||.++..
T Consensus         2 n~l~V~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1           2 NKLYIGNL-SPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCEEEECC-CTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            46999999 899999999999999998865444  6899999999999999999999996 59999999999997653

>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=99.76  E-value=9.9e-19  Score=116.92  Aligned_cols=70  Identities=26%  Similarity=0.559  Sum_probs=64.8

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEY  134 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~  134 (240)
                      +++|||+|| |..+++++|+++|++||+|..+.|.        +|||||+|.++++|+.|++.|||..+.|  .+|.|.|
T Consensus         6 ~~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           6 DANLYVSGL-PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            578999999 8899999999999999999999883        5799999999999999999999999998  5699988


Q ss_pred             e
Q 026341          135 A  135 (240)
Q Consensus       135 a  135 (240)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.76  E-value=1.5e-18  Score=116.07  Aligned_cols=71  Identities=27%  Similarity=0.484  Sum_probs=65.7

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD--RVISVE  133 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~  133 (240)
                      ..++|||+|| |..+++++|+++|++||+|..+.|+        +|||||+|.+.++|+.||+.|||..+.|  ++|.|+
T Consensus         5 ~~t~lfV~nl-p~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           5 KDTNLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTCEEEEESC-CTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            3567999999 8999999999999999999999884        5799999999999999999999999987  889999


Q ss_pred             Ee
Q 026341          134 YA  135 (240)
Q Consensus       134 ~a  135 (240)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            87

>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=99.76  E-value=2.4e-18  Score=117.91  Aligned_cols=78  Identities=23%  Similarity=0.384  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccC--cEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVD--RVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~  136 (240)
                      ...|+++|||+|| |..+++++|+++|++||+|..|.+.  ++||||+|.+.++|+.|++.||+..|.|  .+|.|+||+
T Consensus        13 ~~~Ps~tl~V~nL-p~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          13 KANPTTRLWVGGL-GPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECC-CSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEcCC-CCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            3457899999999 8899999999999999999999995  6899999999999999999999999987  589999998


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      ...
T Consensus        92 ~~~   94 (97)
T d1whya_          92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.75  E-value=3.6e-18  Score=118.27  Aligned_cols=74  Identities=20%  Similarity=0.400  Sum_probs=67.4

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|||+|| |+.+++++|+++|++||+|..|.|.        +|||||+|.+.++|++||+.+|+ .|+|+.|.|++|
T Consensus         9 ~~~~lfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           9 TFTKIFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             SSSEEEEECC-CSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCcEEEEeCC-CCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            4578999999 8999999999999999999999983        68999999999999999998876 799999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      ....
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7653

>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=99.75  E-value=7.8e-19  Score=116.96  Aligned_cols=72  Identities=29%  Similarity=0.579  Sum_probs=65.2

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEE-EE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHV-RI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~-~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |||+|| |..+++++|+++|++||.|..+ .+        .+|||||+|.+.++|+.||+.|||..|+|++|.|+||.++
T Consensus         1 lfV~nL-p~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECC-CTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCC-CCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            799999 8999999999999999998654 44        2689999999999999999999999999999999999876


Q ss_pred             CC
Q 026341          139 DS  140 (240)
Q Consensus       139 ~~  140 (240)
                      ..
T Consensus        80 ~~   81 (83)
T d1x5ta1          80 DS   81 (83)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.4e-18  Score=116.54  Aligned_cols=74  Identities=28%  Similarity=0.559  Sum_probs=68.1

Q ss_pred             CCCEEEEeccCCCCCCHHHHHH----hhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           64 PTKTLFVINFDPIRTRERDIKR----HFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~----~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      |+++|||+|| |..+++++|++    +|++||+|..|.+.     +|||||+|.+.++|+.|+..|||..|+|+.|.|.|
T Consensus         2 P~~tl~V~nL-p~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           2 PNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCSEEEEESC-CTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5789999999 88999998864    58999999999984     79999999999999999999999999999999999


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      |+.+
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9865

>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=2.9e-18  Score=117.76  Aligned_cols=78  Identities=31%  Similarity=0.494  Sum_probs=69.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcC------CCccc
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTD------RSKLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~------g~~~~  126 (240)
                      .....++|||+|| |+.+++++|+++|.+||+|..+.+        .+|||||+|.+.++|+.||+.||      |..|.
T Consensus         4 ~~~~~~tlfV~nL-p~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~   82 (98)
T d1x4ha1           4 DVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   82 (98)
T ss_dssp             CCCCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CCCCCCEEEEcCC-CCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEEC
Confidence            3445789999999 999999999999999999998887        36899999999999999999886      56788


Q ss_pred             CcEEEEEEeecCC
Q 026341          127 DRVISVEYALKDD  139 (240)
Q Consensus       127 g~~l~v~~a~~~~  139 (240)
                      |+.|.|++|.++.
T Consensus        83 gr~l~v~~a~~k~   95 (98)
T d1x4ha1          83 GRQLKVDLAVTRD   95 (98)
T ss_dssp             SCEEEEECCCCCC
T ss_pred             CEEEEEEECCCCC
Confidence            9999999998754

>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=99.75  E-value=9.1e-19  Score=121.22  Aligned_cols=79  Identities=27%  Similarity=0.419  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...|+++|||+|| |..+++++|+++|.+||.|..+.+        .++||||+|.+.++|+.||+.|||..|.|+.|.|
T Consensus        14 ~~~ps~tl~V~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   92 (102)
T d2cpxa1          14 PGEPNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   92 (102)
T ss_dssp             CCSCCSEEEEECC-CTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEE
Confidence            3457899999999 889999999999999998877665        3689999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +||+++..
T Consensus        93 ~~ak~k~~  100 (102)
T d2cpxa1          93 EFGKNKKQ  100 (102)
T ss_dssp             EECCCCSC
T ss_pred             EeCCCccc
Confidence            99987654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.4e-18  Score=120.11  Aligned_cols=77  Identities=19%  Similarity=0.210  Sum_probs=68.1

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE----------------eCCeEEEEecCHHHHHHHHHhcCCCcc
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI----------------RRNFAFVQFETQEEATKALESTDRSKL  125 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~----------------~kg~afV~f~~~~~a~~A~~~l~g~~~  125 (240)
                      .....+|||+|| |..+++++|+++|.+||.|..+.+                .++||||+|.++++|+.||+.|||..|
T Consensus         5 ~~~~~~i~V~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECC-CTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECC-CCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345789999999 999999999999999998854322                258999999999999999999999999


Q ss_pred             cCcEEEEEEeecCC
Q 026341          126 VDRVISVEYALKDD  139 (240)
Q Consensus       126 ~g~~l~v~~a~~~~  139 (240)
                      +|+.|.|++|+++.
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999998654

>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=99.75  E-value=6.3e-18  Score=113.71  Aligned_cols=78  Identities=21%  Similarity=0.383  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc--CCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST--DRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l--~g~~~~g~~l~v~~a~  136 (240)
                      ..+|+.+|||+|| |..+++++|.++|++||.|..+.+.  +++|||+|.+.++|+.|++.|  ++..|.|++|.|.|++
T Consensus         4 ~~~Ps~~l~V~nL-p~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           4 DGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             CSSCCSEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            4678999999999 8899999999999999999999985  799999999999999999865  5778999999999997


Q ss_pred             cCC
Q 026341          137 KDD  139 (240)
Q Consensus       137 ~~~  139 (240)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=1.6e-18  Score=116.15  Aligned_cols=72  Identities=31%  Similarity=0.480  Sum_probs=64.9

Q ss_pred             CCEEEEeccCCCCCC-HHHHHHhhccCCCeEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           65 TKTLFVINFDPIRTR-ERDIKRHFEPYGNVLHVRIR---------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~-~~~l~~~f~~~G~i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      ..+|||+|| |..++ +++|+++|++||.|..|.|.         +|||||+|.+.++|++||+ |||..|+|+.|.|++
T Consensus         4 ~~~l~V~nL-p~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           4 GREIMIRNL-STELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTEEEEEEE-CTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCEEEEECC-CCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            679999999 77765 56699999999999999873         5799999999999999995 999999999999999


Q ss_pred             eecC
Q 026341          135 ALKD  138 (240)
Q Consensus       135 a~~~  138 (240)
                      |+++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>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=99.74  E-value=3e-18  Score=118.50  Aligned_cols=74  Identities=22%  Similarity=0.447  Sum_probs=68.3

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+|||+|| |+.+++++|+++|.+||.|..+.|+        +|||||+|.+.++|++||+ +++..|+|+.|.|.+|.
T Consensus        20 ~~~lfVgnL-p~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGL-SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECC-TTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCC-CCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            478999999 9999999999999999999999983        6899999999999999996 79999999999999998


Q ss_pred             cCCC
Q 026341          137 KDDS  140 (240)
Q Consensus       137 ~~~~  140 (240)
                      ++..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>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=99.74  E-value=1.7e-17  Score=115.12  Aligned_cols=80  Identities=15%  Similarity=0.202  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc--CCCcccCcEEEEEEee
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST--DRSKLVDRVISVEYAL  136 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l--~g~~~~g~~l~v~~a~  136 (240)
                      ..+++.+|||+|| |..+++++|.++|.+||.|..+.+.  +++|||+|++.++|+.||..|  ++..+.|++|.|.|++
T Consensus        11 ~~~ps~~l~v~nl-p~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~   89 (104)
T d1wexa_          11 KVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESC-CSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcC
Confidence            4567899999999 8899999999999999999999995  789999999999999999987  5567889999999998


Q ss_pred             cCCCC
Q 026341          137 KDDSE  141 (240)
Q Consensus       137 ~~~~~  141 (240)
                      .+...
T Consensus        90 ~~~~~   94 (104)
T d1wexa_          90 SKRIT   94 (104)
T ss_dssp             SSSCC
T ss_pred             CCccC
Confidence            75543

>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=99.74  E-value=1.7e-18  Score=120.29  Aligned_cols=73  Identities=25%  Similarity=0.501  Sum_probs=68.0

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.+.++|+.|++.|||..|.|+.|.|+++.
T Consensus         8 ~rtl~V~nL-p~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           8 LRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESC-CTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECC-CCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            468999999 8899999999999999999999883        5799999999999999999999999999999999987


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      +.
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.74  E-value=1e-17  Score=116.29  Aligned_cols=76  Identities=28%  Similarity=0.450  Sum_probs=66.0

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE---------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~---------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..|.++|||+|| |+.+++++|+++|++|| |..+.+         .+|||||+|.+.++|++|+ .||+..|+|+.|.|
T Consensus        12 ~~p~~~v~V~nL-p~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V   88 (104)
T d1wi8a_          12 KSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             SSSCEEEEEESC-CSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCEEEEeCC-CCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEE
Confidence            345689999999 99999999999999998 666655         2579999999999998776 59999999999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      .+|.++..
T Consensus        89 ~~a~~~~~   96 (104)
T d1wi8a_          89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99987643

>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=99.74  E-value=4.6e-18  Score=114.70  Aligned_cols=75  Identities=27%  Similarity=0.508  Sum_probs=67.1

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      .....+|||+|| |+.+++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+.+  ..|+|+.|.|.
T Consensus         5 ~~~~~~lfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~   81 (90)
T d2cqga1           5 VQKTSDLIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEE
T ss_pred             CcCCCeEEEECC-CCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEE
Confidence            345688999999 9999999999999999999999984        589999999999999999854  47999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++.++.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            998754

>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=99.74  E-value=1.9e-18  Score=116.28  Aligned_cols=73  Identities=23%  Similarity=0.352  Sum_probs=67.0

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe---CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecCC
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR---RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDD  139 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~---kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  139 (240)
                      ..++|||+|| |+.+++++|+++|++||.|..|.++   ++||||+|++.++|++||.  ++..|+|++|.|.+|.++.
T Consensus         4 ~s~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           4 GSSGVFVGRC-TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESC-CSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            4789999999 9999999999999999999999884   7999999999999999985  7889999999999997654

>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=99.73  E-value=5.7e-18  Score=112.84  Aligned_cols=71  Identities=27%  Similarity=0.521  Sum_probs=65.5

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+|||+|| |+.+++++|+++|++||.|..+.|+        +|||||+|.+.++|++||+ +++..|+|+.|.|..|
T Consensus         5 ~~~~lfV~nl-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           5 QLRKLFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCcEEEEECC-CCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            3578999999 9999999999999999999999883        6899999999999999997 6999999999999887


Q ss_pred             e
Q 026341          136 L  136 (240)
Q Consensus       136 ~  136 (240)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.73  E-value=9.2e-18  Score=109.32  Aligned_cols=69  Identities=20%  Similarity=0.353  Sum_probs=62.8

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEEEE--eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeecC
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD  138 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  138 (240)
                      |||+|| |..+++++|+++|.+|| +..+.+  .+|+|||+|.+.++|++|++.|||..+.|++|.|+|+...
T Consensus         1 i~V~nL-p~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGL-PGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECC-CTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCC-CCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            799999 89999999999999999 444444  6899999999999999999999999999999999999654

>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=99.73  E-value=1.5e-18  Score=113.64  Aligned_cols=68  Identities=25%  Similarity=0.437  Sum_probs=63.8

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      |.|||+|| |+.+++++|+++|++||+|..+.|+        +|||||+|.++++|++||+ ++++.|+|+.|.|.+|
T Consensus         1 cklfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESC-CSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCC-CCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            57999999 9999999999999999999999883        6899999999999999997 7999999999999987

>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=99.73  E-value=3e-18  Score=118.12  Aligned_cols=72  Identities=26%  Similarity=0.457  Sum_probs=66.8

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |+.+++++|+++|+.||+|..|.|.        +|||||+|.+.++|++|+. |||..|.|+.|.|.++.
T Consensus        18 ~~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          18 ARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECC-CCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            578999999 9999999999999999999999983        6899999999999999995 99999999999999986


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      +.
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.72  E-value=5e-18  Score=117.17  Aligned_cols=74  Identities=18%  Similarity=0.375  Sum_probs=66.4

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...++|||+|| |..+++++|+++|++||.|..+.+.       +|||||+|.+.++|++||+.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34578999999 8899999999999999999988873       579999999999999999999999999998887665


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.72  E-value=7e-18  Score=109.97  Aligned_cols=66  Identities=27%  Similarity=0.557  Sum_probs=61.3

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .|||+|| |+.+++++|.++|++||+|..+.|+        +|||||+|.+.++|++||+ +++..|+|+.|.|..
T Consensus         1 klfV~nl-~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGL-SWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCC-CCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            4899999 8999999999999999999999983        6899999999999999997 799999999998854

>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=99.72  E-value=2e-17  Score=113.55  Aligned_cols=78  Identities=21%  Similarity=0.360  Sum_probs=69.5

Q ss_pred             CCCCCCEEEEeccCCC-CCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHH--hcCCCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPI-RTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALE--STDRSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~--~l~g~~~~g~~l~v~~a  135 (240)
                      ...++++|||+|| |. .+|+++|.++|++||.|..+.+.  +++|||+|.+.++|..|++  .+++..|.|+.|.|.|+
T Consensus        14 ~~~~~~~l~v~nL-p~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          14 KQELGRVIHLSNL-PHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SSCCCCEEEEESC-CCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCC-cCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            4456789999999 76 48999999999999999999995  7999999999999999998  46888999999999999


Q ss_pred             ecCC
Q 026341          136 LKDD  139 (240)
Q Consensus       136 ~~~~  139 (240)
                      +...
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            7643

>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=99.72  E-value=5.4e-18  Score=110.55  Aligned_cols=67  Identities=27%  Similarity=0.494  Sum_probs=62.6

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .|||+|| |..+++++|+++|++||.|..+.+.        +++|||+|.+.++|++|++ |||..|+|++|.|++|
T Consensus         1 rlfV~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGL-SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECC-CSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCC-CCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            4899999 8999999999999999999998873        6899999999999999997 9999999999999886

>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=99.72  E-value=1.6e-17  Score=109.35  Aligned_cols=69  Identities=28%  Similarity=0.437  Sum_probs=63.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .++|||+|| |+.+|+++|+++|++||.|..+.+.        +|||||+|.+.++|++|+. |||..|+|+.|.|+.|
T Consensus         2 ~r~lfV~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGI-KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECC-TTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCC-CCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            468999999 8999999999999999999999883        5899999999999999986 8999999999999876

>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=99.72  E-value=1.1e-18  Score=118.10  Aligned_cols=74  Identities=23%  Similarity=0.293  Sum_probs=66.9

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      .....+|||+|| |+.+++++|+++|.+||.|..+.|       .+|||||+|.+.++|++||+ |||..|.|+.|.|++
T Consensus        10 ~~~~~~ifV~nL-~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECC-CTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCc-cCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            344678999999 999999999999999998877666       37999999999999999996 999999999999999


Q ss_pred             eec
Q 026341          135 ALK  137 (240)
Q Consensus       135 a~~  137 (240)
                      |+.
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>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=99.71  E-value=4.6e-18  Score=118.83  Aligned_cols=78  Identities=18%  Similarity=0.240  Sum_probs=69.6

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCcc--cCcEEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKL--VDRVISVEY  134 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~  134 (240)
                      ...+..+|||+|| ++.+|+++|+++|++||.|..|.+.    +|+|||+|.+.++|+.||..|||..|  .+..|.|.|
T Consensus         3 ~~s~~~~v~V~NL-~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           3 GQSPVLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CCCCEEEEESCSC-CSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CCCCeEEEEEeCc-CCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            3456788999999 9999999999999999999999883    67999999999999999999999998  468899988


Q ss_pred             eecCC
Q 026341          135 ALKDD  139 (240)
Q Consensus       135 a~~~~  139 (240)
                      ++...
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87644

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1.7e-17  Score=108.06  Aligned_cols=68  Identities=22%  Similarity=0.350  Sum_probs=63.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ++|||+|| |+.+++++|+++|..||+|..+.+.      +++|||+|+++++|++|+. ||+..|+|+.|.|+.+
T Consensus         1 Ttv~V~nl-p~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNL-PKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            47999999 9999999999999999999999984      4699999999999999985 8999999999999865

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=4.9e-17  Score=112.28  Aligned_cols=76  Identities=24%  Similarity=0.375  Sum_probs=66.3

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      ......+|||.|| |+++|+++|+++|..||.+ .+.+       .+|||||+|.++++|++|++ ||+..|.|+.|.|.
T Consensus        11 ~~~~~~~v~v~nL-p~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGL-PYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESC-CTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCC-CCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            4456789999999 9999999999999999854 4444       36899999999999999986 89999999999999


Q ss_pred             EeecCC
Q 026341          134 YALKDD  139 (240)
Q Consensus       134 ~a~~~~  139 (240)
                      ++....
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            988654

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.4e-17  Score=112.16  Aligned_cols=69  Identities=19%  Similarity=0.402  Sum_probs=63.0

Q ss_pred             CCCEEEEeccCCCCCCHHHH---HHhhccCCCeEEEEEe-----------CCeEEEEecCHHHHHHHHHhcCCCcccCcE
Q 026341           64 PTKTLFVINFDPIRTRERDI---KRHFEPYGNVLHVRIR-----------RNFAFVQFETQEEATKALESTDRSKLVDRV  129 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l---~~~f~~~G~i~~~~~~-----------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~  129 (240)
                      ..++|||+|| |+.+++++|   .++|.+||+|..|.++           .|||||+|.+.++|++|++.|||..|+|++
T Consensus         7 q~n~vyV~nL-p~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGL-SQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CSSCEEEEEE-CTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             ecCEEEEECC-CCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            3567999999 889999999   7789999999999984           279999999999999999999999999999


Q ss_pred             EEEE
Q 026341          130 ISVE  133 (240)
Q Consensus       130 l~v~  133 (240)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9884

>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=99.70  E-value=3.8e-17  Score=108.97  Aligned_cols=70  Identities=27%  Similarity=0.478  Sum_probs=65.2

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      ..+|||+|| |..+++++|.++|+.||+|..|.|.       +|||||+|.++++|++||+ +++..|.|+.|.|.|..
T Consensus         6 ~rtvfV~nl-p~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECC-CTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECC-CCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            578999999 9999999999999999999999984       5899999999999999996 79999999999999864

>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=99.69  E-value=1.5e-16  Score=110.20  Aligned_cols=77  Identities=22%  Similarity=0.261  Sum_probs=67.7

Q ss_pred             CCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEE
Q 026341           62 QRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVE  133 (240)
Q Consensus        62 ~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  133 (240)
                      .....+|||+|| |+.+++++|+++|..+|.|..+.+        .+|+|||+|.++++|++|++ ||+..|.|+.|.|.
T Consensus        12 ~~~~~~v~v~nL-P~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          12 TANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESC-CTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            344668999999 999999999999999998876544        37999999999999999996 89999999999999


Q ss_pred             EeecCCC
Q 026341          134 YALKDDS  140 (240)
Q Consensus       134 ~a~~~~~  140 (240)
                      ++.....
T Consensus        90 ~~~~~~~   96 (104)
T d1wg5a_          90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHh
Confidence            9987654

>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=99.69  E-value=5.2e-17  Score=109.22  Aligned_cols=77  Identities=18%  Similarity=0.297  Sum_probs=68.7

Q ss_pred             CCCCCCEEEEeccCCCC-CCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhc--CCCcccCcEEEEEEe
Q 026341           61 NQRPTKTLFVINFDPIR-TRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALEST--DRSKLVDRVISVEYA  135 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~-~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l--~g~~~~g~~l~v~~a  135 (240)
                      ...+..+|||+|| |.. +|++||.++|++||.|..|.+.  +++|||+|++.++|+.|+..|  ++..+.|++|.|.||
T Consensus         4 ~~~~sr~v~v~nl-~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s   82 (89)
T d1x4da1           4 RVETRRVVHIMDF-QRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   82 (89)
T ss_dssp             CCCCCCEEEEESC-CCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCcEEEEECC-CCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEEC
Confidence            3456899999999 764 7899999999999999999994  689999999999999999966  677899999999999


Q ss_pred             ecC
Q 026341          136 LKD  138 (240)
Q Consensus       136 ~~~  138 (240)
                      +..
T Consensus        83 ~~~   85 (89)
T d1x4da1          83 QKY   85 (89)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            754

>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=1.6e-17  Score=111.21  Aligned_cols=72  Identities=22%  Similarity=0.275  Sum_probs=64.0

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEE-EEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEE
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEY  134 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~-~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  134 (240)
                      +..++|||+|| |+.+++++|+++|..||.|.. +.+       ++|+|||+|.+.++|++||+.||+..|.|++|.|++
T Consensus         7 p~~~~l~v~nL-p~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESC-CTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999 999999999999999998754 233       368999999999999999999999999999999987


Q ss_pred             e
Q 026341          135 A  135 (240)
Q Consensus       135 a  135 (240)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.69  E-value=1.1e-17  Score=108.77  Aligned_cols=67  Identities=24%  Similarity=0.419  Sum_probs=61.6

Q ss_pred             EEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           67 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        67 ~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      .|||+|| |+.+++++|+++|++||.|..|.|+        +|||||+|.+.++|++||+ +++..|+|+.|.|..|
T Consensus         1 klfVgnL-p~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGL-SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESC-CSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCC-CCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            4899999 9999999999999999999999983        6899999999999999997 4778999999998765

>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=99.69  E-value=4.4e-17  Score=111.32  Aligned_cols=75  Identities=25%  Similarity=0.367  Sum_probs=66.0

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCC-eEEEEEe---------CCeEEEEecCHHHHHHHHHhcCCC--cccCcEEEE
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGN-VLHVRIR---------RNFAFVQFETQEEATKALESTDRS--KLVDRVISV  132 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~-i~~~~~~---------kg~afV~f~~~~~a~~A~~~l~g~--~~~g~~l~v  132 (240)
                      ++.|||+|| |..+++++|+++|++||+ |..+.|.         +|||||+|.+.++|..|++.|++.  .+.|+.|.|
T Consensus         1 n~rLyV~nL-p~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             SEEEEEECC-CTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCEEEEcCC-CCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEE
Confidence            368999999 899999999999999995 8888883         579999999999999999999654  557999999


Q ss_pred             EEeecCCC
Q 026341          133 EYALKDDS  140 (240)
Q Consensus       133 ~~a~~~~~  140 (240)
                      +||++...
T Consensus        80 ~~A~p~~~   87 (96)
T d2disa1          80 DWAEPEID   87 (96)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99987553

>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=99.66  E-value=2.7e-17  Score=106.28  Aligned_cols=62  Identities=21%  Similarity=0.503  Sum_probs=58.5

Q ss_pred             EEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEE
Q 026341           68 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVI  130 (240)
Q Consensus        68 l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l  130 (240)
                      |||+|| |..+++++|.++|.+||.|..+.+.        +|+|||+|.+.++|++|++.|||..|.|+.|
T Consensus         1 lyV~nL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESC-CTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCC-CCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            799999 9999999999999999999998873        6899999999999999999999999999876

>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=99.64  E-value=1.8e-16  Score=109.60  Aligned_cols=77  Identities=9%  Similarity=0.067  Sum_probs=67.2

Q ss_pred             CCCCEEEEeccCCCCC-C----HHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           63 RPTKTLFVINFDPIRT-R----ERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~-~----~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ....+|||+|| +..+ +    .++|+++|++||.|..+.+.  +++|||+|.+.++|++|+..|||..|+|+.|.|.|+
T Consensus         3 ~~~~~L~v~nl-~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   81 (104)
T d1weya_           3 SGSSGLIACVA-NDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA   81 (104)
T ss_dssp             SCCCEEEEECC-CGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECC
T ss_pred             CCCceEEEEeC-CchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeec
Confidence            34788999999 5443 3    36799999999999999996  578999999999999999999999999999999999


Q ss_pred             ecCCC
Q 026341          136 LKDDS  140 (240)
Q Consensus       136 ~~~~~  140 (240)
                      +....
T Consensus        82 ~~~~~   86 (104)
T d1weya_          82 QTLHI   86 (104)
T ss_dssp             CCSSC
T ss_pred             ccCCC
Confidence            76543

>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=99.63  E-value=1.9e-16  Score=109.48  Aligned_cols=72  Identities=22%  Similarity=0.248  Sum_probs=64.3

Q ss_pred             CCCEEEEeccCCCCCCHHHHHHhhccCCCeEE-EEE-------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           64 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLH-VRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        64 ~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~-~~~-------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ...+|||+|| |+.+++++|.++|..||.|.. +.+       .+|+|||+|.+.++|++||+ ||+..|+|+.|.|.++
T Consensus         7 ~~~~v~v~nL-p~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           7 AKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CCCEEEEESC-CTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CceEEEEeCC-CCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            4568999999 999999999999999998865 333       37899999999999999996 8999999999999998


Q ss_pred             ec
Q 026341          136 LK  137 (240)
Q Consensus       136 ~~  137 (240)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>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=99.62  E-value=3e-16  Score=110.10  Aligned_cols=75  Identities=16%  Similarity=0.253  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE--------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~--------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ...+..+|||+|| |+.+++++|.++|..||.|..+.+        .+|+|||+|.+.++|++|++ |||..|+|+.|.|
T Consensus        14 ~~~~~~~i~v~nL-p~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          14 PHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             CCCCCCEEEEECC-CTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCeEEEEecC-CCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            3445779999999 999999999999999998754322        36899999999999999996 8999999999999


Q ss_pred             EEeec
Q 026341          133 EYALK  137 (240)
Q Consensus       133 ~~a~~  137 (240)
                      ..+..
T Consensus        92 ~~~~~   96 (112)
T d1wela1          92 HPITK   96 (112)
T ss_dssp             EEECH
T ss_pred             EEcCh
Confidence            98754

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=5.2e-15  Score=101.58  Aligned_cols=65  Identities=20%  Similarity=0.311  Sum_probs=58.7

Q ss_pred             CCCCCCEEEEec--cCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           61 NQRPTKTLFVIN--FDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~n--l~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      ...|+.+|+|.|  | +..+|+++|+++|++||.|..|.+.  ++||||+|.+.++|+.|+..|||..|.
T Consensus        14 ~~~pt~~l~V~ng~L-~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGL-GNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTG-GGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCC-CCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345688899965  9 8899999999999999999999885  689999999999999999999999873

>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=99.56  E-value=9.1e-15  Score=102.49  Aligned_cols=72  Identities=15%  Similarity=0.185  Sum_probs=62.9

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCH-HHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQ-EEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~-~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      +..+||+|| |..+|+++|+++|++||+|..|.|+  ++||||.|.+. ++|.+|+..||+..|.+..+.|.|+..
T Consensus        11 ~~~~fvgnL-~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDL-DDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESC-CSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCC-CCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            345599999 8899999999999999999999997  68999999985 789999999999988877777777653

>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=99.55  E-value=4e-17  Score=110.17  Aligned_cols=68  Identities=22%  Similarity=0.387  Sum_probs=60.1

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEE-------------eCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~-------------~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      .+|||+|| |+.+++++|+++|++||.|..+.+             .+|||||+|.+.++|+.|++ |||..+.|+.|.|
T Consensus         2 RrlyVgNL-p~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSC-CTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCC
T ss_pred             CEEEEcCC-CCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEE
Confidence            57999999 999999999999999987765543             37899999999999999985 9999999999999


Q ss_pred             EEe
Q 026341          133 EYA  135 (240)
Q Consensus       133 ~~a  135 (240)
                      ..+
T Consensus        80 ~r~   82 (90)
T d1u2fa_          80 RRP   82 (90)
T ss_dssp             BCT
T ss_pred             CCC
Confidence            643

>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=99.45  E-value=2.8e-13  Score=92.43  Aligned_cols=78  Identities=17%  Similarity=0.214  Sum_probs=65.2

Q ss_pred             CCCCCCEEEEeccCC-CCC---------CHHHHHHhhccCCCeEEEEEe----CCeEEEEecCHHHHHHHHHhcCCCccc
Q 026341           61 NQRPTKTLFVINFDP-IRT---------RERDIKRHFEPYGNVLHVRIR----RNFAFVQFETQEEATKALESTDRSKLV  126 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~-~~~---------~~~~l~~~f~~~G~i~~~~~~----kg~afV~f~~~~~a~~A~~~l~g~~~~  126 (240)
                      ......+|+|.||-. ..+         ..++|++.|.+||.|..|.+.    +|+|||+|++.++|.+|+..|||..|+
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            345688999999821 111         126789999999999999884    689999999999999999999999999


Q ss_pred             CcEEEEEEeecC
Q 026341          127 DRVISVEYALKD  138 (240)
Q Consensus       127 g~~l~v~~a~~~  138 (240)
                      |++|.|+++.+.
T Consensus        84 gr~i~v~~~~g~   95 (99)
T d2dita1          84 GRQITAQAWDGT   95 (99)
T ss_dssp             TEECEEEECCSC
T ss_pred             CEEEEEEEeCCc
Confidence            999999998654

>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=99.45  E-value=3.1e-15  Score=103.22  Aligned_cols=69  Identities=19%  Similarity=0.195  Sum_probs=62.9

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe-------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEe
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR-------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA  135 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~-------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  135 (240)
                      ..++|.++ ...+++++|+++|++||+|..|.|+       +|+|||+|.+.++|.+|+..|||..|+|++|.|+|+
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 SDVEMQEH-YDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHH-HHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhh-hhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34777888 6778899999999999999999984       589999999999999999999999999999999985

>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=99.39  E-value=3e-13  Score=88.57  Aligned_cols=70  Identities=24%  Similarity=0.433  Sum_probs=58.8

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--CCeEEEEecCHHHHHHHHHhcCCCcccCcE-EEEEEeec
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--RNFAFVQFETQEEATKALESTDRSKLVDRV-ISVEYALK  137 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--kg~afV~f~~~~~a~~A~~~l~g~~~~g~~-l~v~~a~~  137 (240)
                      .+.|+|+++ |..++++ |..+|++||+|..+.+.  ++||||+|.+.++|++||+ |||..|+|+. |.|..+..
T Consensus         4 ~~wV~V~G~-p~~~~~~-il~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGF-PQASASY-ILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECC-CGGGHHH-HHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECC-ChHHHHH-HHHHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            456999999 7677655 55689999999999985  6999999999999999996 8999999975 56776654

>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=99.38  E-value=1.1e-12  Score=90.34  Aligned_cols=75  Identities=24%  Similarity=0.373  Sum_probs=64.0

Q ss_pred             CCCCEEEEeccCC-CCC--------CHHHHHHhhccCCCeEEEEEe----------CCeEEEEecCHHHHHHHHHhcCCC
Q 026341           63 RPTKTLFVINFDP-IRT--------RERDIKRHFEPYGNVLHVRIR----------RNFAFVQFETQEEATKALESTDRS  123 (240)
Q Consensus        63 ~~~~~l~v~nl~~-~~~--------~~~~l~~~f~~~G~i~~~~~~----------kg~afV~f~~~~~a~~A~~~l~g~  123 (240)
                      +|+.+|.|.||-. ..+        ..++|++.|++||.|..|.|+          .|++||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            5789999999821 111        135789999999999999984          379999999999999999999999


Q ss_pred             cccCcEEEEEEeec
Q 026341          124 KLVDRVISVEYALK  137 (240)
Q Consensus       124 ~~~g~~l~v~~a~~  137 (240)
                      .++|+.|.|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>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=99.22  E-value=1.7e-11  Score=92.63  Aligned_cols=72  Identities=26%  Similarity=0.517  Sum_probs=62.6

Q ss_pred             CCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEe--------CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEee
Q 026341           65 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL  136 (240)
Q Consensus        65 ~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~--------kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  136 (240)
                      .++|||+|| |+.+++++|.++|++||.|..+.+.        +|+|||+|.+.++|++|+.. ++..+.+..+.+....
T Consensus         6 ~r~lfV~nL-p~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           6 LRKLFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CCEEEEECC-CCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            468999999 8899999999999999999999874        57999999999999999984 6677888888777765


Q ss_pred             cC
Q 026341          137 KD  138 (240)
Q Consensus       137 ~~  138 (240)
                      ..
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            44

>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=99.17  E-value=1.6e-11  Score=80.77  Aligned_cols=45  Identities=20%  Similarity=0.294  Sum_probs=41.1

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+++++|||||+|.++++|++|++.|||..|  +|++|.|+||.++.
T Consensus        36 ~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~--~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          36 DTGNSKGYAFINFASFDASDAAIEAMNGQYL--CNRPITVSYAFKKD   80 (83)
T ss_dssp             TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE--TTEECEEEESCCCC
T ss_pred             cccccCceEEEEECCHHHHHHHHHhCCCcEE--CCEEEEEEEecCCC
Confidence            3678899999999999999999999999999  69999999998654

>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=99.14  E-value=3.8e-11  Score=80.78  Aligned_cols=44  Identities=36%  Similarity=0.537  Sum_probs=40.3

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhh-CCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGL-DNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l-~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++||..| ||..|  +|++|.|+||..+.
T Consensus        47 ~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~--~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          47 TGAHRGFGFVDFITKQDAKKAFNALCHSTHL--YGRRLVLEWADSEV   91 (94)
T ss_dssp             SCSSCSEEEEEESSHHHHHHHHHHHHTCCBS--SSCBCEEEECCCCC
T ss_pred             CCCcccEEEEEECCHHHHHHHHHHccCCcEE--CCEEEEEEEcCCCC
Confidence            6788999999999999999999998 88888  69999999998654

>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=99.14  E-value=2.3e-11  Score=81.08  Aligned_cols=45  Identities=36%  Similarity=0.423  Sum_probs=41.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|++|.|+||.+.+
T Consensus        42 ~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i--~g~~l~v~~a~p~~   86 (89)
T d2cqba1          42 ETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVNLAKPMR   86 (89)
T ss_dssp             SSCCCSSEEEECCSSHHHHHHHHHHHTTEEE--TTEEEEEEECCCCC
T ss_pred             ccccccceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEeCCCC
Confidence            4688899999999999999999999999999  69999999998654

>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=99.14  E-value=1.7e-11  Score=81.49  Aligned_cols=44  Identities=20%  Similarity=0.350  Sum_probs=40.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+++++|||||+|.+.++|++|+..|||..|  +|+.|.|+||.++
T Consensus        44 ~tg~~~g~afV~f~~~~~A~~A~~~lng~~l--~g~~l~V~~a~~k   87 (88)
T d1rk8a_          44 RTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQVDWCFVK   87 (88)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEESEEC
T ss_pred             cccccccceeEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEecCC
Confidence            4678899999999999999999999999999  6999999999854

>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=99.14  E-value=2.5e-11  Score=81.06  Aligned_cols=44  Identities=39%  Similarity=0.653  Sum_probs=40.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .++.++|||||+|.+.++|++||+.|||..|  +|+.|.|+||.+.
T Consensus        45 ~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v~~akp~   88 (90)
T d2cq0a1          45 TTGQSKGFAFISFHRREDAARAIAGVSGFGY--DHLILNVEWAKPS   88 (90)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECEEEESSCC
T ss_pred             cccccccceeEEECCHHHHHHHHHHhCCCEE--CCEEEEEEeeeCC
Confidence            3678899999999999999999999999999  6999999999864

>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=99.13  E-value=3.4e-11  Score=80.89  Aligned_cols=45  Identities=27%  Similarity=0.378  Sum_probs=41.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|+.++|||||+|.+.++|++||+.|||..|  +|++|.|+||.+..
T Consensus        46 ~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          46 VTGQHQGYGFVEFLSEEDADYAIKIMDMIKL--YGKPIRVNKASAHN   90 (93)
T ss_dssp             SSCSBCSCEEEEESSHHHHHHHHHHSSSCBC--SSCBCEEEETTTTS
T ss_pred             cccccccceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEcCCCC
Confidence            4678899999999999999999999999999  69999999998754

>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=99.13  E-value=5.9e-11  Score=80.60  Aligned_cols=47  Identities=28%  Similarity=0.279  Sum_probs=42.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .|+.++|||||+|.+.++|++||+.||+..|  +|++|.|+++..+...
T Consensus        45 ~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~--~gr~i~V~~a~~~~~~   91 (99)
T d1whwa_          45 LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             TTCCCCSEEEEEESSHHHHHHHHHHTTTEES--SSCEEEEEECCCCSTT
T ss_pred             cccccCcceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCCcc
Confidence            4678899999999999999999999999998  6999999999976543

>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=99.13  E-value=2.5e-11  Score=79.56  Aligned_cols=43  Identities=35%  Similarity=0.508  Sum_probs=39.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++.++|||||+|.++++|++|+..|||..|  +|++|.|+||.+
T Consensus        39 ~~g~~~g~afV~f~~~~~A~~ai~~lng~~~--~g~~l~v~~a~p   81 (82)
T d1b7fa1          39 KTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYARP   81 (82)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCC
T ss_pred             ccCCccccceEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCC
Confidence            3678899999999999999999999999999  699999999974

>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=99.12  E-value=2.9e-11  Score=82.63  Aligned_cols=46  Identities=22%  Similarity=0.380  Sum_probs=42.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.++++|+.||+.|||..|  +|++|.|+|+.++..
T Consensus        55 ~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~--~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          55 QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI--GMKRLKVQLKRSKND  100 (102)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEECCCCSCC
T ss_pred             ccCCCccceEEEeCCHHHHHHHHHHhCCCEE--CCEEEEEEEeCCCCC
Confidence            4678899999999999999999999999999  699999999987653

>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=99.12  E-value=4.5e-11  Score=77.54  Aligned_cols=42  Identities=29%  Similarity=0.399  Sum_probs=39.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      ++++++|||||+|.++++|++|++.|||..|  +|++|.|+++.
T Consensus        36 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l--~g~~l~V~~a~   77 (78)
T d1no8a_          36 RSGRSLGTADVHFERKADALKAMKQYNGVPL--DGRPMNIQLVT   77 (78)
T ss_dssp             SCCCSCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEEEC
T ss_pred             eccccceeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEee
Confidence            4788899999999999999999999999999  69999999986

>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=99.11  E-value=3.7e-11  Score=78.68  Aligned_cols=43  Identities=30%  Similarity=0.563  Sum_probs=39.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++.++|||||+|.++++|++|+..|||..|  +|++|.|+||++
T Consensus        39 ~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~AkP   81 (82)
T d1fxla1          39 ITGQSLGYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYARP   81 (82)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCC
T ss_pred             cCCCceeeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEeeC
Confidence            3567899999999999999999999999999  699999999975

>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=99.10  E-value=5.4e-11  Score=78.50  Aligned_cols=45  Identities=24%  Similarity=0.332  Sum_probs=41.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|+.++|||||+|.++++|+.|+..|||..|  +|++|.|+||....
T Consensus        38 ~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l--~g~~l~V~~A~~~~   82 (85)
T d2u2fa_          38 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRASVGA   82 (85)
T ss_dssp             SSSCCCCEEEEEESSSHHHHHHHHTSSSCCC--SSSCCEEEECCCCC
T ss_pred             cccccceeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCCC
Confidence            4688999999999999999999999999999  69999999998643

>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=99.09  E-value=3.5e-11  Score=78.46  Aligned_cols=43  Identities=21%  Similarity=0.451  Sum_probs=39.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .|+.++|||||+|.++++|+.|++.|||..|  +|++|+|+|+..
T Consensus        37 ~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~--~gr~i~v~~a~~   79 (80)
T d1cvja1          37 ITRRSLGYAYVNFQQPADAERALDTMNFDVI--KGKPVRIMWSQR   79 (80)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHTTSTTCEE--TTEECEEEECCC
T ss_pred             cccCCCCceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEeCC
Confidence            3678899999999999999999999999999  699999999863

>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=99.09  E-value=4e-11  Score=78.35  Aligned_cols=43  Identities=14%  Similarity=0.170  Sum_probs=36.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ++++++|||||+|.++++|++|++.|||..|  +|++|.|+++.|
T Consensus        38 ~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~--~g~~i~V~~a~P   80 (81)
T d2ghpa1          38 RFNTSRRFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSNP   80 (81)
T ss_dssp             -----CCEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCC
T ss_pred             ccccccceeEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEccC
Confidence            3677899999999999999999999999999  799999999975

>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=99.08  E-value=3.5e-11  Score=80.13  Aligned_cols=43  Identities=23%  Similarity=0.419  Sum_probs=39.1

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..++|||||+|.+.++|++||+.|||..|  +|++|.|+++.++.
T Consensus        45 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~V~~a~~~~   87 (89)
T d1cvja2          45 NGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSRK   87 (89)
T ss_dssp             TBCCSCEEEEESCHHHHHHHTTSSSEEEE--TTEEEEEEECCCTT
T ss_pred             CCCcceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCC
Confidence            34689999999999999999999999999  69999999998654

>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=99.08  E-value=7.9e-11  Score=79.04  Aligned_cols=45  Identities=27%  Similarity=0.547  Sum_probs=40.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++.++|||||+|.+.++|+.|++.|||..|  +|++|.|+|+....
T Consensus        44 ~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          44 MKKTACGFCFVEYYSRADAENAMRYINGTRL--DDRIIRTDWDAGFK   88 (93)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHTTTSEE--TTEECEEEEESCCC
T ss_pred             ccccccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCC
Confidence            3677899999999999999999999999999  69999999997544

>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=99.07  E-value=4.6e-11  Score=77.88  Aligned_cols=45  Identities=24%  Similarity=0.374  Sum_probs=39.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCC-cccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNI-PFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~-~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++..+|||||+|.++++|++|++.|||. .|  +|++|.|+|+.++.+
T Consensus        33 ~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~--~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          33 VLLKSGYAFVDYPDQNWAIRAIETLSGKVEL--HGKIMEVDYSVSKKL   78 (80)
T ss_dssp             EEEETTEEEECCSCHHHHHHHHHHHTTTCEE--TTEECEEEECCCCCC
T ss_pred             EecccceEEEEECCHHHHHHHHHHhCCCeEE--CCEEEEEEEcCCcCc
Confidence            4456999999999999999999999996 47  699999999997654

>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=99.07  E-value=9.5e-11  Score=78.11  Aligned_cols=46  Identities=30%  Similarity=0.449  Sum_probs=41.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.++++|+.|+..|||..|  +|++|.|++|.++..
T Consensus        42 ~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~--~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          42 ETQRSRGFGFVTFENIDDAKDAMMAMNGKSV--DGRQIRVDQAGKSSD   87 (90)
T ss_dssp             SSCSCCSEEEEECSSHHHHHHHHHHHTTCCT--TSCCCEEEEEECCCC
T ss_pred             ccccccceEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEcCCCCC
Confidence            3677899999999999999999999999998  699999999986543

>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=99.06  E-value=9.8e-11  Score=79.73  Aligned_cols=44  Identities=30%  Similarity=0.308  Sum_probs=40.6

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +++++|||||+|.++++|++||+.|||..|  +|++|.|+++.++.
T Consensus        54 ~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~gr~i~V~~a~~~~   97 (101)
T d2cpea1          54 TGKPKGDATVSYEDPPTAKAAVEWFDGKDF--QGSKLKVSLARKKP   97 (101)
T ss_dssp             TCSBCSEEEEEBSSHHHHHHHHHHHTTCEE--TTEECEEECSSCCC
T ss_pred             cccccceeeEEecCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCC
Confidence            577899999999999999999999999999  69999999998654

>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=99.05  E-value=9.4e-11  Score=77.29  Aligned_cols=43  Identities=30%  Similarity=0.385  Sum_probs=38.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .+++++|||||+|.+.++|++||+.|||..+.+.+++|.|+||
T Consensus        43 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          43 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            4678899999999999999999999999988533489999987

>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=99.05  E-value=1.1e-10  Score=79.70  Aligned_cols=46  Identities=17%  Similarity=0.308  Sum_probs=41.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+++++|||||+|.+.++|+.||+.|||..|  .|++|.|+||+++..
T Consensus        55 ~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          55 MTGRMRGQAFITFPNKEIAWQALHLVNGYKL--YGKILVIEFGKNKKQ  100 (102)
T ss_dssp             ECSSSCSEEEEECSSHHHHHHHHHHSTTCBC--SSCBCEEEECCCCSC
T ss_pred             ccccccccceEEeccHHHHHHHHHHhCCCEE--CCEEEEEEeCCCccc
Confidence            3678899999999999999999999999998  699999999997653

>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=99.05  E-value=1.3e-10  Score=78.38  Aligned_cols=48  Identities=33%  Similarity=0.417  Sum_probs=41.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ++.++|||||+|.+.++|..|++.|++..+.++|++|.|+||.++...
T Consensus        41 ~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          41 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             TTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             cccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            567899999999999999999999987655447999999999876543

>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=99.03  E-value=1.1e-10  Score=78.99  Aligned_cols=41  Identities=29%  Similarity=0.471  Sum_probs=37.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++|||||+|++.++|++||+.|||+.|  .|++|.|+|+..+.
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMI--AGQVLDINLAAEPK   89 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEE--TTEECEEEETTSCC
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCC
Confidence            589999999999999999999999999  69999999998644

>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=99.03  E-value=8.8e-11  Score=77.62  Aligned_cols=43  Identities=23%  Similarity=0.322  Sum_probs=37.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+++++|||||+|.+.++|++|++ |||..|  +|++|.|+++.++
T Consensus        43 ~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~--~gr~l~V~~a~~k   85 (86)
T d2ghpa3          43 EHSFNNCCAFMVFENKDSAERALQ-MNRSLL--GNREISVSLADKK   85 (86)
T ss_dssp             ---CCCEEEEEEESSHHHHHHHGG-GTTEEE--TTEEEEEEECCCC
T ss_pred             CccccceeeeEEECCHHHHHHHHh-cCCCEE--CCEEEEEEEcCCC
Confidence            367789999999999999999996 999999  6999999999864

>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=99.03  E-value=1.6e-10  Score=77.42  Aligned_cols=43  Identities=30%  Similarity=0.401  Sum_probs=39.1

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..++|||||+|.++++|++||..|||..|  +|++|.|+||.++.
T Consensus        48 ~~~kg~afV~f~~~~~a~~Ai~~l~~~~~--~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          48 RGSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVNNATARV   90 (93)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEECCSSC
T ss_pred             cCCcceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEecCcCC
Confidence            34699999999999999999999999999  69999999998754

>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=99.03  E-value=9.3e-11  Score=80.35  Aligned_cols=45  Identities=29%  Similarity=0.457  Sum_probs=40.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|++++|||||+|.+.++|++|++.|||..|  +|++|.|+|+....
T Consensus        45 ~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~--~g~~i~V~~a~~~~   89 (104)
T d1p1ta_          45 ETGKPKGYGFCEYQDQETALSAMRNLNGREF--SGRALRVDNAASEK   89 (104)
T ss_dssp             TTTEEEEEEEEECSCHHHHHHHHHHSSSBSC--SSSCBEEEETTCTT
T ss_pred             ceeccCCceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCC
Confidence            4678899999999999999999999999998  69999999988643

>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=99.03  E-value=1.3e-10  Score=74.62  Aligned_cols=43  Identities=28%  Similarity=0.370  Sum_probs=39.5

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +++++|||||+|.+.++|++|+..|||..|  +|++|.|+|+...
T Consensus        29 ~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~--~g~~l~V~~a~~d   71 (75)
T d1wi6a1          29 VDKYKGTAFVTLLNGEQAEAAINTFHQSRL--RERELSVQLQPTD   71 (75)
T ss_dssp             EETTTTEEEEEESSHHHHHHHHHHHTTEES--SSCEEEEEECCST
T ss_pred             ecccceeEEEEECCHHHHHHHHHHhCCccC--CCCEEEEEEeCCC
Confidence            567899999999999999999999999999  6999999999754

>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=99.02  E-value=6.4e-11  Score=79.16  Aligned_cols=45  Identities=29%  Similarity=0.592  Sum_probs=40.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++++++|||||+|++.++|++|++.|||..|  +|+.|.|.||+.+.
T Consensus        41 ~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~--~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          41 RSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPMRIQYAKTDS   85 (91)
T ss_dssp             HHHHHTTCEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSSCC
T ss_pred             eeccCCCceEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEeCCCc
Confidence            4566799999999999999999999999998  69999999998643

>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=99.02  E-value=9.1e-11  Score=77.52  Aligned_cols=44  Identities=25%  Similarity=0.408  Sum_probs=39.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +.+++|||||+|.++++|..|+..|||..|  +|+.|.|+|+.+..
T Consensus        40 ~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i--~g~~i~V~~akP~~   83 (86)
T d2cpda1          40 VKKIRDYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAKPVD   83 (86)
T ss_dssp             EEECSSEEEEEESSHHHHHHHHHHHSSEEE--TTEEEEEECCCCCC
T ss_pred             EccccEEEEEEeCCHHHHHHHHHHcCCCEE--CCEEEEEEeccCCC
Confidence            456799999999999999999999999999  69999999998654

>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=99.02  E-value=1.4e-10  Score=78.02  Aligned_cols=45  Identities=47%  Similarity=0.619  Sum_probs=40.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++...+|||||+|.+.++|++||+.|||+.|  .|++|.|+|+...+
T Consensus        48 ~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~--~g~~l~V~~a~~~r   92 (95)
T d1x4aa1          48 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEFPRSGR   92 (95)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEECCCCCC
T ss_pred             ccccccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEeccCCC
Confidence            3556799999999999999999999999999  69999999998643

>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=99.02  E-value=8.8e-11  Score=77.95  Aligned_cols=44  Identities=20%  Similarity=0.233  Sum_probs=39.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +...+|||||+|.++++|++||+.||++.|  +|++|.|+|+..+.
T Consensus        36 ~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~--~G~~l~V~~a~~~~   79 (88)
T d1wg1a_          36 VDRNKRTAFVTLLNGEQAQNAIQMFHQYSF--RGKDLIVQLQPTDA   79 (88)
T ss_dssp             EEGGGTEEEECCSCHHHHHHHHHHHTTEEE--TTEEEEEEECCCCC
T ss_pred             eeccCCceEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCC
Confidence            456799999999999999999999999999  69999999997544

>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=99.02  E-value=9.4e-11  Score=77.27  Aligned_cols=41  Identities=24%  Similarity=0.418  Sum_probs=37.4

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .++|||||+|.+.++|++|++.|||..|  +|++|.|+|+...
T Consensus        41 ~~kG~afV~f~~~~~A~~A~~~~~~~~~--~g~~i~V~~a~~~   81 (85)
T d2cpfa1          41 LSMGFGFVEYKKPEQAQKALKQLQGHTV--DGHKLEVRISERA   81 (85)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHSTTCEE--TTEECEEECSSCS
T ss_pred             ccceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCC
Confidence            4589999999999999999999999999  6999999998643

>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=99.01  E-value=1.1e-10  Score=78.80  Aligned_cols=46  Identities=20%  Similarity=0.352  Sum_probs=41.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|++|.|+|+.++..
T Consensus        48 ~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~--~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTGEKGG   93 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEE--TTEEEEEEECSSSCC
T ss_pred             ecCccccEEEEEeCCHHHHHHHHHHcCCCEE--CCEEEEEEEeCCCCC
Confidence            4667899999999999999999999999999  699999999997654

>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=99.01  E-value=2.8e-10  Score=82.01  Aligned_cols=47  Identities=30%  Similarity=0.461  Sum_probs=42.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .|+.++|||||+|.+.++|++||+.|||..|  +|+.|.|+|+......
T Consensus        79 ~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          79 ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI--LNKRLKVALAASGHQR  125 (139)
T ss_dssp             TTTEEEEEEEEEESSHHHHHHHHHHTTTEEC--SSCEEEEEESSCCCCC
T ss_pred             ccccccceeeEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCCCC
Confidence            4678899999999999999999999999999  6999999999865543

>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=99.00  E-value=1.9e-10  Score=74.69  Aligned_cols=42  Identities=26%  Similarity=0.304  Sum_probs=38.5

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      .+.+|||||+|.+.++|..|+..|||..|  +|++|+|+|+.++
T Consensus        36 ~~~~~~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~V~~a~~~   77 (79)
T d2bz2a1          36 DPPRNCAFVTYEKMESADQAVAELNGTQV--ESVQLKVNIARKQ   77 (79)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCBC--SSCBCEEEECCSS
T ss_pred             ccCCCEEEEEEcccHHHHHHHHHhCCCEE--CCEEEEEEEecCC
Confidence            45689999999999999999999999999  6999999999754

>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=98.99  E-value=1.3e-10  Score=77.56  Aligned_cols=42  Identities=21%  Similarity=0.332  Sum_probs=38.7

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+++++|||||+|.+.++|++||+ |||..|  +|++|.|++|+.
T Consensus        49 ~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~--~g~~i~V~~ak~   90 (91)
T d1fjeb1          49 RTGTNRKFGYVDFESAEDLEKALE-LTGLKV--FGNEIKLEKPKG   90 (91)
T ss_dssp             EEETTTTEEEEEESSHHHHHHHHH-GGGEEE--TTEEEEEECCCC
T ss_pred             CCCCccEEeEEeeCCHHHHHHHHh-cCCcEE--CCEEEEEEecCC
Confidence            478899999999999999999996 999999  699999999975

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=1.8e-10  Score=80.25  Aligned_cols=44  Identities=27%  Similarity=0.272  Sum_probs=40.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGE   48 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~   48 (240)
                      +++.++|||||+|.+.++|..||+.|||..|  +|+.|.|.|+...
T Consensus        41 ~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~--~gr~l~V~~a~~~   84 (114)
T d2f9da1          41 NTPETRGTAYVVYEDIFDAKNACDHLSGFNV--CNRYLVVLYYNAN   84 (114)
T ss_dssp             CSTTTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCHH
T ss_pred             ccCCcCCeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCC
Confidence            4677899999999999999999999999999  6999999998753

>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=98.99  E-value=2.3e-10  Score=75.38  Aligned_cols=43  Identities=23%  Similarity=0.410  Sum_probs=37.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .++.++|||||+|.++++|++|++.|||..|.+...+|.|.||
T Consensus        43 ~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          43 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            3678899999999999999999999999999523467999986

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.99  E-value=2.9e-10  Score=77.74  Aligned_cols=46  Identities=17%  Similarity=0.104  Sum_probs=40.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      ..+++|||||+|.+.++|++|+..|||..|  .|++|+|.|+......
T Consensus        42 ~~k~~~~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~a~~~~~~   87 (104)
T d1weya_          42 YFKSFKRVRINFSNPLSAADARLRLHKTEF--LGKEMKLYFAQTLHIG   87 (104)
T ss_dssp             EETTTTEEEEECSSTTHHHHHHHTSTTSEE--TTEECEEECCCCSSCC
T ss_pred             EecCCCEEEEEECCHHHHHHHHHHhccccc--CCCEeEEeecccCCCC
Confidence            456799999999999999999999999999  6999999999865543

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=3e-10  Score=75.24  Aligned_cols=43  Identities=19%  Similarity=0.313  Sum_probs=38.7

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +.+.+|||||+|.+.++|.+|+..|||..|. +|++|.|.|+++
T Consensus        44 ~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~-~g~~l~v~~sk~   86 (88)
T d2adca2          44 FQKDRKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVSFSKS   86 (88)
T ss_dssp             CSSSTTCEEEEESSHHHHHHHHHHHTTCBSS-SSCBCEEEECSS
T ss_pred             eecccceeEEEECCHHHHHHHHHhccCCEec-CCCEEEEEeCCC
Confidence            4556899999999999999999999999885 689999999975

>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=98.96  E-value=3e-10  Score=74.93  Aligned_cols=41  Identities=24%  Similarity=0.324  Sum_probs=37.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .+++++|||||+|.++++|++|+..||+..|  +|++|.|.++
T Consensus        46 ~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l--~gr~i~v~l~   86 (86)
T d2cqpa1          46 EKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKLVLG   86 (86)
T ss_dssp             SSSCEEEEEEEEESCHHHHHHHHHHTTTCEE--TTEECEEEES
T ss_pred             CCCCcceEEEEEEcCcHHHHHHHHHcCCCEE--CCEEEEEEEC
Confidence            4678899999999999999999999999999  6999999875

>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=98.96  E-value=2.7e-10  Score=77.49  Aligned_cols=42  Identities=21%  Similarity=0.155  Sum_probs=38.4

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .+++++|||||+|.++++|++|++ |||..|  +|++|.|.++..
T Consensus        55 ~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~--~G~~l~V~~a~~   96 (101)
T d2cq4a1          55 NSRRSKGIAYVEFCEIQSVPLAIG-LTGQRL--LGVPIIVQASQA   96 (101)
T ss_dssp             CSSSCCCCEEEEESCGGGHHHHHH-HTTEEE--TTEEEEEEEHHH
T ss_pred             CCccccceEEEEECCHHHHHHHHH-HCCCEE--CCEEEEEEECCC
Confidence            478899999999999999999996 999999  699999999864

>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=98.95  E-value=5.1e-10  Score=74.45  Aligned_cols=41  Identities=27%  Similarity=0.478  Sum_probs=37.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+|||||+|.+.++|+.|+..|||..|  +|+.|.|.||.++.
T Consensus        47 ~~~~afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v~~a~~~~   87 (90)
T d2cqia1          47 NDPYCFVEFYEHRDAAAALAAMNGRKI--LGKEVKVNWATTPS   87 (90)
T ss_dssp             SCCEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCCTT
T ss_pred             cceeeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEcCCCC
Confidence            489999999999999999999999999  69999999998654

>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=98.94  E-value=3.5e-10  Score=77.32  Aligned_cols=41  Identities=27%  Similarity=0.443  Sum_probs=38.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .+++++|||||+|.+.++|.+|+..|||..|  +|++|.|+|+
T Consensus        63 ~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~--~gr~i~v~~s  103 (104)
T d1jmta_          63 LGDHLVGNVYVKFRREEDAEKAVIDLNNRWF--NGQPIHAELS  103 (104)
T ss_dssp             SSSSSEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECCEEEC
T ss_pred             CCCCEeeEEEEEEechhHHHHHHHHHCCCEE--CCEEEEEEEC
Confidence            4678899999999999999999999999999  7999999985

>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=98.91  E-value=7.3e-10  Score=75.71  Aligned_cols=46  Identities=22%  Similarity=0.380  Sum_probs=39.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERGR   51 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~~   51 (240)
                      .+++++|||||+|.++++|++|++ ||++.|  +|+.|.|+++.++...
T Consensus        52 ~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~--~gr~l~V~~a~~~~~~   97 (104)
T d1wi8a_          52 NPERLKGFGYAEFEDLDSLLSALS-LNEESL--GNKRIRVDVADQAQDK   97 (104)
T ss_dssp             CTTSBCSCEEEEESSHHHHHHHHG-GGTCEE--TTEECEEEECCCCCCC
T ss_pred             cCCCcceeeeEEECCHHHHHHHHH-cCCCEE--CCEEEEEEECCCCCCC
Confidence            367789999999999999987775 999999  6999999999876543

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=7.6e-10  Score=74.50  Aligned_cols=42  Identities=21%  Similarity=0.446  Sum_probs=38.2

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..+|||||+|.+.++|++|+..|||..|  +|++|+|.|++...
T Consensus        52 ~~kg~afV~f~~~~~A~~Ai~~l~~~~i--~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          52 PEKGYSFVRFSTHESAAHAIVSVNGTTI--EGHVVKCYWGKESP   93 (96)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEECCCCCC
T ss_pred             ecceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCC
Confidence            3599999999999999999999999999  69999999997643

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.89  E-value=7.9e-10  Score=72.87  Aligned_cols=42  Identities=31%  Similarity=0.430  Sum_probs=38.6

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      +.+|||||+|.+.++|++|+..|||..|  +|+.|.|+||....
T Consensus        42 ~~k~~afV~f~~~~~A~~A~~~l~g~~i--~g~~l~V~~A~~~~   83 (86)
T d2cpja1          42 KDKGFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFACHSA   83 (86)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCB--TTBCCEEEESSCCS
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCcC
Confidence            4689999999999999999999999999  69999999998643

>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=98.89  E-value=6.5e-10  Score=72.76  Aligned_cols=38  Identities=42%  Similarity=0.646  Sum_probs=35.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEE
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSV   42 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v   42 (240)
                      .+++++|||||+|.+.++|++|+..|||..|  +|++|.|
T Consensus        46 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~gr~i~V   83 (83)
T d2cqca1          46 QSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIRV   83 (83)
T ss_dssp             SSSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEE
T ss_pred             cccccccceEEEECCHHHHHHHHHHcCCCEE--CCEEeEC
Confidence            4678899999999999999999999999999  6999987

>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=98.89  E-value=5.7e-10  Score=71.97  Aligned_cols=40  Identities=20%  Similarity=0.365  Sum_probs=36.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .|++++|||||+|.++++|++|++ +|+..|  +|++|.|+.|
T Consensus        37 ~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i--~Gr~i~V~~A   76 (77)
T d1uawa_          37 LTKRSRGFGFVTFMDQAGVDKVLA-QSRHEL--DSKTIDPKVA   76 (77)
T ss_dssp             CSSSCSSEEEECCCCTTHHHHHHH-TTTCCC--SSCCCEEEEC
T ss_pred             CCCCccceEEEEECCHHHHHHHHH-cCCCEE--CCeEEEEEEC
Confidence            368899999999999999999997 799988  6999999876

>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=98.88  E-value=1e-09  Score=70.32  Aligned_cols=40  Identities=18%  Similarity=0.268  Sum_probs=36.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .++.++|||||+|.++++|++|++ |||..|  +|++|.|++|
T Consensus        36 ~~~~~~~~afV~F~~~~~a~~al~-~~~~~l--~gr~i~V~~A   75 (75)
T d2msta_          36 TTNRHRGFGFVTFESEDIVEKVCE-IHFHEI--NNKMVECKKA   75 (75)
T ss_dssp             TCTTSCCEEEEECSCHHHHHHHHH-CSSCCB--TTBCCEEEEC
T ss_pred             cccccCceeEEEECCHHHHHHHHh-cCCCEE--CCeEEEEEEC
Confidence            367789999999999999999997 999999  6999999876

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=98.86  E-value=1.3e-09  Score=71.32  Aligned_cols=39  Identities=18%  Similarity=0.325  Sum_probs=35.9

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .+|||||+|.+.++|+.|+..|||..|. +|++|.|.||+
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~-~~~~i~v~~ak   82 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAKEALQGFKIT-PTHAMKITFAK   82 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHTTCBSS-TTCBCEEEECC
T ss_pred             cceeEEEecCCHHHHHHHHHHhCCcEeC-CCcEEEEEEec
Confidence            4799999999999999999999999885 57899999986

>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=98.86  E-value=1.3e-09  Score=74.36  Aligned_cols=44  Identities=23%  Similarity=0.243  Sum_probs=38.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .|++++|||||+|.+.++|++||+.+|+ .|  +|++|.|+++....
T Consensus        47 ~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l--~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          47 QTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKANVNLAYLGA   90 (103)
T ss_dssp             SSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECEEEESTTTC
T ss_pred             cccccCCeEEEEECCHHHHHHHHHHCCC-cC--CCEEEEEEEcCCCC
Confidence            3688999999999999999999998886 56  69999999998643

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=1.9e-09  Score=74.12  Aligned_cols=45  Identities=16%  Similarity=0.076  Sum_probs=39.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +.+|||||+|.++++|++||..|||..|...+.+|.|.|+.....
T Consensus        43 ~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            458999999999999999999999999866789999999986543

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=4.1e-10  Score=76.64  Aligned_cols=43  Identities=12%  Similarity=0.006  Sum_probs=37.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++.++|||||+|.+.++|++||+.|||..|  .|++|.|.++.+
T Consensus        54 ~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i--~gr~~~v~~~~P   96 (101)
T d1x5oa1          54 SSGTSRGVGFARMESTEKCEAVIGHFNGKFI--KTPPGVSAPTEP   96 (101)
T ss_dssp             SSSCEEEEEEEEESCHHHHHHHHHHHBTCCC--CCCTTSCCCSSC
T ss_pred             cccccccceeEEeCCHHHHHHHHHHhCCCEE--CCcCCccCCCCC
Confidence            3667899999999999999999999999999  699988877653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=2.2e-09  Score=73.82  Aligned_cols=41  Identities=15%  Similarity=0.206  Sum_probs=37.5

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .+|||||+|+++++|++||+.|||..|  .|+.|.|+|+....
T Consensus        39 ~kg~afV~f~~~~~A~~ai~~lng~~l--~g~~l~v~~s~~~~   79 (109)
T d2adca1          39 KKENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITLSKHQN   79 (109)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHTTCBC--SSSBCEEECCSCCC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCCC
Confidence            489999999999999999999999999  59999999997543

>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=98.85  E-value=1.8e-09  Score=72.79  Aligned_cols=44  Identities=25%  Similarity=0.359  Sum_probs=37.8

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCC------CcccCCCceEEEEeccCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDN------IPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g------~~~~~~g~~l~v~~a~~~~   49 (240)
                      ++.++|||||+|.+.++|++||+.||+      ..|  +|+.|.|+|+.++.
T Consensus        46 ~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~--~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          46 TEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--DGRQLKVDLAVTRD   95 (98)
T ss_dssp             SCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--SSCEEEEECCCCCC
T ss_pred             cccccceEEEEEcCHHHHHHHHHHcccccccCCcEE--CCEEEEEEECCCCC
Confidence            566799999999999999999999874      445  69999999998654

>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=98.85  E-value=1.3e-09  Score=72.44  Aligned_cols=44  Identities=18%  Similarity=0.286  Sum_probs=37.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .|+.++|||||+|.++++|++||+.++  .|  +|+.|.|.++.++..
T Consensus        45 ~tg~srG~aFV~f~~~~~a~~al~~~~--~l--~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          45 KTGHSKGFGFVRFTEYETQVKVMSQRH--MI--DGRWCDCKLPNSKQS   88 (90)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHSCE--EE--TTEEEEEECCCTTCC
T ss_pred             CCcccCCEEEEEECCHHHHHHHHhcCC--cc--CCEEeEEEeCCCCCC
Confidence            478899999999999999999998544  55  799999999987553

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=1.5e-09  Score=73.36  Aligned_cols=43  Identities=30%  Similarity=0.356  Sum_probs=39.0

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ...+|||||+|.++++|.+|+..|||..|  +|++|.|+|+.++.
T Consensus        54 ~~~~G~~fV~f~~~e~A~~A~~~lng~~~--~gr~i~v~~~~g~~   96 (99)
T d2dita1          54 RHPDGVASVSFRDPEEADYCIQTLDGRWF--GGRQITAQAWDGTT   96 (99)
T ss_dssp             TCTTCEEEEECSCHHHHHHHHHHSTTCEE--TTEECEEEECCSCC
T ss_pred             CCCccEEEEEECCHHHHHHHHHHhCCcEE--CCEEEEEEEeCCcC
Confidence            35689999999999999999999999999  79999999987654

>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=98.85  E-value=1.3e-09  Score=69.91  Aligned_cols=40  Identities=18%  Similarity=0.360  Sum_probs=35.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .|++++|||||+|.++++|++|++ +++..|  +|+.|.|..|
T Consensus        36 ~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l--~Gr~i~V~rA   75 (75)
T d1hd0a_          36 ITGRSRGFGFVLFKESESVDKVMD-QKEHKL--NGKVIDPKRA   75 (75)
T ss_dssp             TTTBCCSEEEEEESSHHHHHHHHH-TCCCCB--TTBCCEECCC
T ss_pred             CCCCcCceEEEEECCHHHHHHHHh-cCCCEE--CCCEEEeeEC
Confidence            467889999999999999999997 788888  6999998654

>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=98.85  E-value=7.9e-10  Score=75.30  Aligned_cols=44  Identities=20%  Similarity=0.140  Sum_probs=39.3

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      .++..+|||||+|.++++|++|++ ||+..|  +|+.|.|.++....
T Consensus        50 ~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i--~gR~I~V~~s~~~~   93 (102)
T d1weza_          50 PDGRVTGEADVEFATHEDAVAAMA-KDKANM--QHRYVELFLNSTAG   93 (102)
T ss_dssp             SSSCEEEEEEEECSSSHHHHHHHT-TSSCCS--SSSCCEEEEECCCC
T ss_pred             cCCcceEEEEEEECCHHHHHHHHH-cCCCEE--CCEEEEEEEcCCCC
Confidence            356779999999999999999986 899999  69999999998654

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.84  E-value=2.6e-09  Score=73.70  Aligned_cols=43  Identities=28%  Similarity=0.223  Sum_probs=38.8

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ...+|||||+|.+.++|++||+.|||..|  .|++|.|+|+....
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~--~gr~l~v~~a~~~~   85 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKF--HHVPLYLEWAPIGV   85 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBS--SSSBCEEEEEETTT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCcc--CCCeEEEEECCCCc
Confidence            34689999999999999999999999999  69999999997544

>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=98.83  E-value=1.4e-09  Score=74.06  Aligned_cols=44  Identities=23%  Similarity=0.269  Sum_probs=39.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ++.++|||||+|.+.++|++|++ +++..|  +|+.|.|.+|.++.+
T Consensus        58 ~~~~kg~aFV~f~~~~~a~~al~-~~~~~l--~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          58 SKRSRGFGFVTFSSMAEVDAAMA-ARPHSI--DGRVVEPKRAVAREE  101 (103)
T ss_dssp             TSSCCSEEEEECSSHHHHHHHHT-SCSEEE--TTEEEEEECCSSCCC
T ss_pred             CCCccCeEEEEECCHHHHHHHHH-hCCCeE--CCEEEEEEECcccCC
Confidence            56789999999999999999996 899988  699999999987553

>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=98.80  E-value=2.3e-09  Score=70.20  Aligned_cols=41  Identities=20%  Similarity=0.236  Sum_probs=36.9

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .+++++|||||+|.++++|++|++ +++..|  +|+.|.|..|.
T Consensus        43 ~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i--~Gr~i~V~~A~   83 (84)
T d1l3ka1          43 NTKRSRGFGFVTYATVEEVDAAMN-ARPHKV--DGRVVEPKRAV   83 (84)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHH-TCSCEE--TTEECEEEECC
T ss_pred             cCCCcccEEEEEEcCHHHHHHHHH-hCCCEE--CCEEEEEEeee
Confidence            468889999999999999999998 688888  69999999875

>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=98.79  E-value=2.6e-09  Score=69.05  Aligned_cols=40  Identities=25%  Similarity=0.251  Sum_probs=36.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .++.++|||||+|.++++|++|++ |||..|  +|++|.|+.|
T Consensus        39 ~~~~~~g~afV~f~~~e~~~~al~-~~~~~l--~Gr~i~V~~A   78 (79)
T d1l3ka2          39 GSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV--NGHNCEVRKA   78 (79)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHH-CSCCEE--TTEECEEEEC
T ss_pred             CCcccccEEEEEEcCHHHHHHHHH-hCCCEE--CCEEEEEEEC
Confidence            467789999999999999999996 899999  6999999876

>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=98.78  E-value=3.7e-09  Score=72.09  Aligned_cols=45  Identities=18%  Similarity=0.161  Sum_probs=39.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+++.+|||||+|.++++|++|++ ||+..|  +|+.|.|.++.....
T Consensus        52 ~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i--~gR~i~V~~~~~~~~   96 (104)
T d1wg5a_          52 FQGRSTGEAFVQFASQEIAEKALK-KHKERI--GHRYIEIFKSSRAEV   96 (104)
T ss_dssp             SSSCBCSEEEEEESSHHHHHHHHT-TTTCCS--SSSCCEEEEECTTTS
T ss_pred             CCCCcceEEEEEeCCHHHHHHHHh-hCCCEE--cceEEEEEECCHHHh
Confidence            467789999999999999999996 999988  799999999986653

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.78  E-value=4.2e-09  Score=70.88  Aligned_cols=44  Identities=27%  Similarity=0.459  Sum_probs=38.2

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..++||||+|.+.++|++|++.||+..|...+.+|.|+|++..+
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            45899999999999999999999999995334689999998643

>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=98.77  E-value=2.4e-09  Score=72.91  Aligned_cols=42  Identities=24%  Similarity=0.206  Sum_probs=38.2

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++.++|||||+|.++++|++||. ||+..|  +|+.|.|.++..
T Consensus        45 ~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i--~gr~i~V~~~~~   86 (103)
T d2cpya1          45 NNGQGLGQALVQFKNEDDARKSER-LHRKKL--NGREAFVHVVTL   86 (103)
T ss_dssp             TTSSCSSCEEEECSSHHHHHHHGG-GCSEEE--TTEEEEEEEECH
T ss_pred             CCCCcCccEEEEECCHHHHHHHHh-cCCCeE--CCcEEEEEECCH
Confidence            478889999999999999999996 999999  699999998763

>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=98.77  E-value=2.7e-09  Score=70.06  Aligned_cols=41  Identities=15%  Similarity=0.280  Sum_probs=37.0

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      .++.++|||||+|.++++|++||+ +++..|  .|+.|.|.|..
T Consensus        42 ~~~~~kG~afV~f~~~e~a~~al~-~~~~~~--~g~~l~v~~~~   82 (85)
T d1zh5a2          42 LHKAFKGSIFVVFDSIESAKKFVE-TPGQKY--KETDLLILFKD   82 (85)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHT-CCCCEE--TTEECEEEEGG
T ss_pred             ccCCcceEEEEEEcCHHHHHHHHH-HCCCEE--CCEEEEEEEcC
Confidence            467789999999999999999996 799998  69999999875

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.75  E-value=6.4e-09  Score=70.90  Aligned_cols=46  Identities=15%  Similarity=0.236  Sum_probs=38.0

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      .+.+|||||+|.+.++|+.||..|++..+.++|++|.|.|++.+..
T Consensus        48 ~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          48 MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCcc
Confidence            3568999999999999999999886554444799999999986543

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.73  E-value=6.1e-09  Score=68.91  Aligned_cols=34  Identities=29%  Similarity=0.433  Sum_probs=31.8

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEE
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVE   43 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~   43 (240)
                      .|||||+|.++++|++|++.|||..|  +|+.|+|.
T Consensus        56 ~g~aFV~f~~~~~A~~Ai~~lng~~~--~gr~lkvS   89 (89)
T d2cpia1          56 SASAYVTYIRSEDALRAIQCVNNVVV--DGRTLKAS   89 (89)
T ss_dssp             CEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEE
T ss_pred             ceEEEEecccchhHHHHHHHhCCCEE--CCEEEEEC
Confidence            59999999999999999999999999  69999873

>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=98.72  E-value=3e-09  Score=68.06  Aligned_cols=40  Identities=13%  Similarity=0.249  Sum_probs=34.5

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      .|++++|||||+|.+.++|++||+ +++..|  +|+.|.|..|
T Consensus        36 ~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i--~g~~i~vk~A   75 (75)
T d1x0fa1          36 KTNKRRGFCFITFKEEEPVKKIME-KKYHNV--GLSKCEIKVA   75 (75)
T ss_dssp             TTCCTTCCEEEEESSSHHHHHHTT-CSSCCB--TTBCCEEECC
T ss_pred             cccccccEEEEEECCHHHHHHHHh-hCCCEE--CCEEeEEEEC
Confidence            478899999999999999999997 566677  6999998865

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=4.6e-09  Score=69.36  Aligned_cols=43  Identities=9%  Similarity=0.179  Sum_probs=36.2

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhC--CCcccCCCceEEEEeccCCC
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLD--NIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~--g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ...+|||||+|.+.++|+.|++.|+  +..|  +|++|.|.|++.+.
T Consensus        41 ~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~--~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          41 LKGKNQAFLELATEEAAITMVNYYSAVTPHL--RNQPIYIQYSNHKE   85 (88)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEECSCSS
T ss_pred             cccceEEEEEeCCHHHHHHHHHHHccCCCcc--CCCEEEEEECCCCC
Confidence            3468999999999999999999765  4555  79999999998654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=2.2e-09  Score=70.80  Aligned_cols=42  Identities=26%  Similarity=0.291  Sum_probs=37.2

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..+|||||+|.+.++|++||..|||..|  +|+.|.|.++....
T Consensus        33 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~i~v~~~~~~~   74 (87)
T d3begb1          33 YRDGTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKV   74 (87)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHTTCBC--CCTTSCCCBCEEEE
T ss_pred             cccceeeEEeCCHHHHHHHHHHhCCCEE--CCcEeEEeEEecCc
Confidence            3469999999999999999999999999  69999998876544

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.70  E-value=2.5e-09  Score=72.17  Aligned_cols=43  Identities=21%  Similarity=0.282  Sum_probs=38.5

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      ..+|||||+|.++++|++||+.|||..|  .|+.|.|.++.....
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~~lng~~~--~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          48 QKDGMGMVEYLRKEDMEYALRKLDDTKF--RSHEGETSYIRVYPE   90 (98)
T ss_dssp             ETTTEEEEEESSHHHHHHHHHHHSSEEE--ECTTSCEEEEEEECC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEe--CCeEEEEEEEecCCC
Confidence            3589999999999999999999999999  699999999876543

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=2.1e-09  Score=68.26  Aligned_cols=37  Identities=19%  Similarity=0.315  Sum_probs=32.8

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEE
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLS   41 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~   41 (240)
                      .++.++|||||+|.+.++|++|++.|||..|  +|+.|+
T Consensus        35 ~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~--~Gr~~k   71 (72)
T d1x4ea1          35 TTNKCKGYGFVDFDSPSAAQKAVTALKASGV--QAQMAK   71 (72)
T ss_dssp             SSCSCCSEEEEEESCHHHHHHHHHHHHHHTC--CEESCC
T ss_pred             ccccccceeEEEECCHHHHHHHHHHhCCCEE--CCEECc
Confidence            3677899999999999999999999999999  687653

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=1.4e-09  Score=72.26  Aligned_cols=41  Identities=22%  Similarity=0.380  Sum_probs=36.1

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      +++++|||||+|.++++|++|++ |||..|  .|+.|.|..++.
T Consensus        44 ~~~~kg~afV~f~~~e~a~~a~~-l~g~~~--~Gr~l~V~r~k~   84 (90)
T d1u2fa_          44 INQDKNFAFLEFRSVDETTQAMA-FDGIIF--QGQSLKIRRPHD   84 (90)
T ss_dssp             EETTTTEEEEEESSCTTTTTGGG-GSSCCS--SSSCCCCBCTTC
T ss_pred             cCCCceEEEEEeCCHHHHHHHHh-hCCcEE--CCEEEEECCCCC
Confidence            56779999999999999999995 999999  699999976553

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.60  E-value=2.4e-08  Score=67.31  Aligned_cols=42  Identities=19%  Similarity=0.238  Sum_probs=36.3

Q ss_pred             CccceEEEEeCChhHHHHHHH--hhCCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIR--GLDNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~--~l~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..+|||||+|.+.++|..||+  .+++..|  +|+.|.|.|+....
T Consensus        53 ~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~--~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          53 RMKSQAFIEMETREDAMAMVDHCLKKALWF--QGRCVKVDLSEKYK   96 (99)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCS--SSSCCEEEEECSCS
T ss_pred             ecCCcEEEEecchHHHHHHHHHHhcCCceE--CCEEEEEEEcCCcc
Confidence            468999999999999999998  4677777  79999999997544

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=1.5e-08  Score=70.00  Aligned_cols=42  Identities=19%  Similarity=0.141  Sum_probs=37.6

Q ss_pred             ccCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            3 ISLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         3 ~t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      .++..+|||||+|.+.++|++|++ |||..|  +|+.|.|..+..
T Consensus        55 ~~g~~~G~afVeF~~~e~a~~al~-~~~~~i--~gR~i~V~~~~~   96 (112)
T d1wela1          55 PNGKATGEGFVEFRNEADYKAALC-RHKQYM--GNRFIQVHPITK   96 (112)
T ss_dssp             TTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS--TTSCBEEEEECH
T ss_pred             cccceeeEEEEEECCHHHHHHHHH-cCCCcC--CCEEEEEEEcCh
Confidence            467889999999999999999996 999998  799999988763

>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=98.57  E-value=1e-08  Score=67.58  Aligned_cols=43  Identities=21%  Similarity=0.322  Sum_probs=36.4

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccCCCC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARGERG   50 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~~~~   50 (240)
                      +..++|||||+|.++++|++|+.  ++..|  +|++|.|.++.++..
T Consensus        38 ~~~~~gfafV~f~~~~~a~~a~~--~~~~i--~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_          38 PKPFRAFAFVTFADDQIAQSLCG--EDLII--KGISVHISNAEPKHN   80 (88)
T ss_dssp             CSSCCSCCEEECSCHHHHHHTTT--CEEEE--TTEEEEEECCCCCCC
T ss_pred             eeccCceEEEEECCHHHHHHHHh--CCCEE--CCEEeEEEeCCCCCC
Confidence            44579999999999999999985  67777  799999999986553

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.56  E-value=2.3e-08  Score=65.98  Aligned_cols=42  Identities=14%  Similarity=0.105  Sum_probs=35.7

Q ss_pred             CccceEEEEeCChhHHHHHHHhh--CCCcccCCCceEEEEeccCCC
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGL--DNIPFGYDRRRLSVEWARGER   49 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l--~g~~~~~~g~~l~v~~a~~~~   49 (240)
                      ..++||||+|++.++|+.|++.|  ++..|  .|++|.|.|+....
T Consensus        43 ~~k~~afV~f~~~~~A~~A~~~l~~~~~~~--~gr~l~V~~s~~~~   86 (89)
T d1x4da1          43 NKINEAFIEMATTEDAQAAVDYYTTTPALV--FGKPVRVHLSQKYK   86 (89)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEEECCCT
T ss_pred             ccceEEEEEEcchhhHHHHHHHHhhCCCcc--CCceEEEEECCCcc
Confidence            45899999999999999999976  45566  79999999998543

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.55  E-value=2.9e-08  Score=63.32  Aligned_cols=37  Identities=19%  Similarity=0.124  Sum_probs=32.9

Q ss_pred             CccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            6 HYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         6 ~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      ..+|||||+|.++++|++|+. ||++.|  +|++|.|+.+
T Consensus        38 ~~~~~afV~F~~~~~a~~Al~-~~~~~i--~g~~i~V~~~   74 (75)
T d2ghpa2          38 KNFRFARIEFARYDGALAAIT-KTHKVV--GQNEIIVSHL   74 (75)
T ss_dssp             SSSEEEEEEESSHHHHHHHHT-TTTCEE--TTEECEEEEC
T ss_pred             ccceEEEEEEcchHHhHHHHH-hcCcEE--CCEEEEEEEC
Confidence            346899999999999999996 899988  7999999865

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.53  E-value=5.3e-08  Score=66.15  Aligned_cols=39  Identities=26%  Similarity=0.363  Sum_probs=36.2

Q ss_pred             ccceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            7 YAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         7 ~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      ..|++||+|.++++|.+|+..|||..|  +|++|.|.|+..
T Consensus        57 ~~g~vfV~f~~~e~A~~A~~~l~Gr~f--~gR~v~v~f~~~   95 (104)
T d1o0pa_          57 GCGKIFVEFTSVFDCQKAMQGLTGRKF--ANRVVVTKYCDP   95 (104)
T ss_dssp             TCCEEEEEESCHHHHHHHHHHHSSCCS--SSSCCEEEEECH
T ss_pred             CceEEEEEECCHHHHHHHHHHHCCCEE--CCeEEEEEEcCH
Confidence            369999999999999999999999999  799999999863

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.37  E-value=1.4e-07  Score=60.86  Aligned_cols=41  Identities=12%  Similarity=0.152  Sum_probs=33.9

Q ss_pred             cCCccceEEEEeCChhHHHHHHHhhCCCcccCCCce-EEEEeccC
Q 026341            4 SLHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRR-LSVEWARG   47 (240)
Q Consensus         4 t~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~-l~v~~a~~   47 (240)
                      .+..+|||||+|.++++|++||. |||..|  +|+. |.|..+..
T Consensus        35 ~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~--~g~~~vgV~~~~~   76 (81)
T d1wwha1          35 MSNTGNWMHIRYQSKLQARKALS-KDGRIF--GESIMIGVKPCID   76 (81)
T ss_dssp             ECSSSSEEEEEESSHHHHHHHHT-TTTCEE--TTTEECEEEECCC
T ss_pred             ecCCCCEEEEEEcccHHHHHHHh-cCCCeE--CCcEEEEEEeCCC
Confidence            45679999999999999999996 999999  5764 56776653

>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=98.32  E-value=2.1e-07  Score=62.70  Aligned_cols=34  Identities=12%  Similarity=0.142  Sum_probs=28.8

Q ss_pred             CCccceEEEEeCChhHHHHHHHhhCCCcccCCCce
Q 026341            5 LHYAGFAFVYFEDDRDAADAIRGLDNIPFGYDRRR   39 (240)
Q Consensus         5 ~~~kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~   39 (240)
                      ...+|||||+|.+.++|++|+..|||..|. ++..
T Consensus        53 ~~~k~~aFV~f~~~e~A~~A~~~lng~~i~-~~~~   86 (101)
T d2cq2a1          53 PPNKPYSFARYRTTEESKRAYVTLNGKEVV-DDLG   86 (101)
T ss_dssp             CTTCSCEEEEESSHHHHHHHHHHTTTCEEE-CTTS
T ss_pred             ccCccEEEEEECCHHHHHHHHHHhCCCCCC-CCCC
Confidence            345899999999999999999999999875 4433

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=5.5e-06  Score=53.10  Aligned_cols=73  Identities=21%  Similarity=0.323  Sum_probs=57.8

Q ss_pred             CCCCCCEEEEeccCCC-----CCC---HHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcCCCcccCcEEEE
Q 026341           61 NQRPTKTLFVINFDPI-----RTR---ERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISV  132 (240)
Q Consensus        61 ~~~~~~~l~v~nl~~~-----~~~---~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  132 (240)
                      ..+|.-+|.|.-..+.     ...   ..+|.+.|..||+|.-+++..+...|+|.+-+.|.+|+. |+|.++.|+.|+|
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~I   89 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCeEEEEECCcHHHHHHhc-cCCeEEcceEEEE
Confidence            4556667776433110     111   246888899999999999999999999999999999998 7999999999998


Q ss_pred             EE
Q 026341          133 EY  134 (240)
Q Consensus       133 ~~  134 (240)
                      ..
T Consensus        90 t~   91 (95)
T d1ufwa_          90 SG   91 (95)
T ss_dssp             EC
T ss_pred             ec
Confidence            65

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.79  E-value=1.6e-05  Score=54.23  Aligned_cols=39  Identities=18%  Similarity=0.302  Sum_probs=30.5

Q ss_pred             CccceEEEEeCCh-hHHHHHHHhhCCCcccCCCceEEEEecc
Q 026341            6 HYAGFAFVYFEDD-RDAADAIRGLDNIPFGYDRRRLSVEWAR   46 (240)
Q Consensus         6 ~~kG~aFV~F~~~-~~A~~A~~~l~g~~~~~~g~~l~v~~a~   46 (240)
                      +.+|||||.|.++ ++|..|+..||+..|.  +..+.|.|+.
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~--~~~~~v~~~~   84 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQ--LRNKEVTWEV   84 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBC--TTSSSEEEEE
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCcee--cCceEEEEee
Confidence            4689999999996 6899999999999885  4455555444

>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=97.73  E-value=6e-05  Score=45.75  Aligned_cols=57  Identities=28%  Similarity=0.306  Sum_probs=50.7

Q ss_pred             HHHHHhhccCCCeEEEEEe-----CCeEEEEecCHHHHHHHHHhcCCCcccCcEEEEEEeec
Q 026341           81 RDIKRHFEPYGNVLHVRIR-----RNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALK  137 (240)
Q Consensus        81 ~~l~~~f~~~G~i~~~~~~-----kg~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  137 (240)
                      +.|.+.|.+++.|..+.+.     .-.|-|...+.++|.-|+..||..+|+++.|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            4567788999999999994     34799999999999999999999999999999999864

>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=97.63  E-value=0.00017  Score=46.64  Aligned_cols=70  Identities=17%  Similarity=0.260  Sum_probs=57.6

Q ss_pred             CEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeC----------CeEEEEecCHHHHHHHHHhcCCCcccC-----cEE
Q 026341           66 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR----------NFAFVQFETQEEATKALESTDRSKLVD-----RVI  130 (240)
Q Consensus        66 ~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~k----------g~afV~f~~~~~a~~A~~~l~g~~~~g-----~~l  130 (240)
                      +.|.|..| |..+|++++.+.+...|++.......          .-|+|.|.+.++.....+.++|..+.+     .+-
T Consensus         2 tKvVvRrL-PP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a   80 (91)
T d1uw4a_           2 SKVVIRRL-PPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             ceEEEecC-CCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeee
Confidence            57899999 77999999999999999888776632          479999999999999999999997753     244


Q ss_pred             EEEEee
Q 026341          131 SVEYAL  136 (240)
Q Consensus       131 ~v~~a~  136 (240)
                      .|++|-
T Consensus        81 ~VE~AP   86 (91)
T d1uw4a_          81 IVEFAP   86 (91)
T ss_dssp             EEEECS
T ss_pred             EEEEcC
Confidence            566664

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.90  E-value=0.0024  Score=41.23  Aligned_cols=58  Identities=21%  Similarity=0.394  Sum_probs=50.6

Q ss_pred             CCCCEEEEeccCCCCCCHHHHHHhhccCCCeEEEEEeCCeEEEEecCHHHHHHHHHhcC
Q 026341           63 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD  121 (240)
Q Consensus        63 ~~~~~l~v~nl~~~~~~~~~l~~~f~~~G~i~~~~~~kg~afV~f~~~~~a~~A~~~l~  121 (240)
                      +.-..||.-.+ |..+...||.++|+.||.|.-..|...-|||...+.++|+.++..+.
T Consensus        13 p~RdHVf~~tF-P~~Wk~~dI~~lFSpfG~V~VswIddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEEC-CTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeC-CcccchhHHHHHhcCCCceEEEEecCceEEEEecCHHHHHHHHHHhc
Confidence            34566888888 88999999999999999998888888999999999999999987654

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.99  E-value=0.048  Score=32.68  Aligned_cols=37  Identities=27%  Similarity=0.327  Sum_probs=33.5

Q ss_pred             ceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEeccC
Q 026341            9 GFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWARG   47 (240)
Q Consensus         9 G~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a~~   47 (240)
                      =.|-|...+.++|..|+..|+-..|  +++.|.|.++..
T Consensus        36 ~~A~V~v~~~q~A~~~v~~LhR~Ki--G~KRI~Vs~~~~   72 (73)
T d2dgxa1          36 LKAVVQMENLQDAIGAVNSLHRYKI--GSKKILVSLATG   72 (73)
T ss_dssp             CCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCC
T ss_pred             EEEEEEcCCHHHHHHHHHHHHHHhc--CCeEEEEEEecC
Confidence            3689999999999999999999999  799999998763

>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=92.84  E-value=0.065  Score=33.77  Aligned_cols=35  Identities=20%  Similarity=0.350  Sum_probs=30.2

Q ss_pred             cceEEEEeCChhHHHHHHHhhCCCcccCCCceEEEEec
Q 026341            8 AGFAFVYFEDDRDAADAIRGLDNIPFGYDRRRLSVEWA   45 (240)
Q Consensus         8 kG~aFV~F~~~~~A~~A~~~l~g~~~~~~g~~l~v~~a   45 (240)
                      -+...|+|.+-++|-+|+. |+|+.++  |+.|+|...
T Consensus        58 ~d~mwVTF~dG~SAL~al~-l~g~~v~--G~~l~It~~   92 (95)
T d1ufwa_          58 QGQMLVTFADSHSALSVLD-VDGMKVK--GRAVKISGP   92 (95)
T ss_dssp             TTEEEEECSCSHHHHHHHH-GGGSEET--TEEEEEECC
T ss_pred             CCeEEEEECCcHHHHHHhc-cCCeEEc--ceEEEEecC
Confidence            3567899999999999998 9999994  999998754