Psyllid ID: psy3343

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270----
Protein Sequence
PGIDEGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccHHccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEcccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccHHHHHHHccccccccccccccHHHHHcccHHHcccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHcccccccHHHcccHHHHHHHHHHHHcccHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHHcccccEEEcccccEEEEEEEccHHHHHHHHHHHHHHHcccccEEEEEcccccccccccccccccccccccccccccccHccHHHcHHcccccccccHHccccccccccEEEEEEEccccccHHHHHHHHcccccEEEEEEEEcccccccccEccc
Coil and Loop (DISEMBL)
pgidegssyktKKAKELKKIAGhvhtwnslfLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIIlvknlpyrtlptdlkalfepfgdlgrvlvppygiTGLVEFLQKNQAKAAFNSLaytkfkevplylewapegvfaeakekskgkekekneegegeeekkentaeednqqgvpeveenveedeerepepdttlyiknlnfnsTEDSIRRHFkkcgpiasvtvarkkdpkspgqflsm
Flexible Loop (DISEMBL)
pgidegssyktKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSkriilvknlpyrtlPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVfaeakekskgkekekneegegeeekkentaeednqqgvpeveenveedeerepepdttlyiknLNFNSTEDSIRRHFKKcgpiasvtvarkkdpkspgqflsm
Low Complexity Region (SEG)
PGIDEGSSYktkkakelkkIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFaeakekskgkekekneegegeeekkentaeeDNQQGvpeveenveedeerepepDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM
Disordered region (IsUnstruct)
*****************KKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF*********************************************************LYIKNLNFNST**SIRRHFKKCGPIAS******************
Disordered Region (DISOPRED)
***************************NSLFLGTNAIAEAMAETYN***********AATRLAMGETEIVEKTRAFLEENGVQ**AF*****ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG**********************************************************TLYIKNLNFNSTEDSIRRHFKKCGPIASV*****************
Disordered Region (DISEMBL)
**************KELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE****************************************************DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA**************
Disordered Region (DISPRO)
*******SYK******LKK*AGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFA***************************************************EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK***********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
PGIDEGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM
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	274	2.2.26 [Sep-21-2011]
Q8R3C6	952	Probable RNA-binding prot	yes	N/A	0.974	0.280	0.462	6e-57
Q9Y4C8	960	Probable RNA-binding prot	yes	N/A	0.970	0.277	0.452	3e-55
O13620	833	Multiple RNA-binding doma	yes	N/A	0.886	0.291	0.369	7e-43
Q54PB2	895	Multiple RNA-binding doma	yes	N/A	0.948	0.290	0.337	5e-39
Q5BGA9	819	Multiple RNA-binding doma	yes	N/A	0.857	0.286	0.363	1e-37
Q4WJT7	825	Multiple RNA-binding doma	yes	N/A	0.912	0.303	0.352	2e-36
Q5AJS6	841	Multiple RNA-binding doma	N/A	N/A	0.923	0.300	0.342	4e-34
Q6CQR6	878	Multiple RNA-binding doma	yes	N/A	0.959	0.299	0.322	5e-34
Q4PC17	858	Multiple RNA-binding doma	N/A	N/A	0.952	0.304	0.317	1e-33
Q7SG09	827	Multiple RNA-binding doma	N/A	N/A	0.861	0.285	0.338	2e-33

>sp|Q8R3C6|RBM19_MOUSE Probable RNA-binding protein 19 OS=Mus musculus GN=Rbm19 PE=1 SV=1

 Score =  221 bits (562), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 129/279 (46%), Positives = 179/279 (64%), Gaps = 12/279 (4%)

Query: 6   GSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRL 62
           GSSYK KK    K  +   H WN+LF+G NA+A+A+A+ YNATK++V    T    A R+
Sbjct: 490 GSSYKKKKEAMDKANSSSSHNWNTLFMGPNAVADAIAQKYNATKSQVFDHETRGSVAVRV 549

Query: 63  AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
           A+GET++V++ R+FL +NGV LD+F+Q    RSK +IL KNLP  TL  +++  F  FG 
Sbjct: 550 ALGETQLVQEVRSFLIDNGVCLDSFSQAAAERSKTVILAKNLPAGTLAAEIQETFSRFGS 609

Query: 123 LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGK 182
           LGRVL+P  GIT +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF  A +K   +
Sbjct: 610 LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 669

Query: 183 EKEKNEEGEGEEE-------KKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNL 235
            ++  E+ E E+E       +K +    +   G  E EE  EE+EE E  P  TL+IKNL
Sbjct: 670 HEQPAEKAEVEQETVLDPEGEKASVEGAEASTGKMEEEEEEEEEEEEESIPGCTLFIKNL 729

Query: 236 NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           NF++TE++++  F K G I S T+++KK+    G  LSM
Sbjct: 730 NFSTTEETLKGVFSKVGAIKSCTISKKKN--KAGVLLSM 766

Plays a role in embryo pre-implantation development.
Mus musculus (taxid: 10090)

>sp|Q9Y4C8|RBM19_HUMAN Probable RNA-binding protein 19 OS=Homo sapiens GN=RBM19 PE=1 SV=3

 Score =  215 bits (547), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 128/283 (45%), Positives = 175/283 (61%), Gaps = 17/283 (6%)

Query: 7   SSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRLA 63
           SSYK KK  + K  +   H WN+LF+G NA+A+A+A+ YNATK++V    T    A R+A
Sbjct: 494 SSYKKKKEAQDKANSASSHNWNTLFMGPNAVADAIAQKYNATKSQVFDHETKGSVAVRVA 553

Query: 64  MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
           +GET++V++ R FL +NGV LD+F+Q    RSK +ILVKNLP  TL   L+  F  FG L
Sbjct: 554 LGETQLVQEVRRFLIDNGVSLDSFSQAAAERSKTVILVKNLPAGTLAAQLQETFGHFGSL 613

Query: 124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKE 183
           GRVL+P  GIT +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF+    + K  +
Sbjct: 614 GRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPVGVFSSTAPQKKKLQ 673

Query: 184 KEKNEEGE-----------GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPE-PDTTLY 231
              +E  E           GE  + EN  EE       ++EE  EE+EE E   P  TL+
Sbjct: 674 DTPSEPMEKDPAEPETVPDGETPEDENPTEEGADNSSAKMEEEEEEEEEEEESLPGCTLF 733

Query: 232 IKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           IKNLNF++TE+ ++  F K G + S ++++KK+    G  LSM
Sbjct: 734 IKNLNFDTTEEKLKEVFSKVGTVKSCSISKKKN--KAGVLLSM 774

Plays a role in embryo pre-implantation development.

Homo sapiens (taxid: 9606)

>sp|O13620|MRD1_SCHPO Multiple RNA-binding domain-containing protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mrd1 PE=3 SV=1

 Score =  174 bits (441), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 99/268 (36%), Positives = 149/268 (55%), Gaps = 25/268 (9%)

Query: 12  KKAKELKK---IAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL--TGSGAATRLAMGE 66
           KK +ELK+    A    +WNSL++  +A+  ++A      K ++L  T S +A + A+ E
Sbjct: 418 KKQRELKRKNTAASSTFSWNSLYMNADAVVTSLASRLGVKKTDILDPTSSDSAVKQALTE 477

Query: 67  TEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV 126
           T ++++T+ F EE+GV LDAF     ARS  ++LVKN PY T   +L +LF PFG+LGR+
Sbjct: 478 THVIQETKNFFEEHGVDLDAFKNA--ARSDNVLLVKNFPYGTSAEELTSLFSPFGELGRI 535

Query: 127 LVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 186
           L+PP G   ++EFL     + AF+ LAYT+ K   LYLE AP  VF  + ++S       
Sbjct: 536 LIPPAGTIAIIEFLNAPDCRQAFSKLAYTRIKSSILYLEKAPRDVFTTSFKQS------- 588

Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR 246
              G+ E  +K N  E    + V          E+ E     T+Y+KNLNF++ ++  ++
Sbjct: 589 ---GKPELAQKVNAVEATTSEKVGT--------EDIESLDTATIYVKNLNFSTKQEEFQK 637

Query: 247 HFKKCGPIASVTVARKKDPKSPGQFLSM 274
            FK      S  +  K DPK PG++LSM
Sbjct: 638 VFKPLEGYLSAVIRAKPDPKRPGKYLSM 665

Involved in pre-rRNA processing.

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

>sp|Q54PB2|MRD1_DICDI Multiple RNA-binding domain-containing protein 1 OS=Dictyostelium discoideum GN=mrd1 PE=3 SV=1

 Score =  161 bits (407), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 91/270 (33%), Positives = 151/270 (55%), Gaps = 10/270 (3%)

Query: 6   GSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGS--GAATRLA 63
            SS+K +K ++ K  +G  H WN+LF+ ++AI  ++AE Y  T+ ++L  +    A R+ 
Sbjct: 460 SSSFKAEKEQKQKTTSGSTHNWNALFMRSDAIVSSLAERYKMTQGQLLDPNQMDLAVRMT 519

Query: 64  MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
           + ET ++ +T+ FLE+ GV +         RS  ++LVKN+P++T   +L  LF  FG+L
Sbjct: 520 LMETHVINETKKFLEDQGVIIQDIGNKGSKRSNTVLLVKNIPFKTQEHELHELFSKFGEL 579

Query: 124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFA-EAKEKSKGK 182
            RV++ P     L+E++  N+AK  F +LAY+KF  VPLYLEWAPEGVF   A  K   K
Sbjct: 580 SRVVLSPARTIALIEYIHPNEAKVGFKNLAYSKFHHVPLYLEWAPEGVFKLPAPPKEIKK 639

Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTED 242
            ++  +  +   +KKE  +           ++  + + +        +YIKNLN+ +T +
Sbjct: 640 SEKSEKSSDSSNDKKEVESTTKTAATTTTTKKGTDNNTQ-------FVYIKNLNWKTTNE 692

Query: 243 SIRRHFKKCGPIASVTVARKKDPKSPGQFL 272
           ++   FK      +V +A K +PK+P + L
Sbjct: 693 TLVGKFKSLKDYVNVNIATKANPKNPSERL 722

Dictyostelium discoideum (taxid: 44689)

>sp|Q5BGA9|MRD1_EMENI Multiple RNA-binding domain-containing protein 1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=mrd1 PE=3 SV=1

 Score =  156 bits (395), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 93/256 (36%), Positives = 138/256 (53%), Gaps = 21/256 (8%)

Query: 21  AGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL--TGSGAATRLAMGETEIVEKTRAFLE 78
           A    +WNSL++  +A+  ++AE    +KA++L  T S AA + A  ET ++++T+A+ +
Sbjct: 402 ASSTFSWNSLYMNADAVMSSVAERIGVSKADLLDPTSSDAAVKQAHAETHVIQETKAYFK 461

Query: 79  ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVE 138
            NGV LDAF Q    R    ILVKN  Y T   DL+ LFEPFG + R+L+PP G   +V 
Sbjct: 462 ANGVNLDAFKQ--RERGNLAILVKNFSYGTKTEDLRKLFEPFGQITRLLMPPSGTIAIVA 519

Query: 139 FLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKE 198
           F + ++A+ AF SLAY K  +  L+LE AP+ +F EA    +    E     +G      
Sbjct: 520 FARPDEAQKAFKSLAYRKLGDSILFLEKAPKDLF-EADVPPQNPLPETKAVSQGFSTADT 578

Query: 199 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
             A+E +++ +                   TL+IKNLNF++T  S+   F+      S  
Sbjct: 579 FAADEGDEEVMATA----------------TLFIKNLNFSTTNQSLIEAFRPLDGFVSAR 622

Query: 259 VARKKDPKSPGQFLSM 274
           +  K DPK+PGQ LSM
Sbjct: 623 IKTKPDPKNPGQTLSM 638

Involved in pre-rRNA processing.

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

>sp|Q4WJT7|MRD1_ASPFU Multiple RNA-binding domain-containing protein 1 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=mrd1 PE=3 SV=1

 Score =  152 bits (385), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 99/281 (35%), Positives = 147/281 (52%), Gaps = 31/281 (11%)

Query: 3   IDEG--SSYKTKKAKELKK---IAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL--TG 55
           IDE   S    KK K++K+    +    +WNSL++ T+A+  ++AE    +KA++L  T 
Sbjct: 385 IDEHELSKLPLKKQKQIKRKLEASSSTFSWNSLYMNTDAVMSSVAERLGVSKADLLDPTS 444

Query: 56  SGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKA 115
           + AA + A  ET ++++T+A+   NGV LDAF Q    R    ILVKN  Y     DL+ 
Sbjct: 445 ADAAVKQAHAETHVIQETKAYFTANGVNLDAFKQ--RERGNTAILVKNFSYGVKVDDLRK 502

Query: 116 LFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF--A 173
           LFEP+G + R+L+PP G   +VEF + ++A+ AF  LAY K  +  L+LE AP  +F   
Sbjct: 503 LFEPYGQITRLLMPPSGTIAIVEFARPDEAQKAFKGLAYRKVGDSILFLEKAPANLFDAT 562

Query: 174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIK 233
            A + S  + K  +                   QG    +    ED + EP   +TL++K
Sbjct: 563 TAPQTSVLETKAVS-------------------QGFSTADTFAAEDGD-EPVVTSTLFVK 602

Query: 234 NLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           NLNF++T +     FK      S  +  K DPK PG+ LSM
Sbjct: 603 NLNFSTTNERFTEVFKPLDGFVSARIKTKPDPKRPGKTLSM 643

Involved in pre-rRNA processing.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

>sp|Q5AJS6|MRD1_CANAL Multiple RNA-binding domain-containing protein 1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=MRD1 PE=3 SV=1

 Score =  145 bits (365), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 92/269 (34%), Positives = 144/269 (53%), Gaps = 16/269 (5%)

Query: 12  KKAKELKKIAGHVHT---WNSLFLGTNAIAEAMAETYNATKAEVLT--GSGAATRLAMGE 66
           KK +ELKK A    T   WNSL++ ++A+ E++A     TK++++    S +A + A+ E
Sbjct: 405 KKQRELKKKAQAAKTQFSWNSLYMNSDAVLESVASKLGVTKSQLIDPENSSSAVKQALAE 464

Query: 67  TEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV 126
             ++   R + E+ GV L +F++  + R  +IILVKN P+ T   ++  LF  +G L R+
Sbjct: 465 AHVIGDVRKYFEDRGVDLTSFDK--KERDDKIILVKNFPFGTTIDEIGELFSAYGQLKRM 522

Query: 127 LVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 186
           L+PP G   ++EF     A+AAF+ LAY +FK   LYLE  P+ +F         +E   
Sbjct: 523 LMPPAGTIAIIEFRDAPSARAAFSKLAYKRFKSSILYLEKGPKDLFT--------REPTT 574

Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDE-EREPEPDTTLYIKNLNFNSTEDSIR 245
           NE     E+++   A E        + E+ E+DE E    P   +++KNLNF +T  ++ 
Sbjct: 575 NEVATIPEQQQNEHAVEAKISANEILGESKEDDEIESVQGPTVAVFVKNLNFATTVQALS 634

Query: 246 RHFKKCGPIASVTVARKKDPKSPGQFLSM 274
             FK        TV  K DPK+ G+ LSM
Sbjct: 635 DLFKPLPGFVVATVKTKPDPKNSGKTLSM 663

Involved in pre-rRNA processing.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

>sp|Q6CQR6|MRD1_KLULA Multiple RNA-binding domain-containing protein 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=MRD1 PE=3 SV=1

 Score =  144 bits (364), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 88/273 (32%), Positives = 145/273 (53%), Gaps = 10/273 (3%)

Query: 12  KKAKELKKIAG---HVHTWNSLFLGTNAIAEAMAETYNATKAEVLTG--SGAATRLAMGE 66
           KK +ELK+ A       +WNSL++  +A+  ++A+     K+E++    S +A + A+ E
Sbjct: 425 KKQRELKRKANSAQQTFSWNSLYMNQDAVLSSVADKLGMKKSELIDAENSSSAVKQALAE 484

Query: 67  TEIVEKTRAFLEENGVQLDAFNQVVEA-RSKRIILVKNLPYRTLPTDLKALFEPFGDLGR 125
             ++   R F E  GV L  F Q+  + R  R+ILVKN PY T   ++  LF PFG L R
Sbjct: 485 ASVIGDVRKFFETRGVDLTKFAQLKNSERDDRVILVKNFPYGTTREEIAELFLPFGKLQR 544

Query: 126 VLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKE 185
           +L+PP G   +++F     A+AAF+ ++Y +FK+  +YLE  P   F    +  +  E E
Sbjct: 545 LLLPPSGTIAILQFRDVPAARAAFSKISYKRFKDGIIYLEKGPSDCFTRDAQGDELVESE 604

Query: 186 KNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEER----EPEPDTTLYIKNLNFNSTE 241
            + +    +E K + A+    Q +P  +++  +D++     +  P  +++IKNLNF++T 
Sbjct: 605 TDIQKATAKEAKISGADLLEAQSLPAADKDDHDDDDDDDDVQAGPTVSIFIKNLNFSTTS 664

Query: 242 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
             +   FK         V  K DPK PG+ LSM
Sbjct: 665 QQLTEKFKPFNGFVVAQVKTKPDPKQPGKTLSM 697

Involved in pre-rRNA processing.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|Q4PC17|MRD1_USTMA Multiple RNA-binding domain-containing protein 1 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=MRD1 PE=3 SV=1

 Score =  144 bits (362), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 19/280 (6%)

Query: 2   GIDEGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLT------G 55
           G  + ++ K  +A++ K+ A     W+ L++ ++A+A ++A+     K+++L        
Sbjct: 400 GSKKTATLKQARAEQKKQDATKDFNWSMLYMSSDAVASSIADRLGVNKSDILNPGANGGA 459

Query: 56  SGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKA 115
             AA RLA+ ET I+++T+ FL + G+ +DAF      RS   ILVKN+PY T   +++ 
Sbjct: 460 DNAAVRLALAETRIIQETKEFLAQQGINVDAFQGAKGPRSDTTILVKNIPYGTSAEEVEK 519

Query: 116 LFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEA 175
           LF   G++ +VL+PP G   +VE    N+A+ AF ++AY +FK   LYLE AP G+  + 
Sbjct: 520 LFGEHGEVDKVLIPPSGTIAVVEMPVVNEARLAFRAIAYKRFKGGILYLEKAPVGLLTQH 579

Query: 176 KEKSKGKEKEKNEEGEGEEEKKEN-TAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKN 234
           K    G++  K     G+     N + + D   G    +E V+           TLY+KN
Sbjct: 580 K---VGEKVVKQAPIVGKSIDSSNPSVDLDGPAGAGAGDEAVD---------GATLYVKN 627

Query: 235 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           L+F++T++ +   F      A   +  K DP+ PG  LSM
Sbjct: 628 LSFSTTDERLTAFFHGLSDFAFARIQTKPDPRRPGARLSM 667

Involved in pre-rRNA processing.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|Q7SG09|MRD1_NEUCR Multiple RNA-binding domain-containing protein 1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=mrd-1 PE=3 SV=1

 Score =  142 bits (359), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 140/272 (51%), Gaps = 36/272 (13%)

Query: 12  KKAKELKK---IAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL--TGSGAATRLAMGE 66
           KK + L+K    A     WNSLF+  +A+  AMAE    +KAE+L  T + AA + A+ E
Sbjct: 401 KKQQLLRKKAEAASSTFNWNSLFMSQDAVNTAMAERLGVSKAELLDPTDASAAVKQAVAE 460

Query: 67  TEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV 126
           T ++++ + +   NGV ++AF    + R    ILVKN+   T+  +L+ LFE  G + RV
Sbjct: 461 TTVIQEAKQYFAANGVNIEAFK--TQQRGDTTILVKNIKNTTI-EELRTLFEEHGTVLRV 517

Query: 127 LVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 186
           L+PP G   +V+F Q  Q + AF   AY++FK+  L+LE  P+G+F +            
Sbjct: 518 LMPPSGTIAIVQFAQPVQCRTAFARKAYSRFKDSVLFLEKGPKGLFTD------------ 565

Query: 187 NEEGEGEEEKKENTAEEDNQQ--GV--PEVEENVEEDEEREPEPDTTLYIKNLNFNSTED 242
                       N A   + +  GV  P V + +E D+  E    ++L+++NLNF++T  
Sbjct: 566 ------------NVAVPTDARPAGVQKPSVADLLERDDAEEQLETSSLFVRNLNFSTTSQ 613

Query: 243 SIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
            +   FK         V  K DPK PGQ LSM
Sbjct: 614 GLTDAFKHLDGFVQAKVKTKTDPKKPGQVLSM 645

Involved in pre-rRNA processing.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	274
321476727	845	hypothetical protein DAPPUDRAFT_306569 [	0.948	0.307	0.518	4e-69
193624932	831	PREDICTED: probable RNA-binding protein	0.897	0.296	0.516	1e-68
307192625	863	Probable RNA-binding protein 19 [Harpegn	0.970	0.308	0.479	4e-66
427792771	687	Hypothetical protein, partial [Rhipiceph	0.952	0.379	0.534	6e-66
307180956	903	Probable RNA-binding protein 19 [Campono	0.967	0.293	0.467	1e-65
427792715	841	Hypothetical protein, partial [Rhipiceph	0.952	0.310	0.531	4e-65
405963583	878	Putative RNA-binding protein 19 [Crassos	0.912	0.284	0.473	7e-65
322787083	859	hypothetical protein SINV_16564 [Solenop	0.974	0.310	0.464	4e-63
357616005	888	hypothetical protein KGM_10362 [Danaus p	0.970	0.299	0.474	9e-63
332024948	862	Putative RNA-binding protein 19 [Acromyr	0.967	0.307	0.462	3e-62

>gi|321476727|gb|EFX87687.1| hypothetical protein DAPPUDRAFT_306569 [Daphnia pulex]

 Score =  267 bits (682), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 143/276 (51%), Positives = 191/276 (69%), Gaps = 16/276 (5%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSG------A 58
           EG+SYK KK KELK  A   H WN+LFLGTNA+A  MAE Y+ TK +VL   G       
Sbjct: 402 EGTSYKKKKLKELKNKAASAHNWNTLFLGTNAVATLMAERYSTTKQQVLLEGGDGQQQSV 461

Query: 59  ATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFE 118
           A RLA+GET++V +T+ FL ENG+ LDAF    + RSK ++LVKNL  ++   +L+ LF 
Sbjct: 462 AVRLALGETQLVAETKQFLVENGIHLDAFQDAPKQRSKTVMLVKNLDAQSNVDELRDLFS 521

Query: 119 PFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEK 178
           PFG+LGRVL+PP G+T +VEFL+  +AKAAF  LAY+KF+ +PLYLEWAP  VF  A ++
Sbjct: 522 PFGELGRVLLPPRGVTAIVEFLEPTEAKAAFRKLAYSKFRHMPLYLEWAPMDVFRTAAQR 581

Query: 179 SKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN 238
            + K  E   + + ++     T EE+N    P + + VEE    +PE DTT+++KN+NF 
Sbjct: 582 VESKPSE--NKTKVKDASAVATLEENN----PILSDKVEE----QPEQDTTIFVKNVNFA 631

Query: 239 STEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +T+ S+R+HF+ CGPI S TVARKKDPK+PGQFLSM
Sbjct: 632 TTDQSMRKHFESCGPIFSATVARKKDPKNPGQFLSM 667

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193624932|ref|XP_001949363.1| PREDICTED: probable RNA-binding protein 19-like [Acyrthosiphon pisum]

 Score =  266 bits (679), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 140/271 (51%), Positives = 178/271 (65%), Gaps = 25/271 (9%)

Query: 4   DEGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLA 63
           DE SS+K KK  +LK  AG  H WNSLFLG NA+A+ +A+TYN TK  VLTG  AA RLA
Sbjct: 409 DECSSFKKKKMAKLKSEAGLSHNWNSLFLGQNAVADIIAKTYNTTKENVLTGDNAAVRLA 468

Query: 64  MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
           +GE++IV  T+ +LE  GV+LD FNQ V  RSK +ILVKNLP  T   +LK +F  +G +
Sbjct: 469 LGESQIVSDTKIYLENQGVKLDIFNQTVINRSKNVILVKNLPADTTELELKDIFSKYGLV 528

Query: 124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKE 183
            RV++PP G+TGL+EF+Q ++AK AF  LAY+KFK +PLYLEWAP+ V  +         
Sbjct: 529 NRVVLPPSGVTGLIEFVQNSEAKTAFRQLAYSKFKHLPLYLEWAPDKVLTDV-------- 580

Query: 184 KEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS 243
                         +N  EE      P       ED+  EPE DTTL+IKN+NFN+TE+ 
Sbjct: 581 -------------PQNIHEE----TFPSYTNKDTEDDIDEPESDTTLFIKNINFNTTEEH 623

Query: 244 IRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           I +HF+ CG IA+VTVARKKDP  PG+FLSM
Sbjct: 624 ITKHFEPCGKIANVTVARKKDPNLPGKFLSM 654

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192625|gb|EFN75799.1| Probable RNA-binding protein 19 [Harpegnathos saltator]

 Score =  257 bits (656), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 131/273 (47%), Positives = 182/273 (66%), Gaps = 7/273 (2%)

Query: 8   SYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL----TGSGAATRLA 63
           SYK KK  + K  A   H WN+LFLG NA+ +A+A TYN TK +VL     G  AA +LA
Sbjct: 414 SYKQKKELQNKATANSSHNWNTLFLGQNAVMDAIATTYNTTKEKVLEDESKGMSAAVKLA 473

Query: 64  MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
           +GET+I   T+AFLEENGV L+ FNQ  + RS  +ILVKNLP +T P D++ +F   G+L
Sbjct: 474 LGETQIAHDTKAFLEENGVCLNTFNQAPKQRSNTVILVKNLPAQTKPADIREMFVKHGEL 533

Query: 124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKE 183
           GR+++PP GIT LVEFL+ ++A+ AF  LAYTKFK +PLYLEWAP+  F     K KGK 
Sbjct: 534 GRIVLPPSGITALVEFLEPSEARKAFTKLAYTKFKHLPLYLEWAPDNSFTAPASKCKGK- 592

Query: 184 KEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEER--EPEPDTTLYIKNLNFNSTE 241
           ++  +    EE K E   ++++++ V    +  + D+    EPE DTTL++KN+NF++T 
Sbjct: 593 RDTKKSSNAEEAKGEEATQKESKENVNNANKKADADDADDEEPESDTTLFVKNINFSTTT 652

Query: 242 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           + ++ +F KCG +  V +A KKDPK+PG  LSM
Sbjct: 653 EELKSYFSKCGRLHYVMIATKKDPKNPGNNLSM 685

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792771|gb|JAA61837.1| Hypothetical protein, partial [Rhipicephalus pulchellus]

 Score =  256 bits (655), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 146/273 (53%), Positives = 190/273 (69%), Gaps = 12/273 (4%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATR 61
           E  SYK KK +ELKK +G  H WN+LFLG NA+A+ MAE Y  +K E+L   TG   A R
Sbjct: 389 EAKSYKDKKEEELKKSSGRSHNWNTLFLGANALADVMAERYATSKQELLGTETGESVAVR 448

Query: 62  LAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG 121
           +A+GET++V +TR FLE NGV LDAFN+    RSK +ILVKNLP +T P DL ++F  FG
Sbjct: 449 MALGETQVVAETREFLESNGVVLDAFNRPATERSKTVILVKNLPAKTPPKDLHSVFGKFG 508

Query: 122 DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKG 181
            L RV++PP+G+T L+EF    +A+AAF  LAY+KFK VPLYLEWAP GVF+  K   K 
Sbjct: 509 ILSRVVLPPWGVTALIEFQDPTEARAAFRRLAYSKFKHVPLYLEWAPTGVFSTEKSADKS 568

Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE 241
           K        EGE + K+   E+ + +   + EE  E +EE  PEPDTTL+IKNLNF++ E
Sbjct: 569 KT-------EGETKTKDT--EQKHAEQPADEEEEAENEEEIPPEPDTTLFIKNLNFSTDE 619

Query: 242 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +++R HF++CGPI  VT+A+KKD K+PGQ LSM
Sbjct: 620 EAVREHFEQCGPIHEVTIAKKKDTKNPGQLLSM 652

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180956|gb|EFN68744.1| Probable RNA-binding protein 19 [Camponotus floridanus]

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 130/278 (46%), Positives = 191/278 (68%), Gaps = 13/278 (4%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL----TGSGAAT 60
           E  +YK KK  + K  AG  H WN+LFLG NA+A+A+A  YN TK ++L     G  AA 
Sbjct: 450 ENLTYKQKKELQNKATAGSSHNWNTLFLGQNAVADAIASCYNTTKEKLLEDGSNGMSAAV 509

Query: 61  RLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPF 120
           +LA+GET++ + T+AFLEENGV L+AFNQ  + RS  IIL+KNLP +T  ++++ +F   
Sbjct: 510 KLALGETQLAQDTKAFLEENGVCLNAFNQAPKKRSTTIILIKNLPAQTKSSEIREMFAKH 569

Query: 121 GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKS- 179
           G+L R+++PP GIT LVEFL+ ++A+ AF++LAY K+K +PLYLEWAP+  F     K+ 
Sbjct: 570 GELARIVMPPAGITALVEFLEPSEARKAFHALAYKKYKHLPLYLEWAPDNSFTRPASKTD 629

Query: 180 --KGKEKEKNEEG-EGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLN 236
             K K +E+ +E  + +E KKE   EE  +      + + +ED+E  PEPDTTL++KN+N
Sbjct: 630 MIKSKSRERRKESTDSKEAKKEIITEESKENE----KMHTKEDDE-PPEPDTTLFVKNIN 684

Query: 237 FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           F++TE+ ++ +F KCGP+  +T+A KKDP++P   LSM
Sbjct: 685 FSTTEEQLKDYFGKCGPLHYITIATKKDPENPTNKLSM 722

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792715|gb|JAA61809.1| Hypothetical protein, partial [Rhipicephalus pulchellus]

 Score =  254 bits (648), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 145/273 (53%), Positives = 189/273 (69%), Gaps = 12/273 (4%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATR 61
           E  SYK KK +ELKK +G  H WN+LFLG NA+A+ MAE Y  +K E+L   TG   A R
Sbjct: 389 EAKSYKDKKEEELKKSSGRSHNWNTLFLGANALADVMAERYATSKQELLGTETGESVAVR 448

Query: 62  LAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG 121
           +A+GET++V +TR FLE NGV LDAFN+    RSK +ILVKNLP +T P DL ++F  FG
Sbjct: 449 MALGETQVVAETREFLESNGVVLDAFNRPATERSKTVILVKNLPAKTPPKDLHSVFGKFG 508

Query: 122 DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKG 181
            L RV++PP+G+T L+EF    +A+AAF  LAY+KFK VPLYLEWAP GVF+  K   K 
Sbjct: 509 ILSRVVLPPWGVTALIEFQDPTEARAAFRRLAYSKFKHVPLYLEWAPTGVFSTEKSADKS 568

Query: 182 KEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE 241
           K        EGE + K+   E+ + +   + EE  E +EE  PEPDTTL+IKNLNF++ E
Sbjct: 569 KT-------EGETKTKDT--EQKHAEQPADEEEEAENEEEIPPEPDTTLFIKNLNFSTDE 619

Query: 242 DSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +++R HF++CGPI  VT+A+KKD K+ GQ LSM
Sbjct: 620 EAVREHFEQCGPIHEVTIAKKKDTKNAGQLLSM 652

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405963583|gb|EKC29145.1| Putative RNA-binding protein 19 [Crassostrea gigas]

 Score =  253 bits (646), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 132/279 (47%), Positives = 177/279 (63%), Gaps = 29/279 (10%)

Query: 6   GSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRL 62
           GSSYK+KKA + K  A   H WN++FLG NA+A+ MA  YN  K+ +L          R+
Sbjct: 461 GSSYKSKKAAQQKAEASSSHNWNTMFLGINAVADVMATKYNTEKSHILDPEAPQSLGVRM 520

Query: 63  AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
           A+GET+IV +TR FL ENGV LD+F+Q    RSK ++LVKNLP  T P DL+ +F   G 
Sbjct: 521 ALGETQIVAETRDFLTENGVVLDSFSQAAAPRSKTVLLVKNLPANTDPEDLQEVFSKHGA 580

Query: 123 LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGK 182
           LGRVL+PP G+T +VE+L   +AK  F +LAYTKF+ VPLYLEWAP  VF +        
Sbjct: 581 LGRVLMPPSGVTAIVEYLDPTEAKLGFRNLAYTKFQHVPLYLEWAPMEVFRKPA------ 634

Query: 183 EKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE-------PEPDTTLYIKNL 235
                         +EN  +E    G+PE E   +E+   E       PEPD+TL++KNL
Sbjct: 635 -------------VRENKKQESADSGIPEKEAGADEESSGESGEEDAGPEPDSTLFVKNL 681

Query: 236 NFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           NF++TE+ +R+ FKKCG I +V+VA+KKD K+PG++LSM
Sbjct: 682 NFSTTEEGLRQKFKKCGAIRAVSVAKKKDMKNPGKYLSM 720

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|322787083|gb|EFZ13307.1| hypothetical protein SINV_16564 [Solenopsis invicta]

 Score =  247 bits (631), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 129/278 (46%), Positives = 181/278 (65%), Gaps = 11/278 (3%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL----TGSGAAT 60
           E  +YK KK  + K  AG  H WN+LFLG NA+A+A+A  YN TK ++L     G  AA 
Sbjct: 403 ENLTYKQKKELQTKATAGSSHNWNTLFLGQNAVADAIASRYNTTKEKLLEDGSNGMSAAV 462

Query: 61  RLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPF 120
           +LA+GET++ +  + FLEENGV LDAFN   + RS  IILVKNLP  T P +L+  F   
Sbjct: 463 KLALGETQLAQDAKTFLEENGVCLDAFNGAPKKRSNTIILVKNLPAETKPNELQERFAKH 522

Query: 121 GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSK 180
           G+L R+++PP GIT LVEFL+ ++A+ AF +LAYTK+K +PLYLEWAP+  F  +  K+K
Sbjct: 523 GELARIVMPPAGITALVEFLEPSEARKAFQALAYTKYKHLPLYLEWAPDNSFTTSASKTK 582

Query: 181 GKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENV---EEDEEREP-EPDTTLYIKNLN 236
                KN+    +    E   +E   +   E E+N    E +E  EP EPDTTL++KN+N
Sbjct: 583 A---TKNKATTKKSTDSEKVKDEKTIEQSKEKEKNTRKKENNESTEPVEPDTTLFVKNIN 639

Query: 237 FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           F++TE+ ++ +F KCGP+  VT+A K +P++P + LSM
Sbjct: 640 FSTTEEQLKDYFGKCGPLHYVTIATKMNPENPAEKLSM 677

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357616005|gb|EHJ69949.1| hypothetical protein KGM_10362 [Danaus plexippus]

 Score =  246 bits (627), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 131/276 (47%), Positives = 181/276 (65%), Gaps = 10/276 (3%)

Query: 3   IDEGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLT----GSGA 58
           IDE   +K KKA +LK+ A   H WN LFLG NAIA+ +A +YN TK ++L+     + A
Sbjct: 437 IDEDLPFKEKKALKLKQQAKSSHNWNVLFLGANAIADVVASSYNTTKEQLLSDNNKNTSA 496

Query: 59  ATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFE 118
           A RLA+GET++V +T+ FLE NGV LDAFN+  + RSK  ILVKNLP  T   +++ LF 
Sbjct: 497 AVRLALGETQLVAETKEFLESNGVHLDAFNRPAKKRSKTCILVKNLPAGTDKEEIRNLFV 556

Query: 119 PFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEK 178
             G L R L+P +GIT LV+F++  +AK AF  LAY+++K  PLYLEWAPE VF +  + 
Sbjct: 557 KHGQLARFLMPRHGITALVDFIEPFEAKKAFGKLAYSQYKSAPLYLEWAPENVFVKDAKT 616

Query: 179 SKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN 238
                KE ++  + E E  + T+ ++     PE  + VEE    +PE DTTL+IKNLNF 
Sbjct: 617 ETVSGKETSDVNKTEAESGDETSVKE-----PET-KMVEEPSNEQPENDTTLFIKNLNFK 670

Query: 239 STEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +TE++++ HF  CG + SV +A+KKDPK+  Q LSM
Sbjct: 671 TTEETLKSHFSACGKVHSVVIAKKKDPKNQTQLLSM 706

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332024948|gb|EGI65135.1| Putative RNA-binding protein 19 [Acromyrmex echinatior]

 Score =  244 bits (623), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 128/277 (46%), Positives = 181/277 (65%), Gaps = 12/277 (4%)

Query: 5   EGSSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL----TGSGAAT 60
           E  +YK KK  + K  A   H WN+LFLG NA+A A+   YN TK ++L     G  AA 
Sbjct: 409 ENLTYKQKKELQTKATASSSHNWNTLFLGQNAVANAIVSRYNTTKEKLLEDESNGMSAAV 468

Query: 61  RLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPF 120
           +LA+GET++V+ T+ FLEENGV LDAFN+  + RS  IILVKNLP  T P +L+ +F   
Sbjct: 469 KLALGETQLVQDTKIFLEENGVCLDAFNETPKKRSSTIILVKNLPAETKPNELQEMFAKH 528

Query: 121 GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSK 180
           G+L R+++PP GIT LVEFL+  +A+ AF +LAYTK+K +PLYLEWAP+  F     K+ 
Sbjct: 529 GELARIILPPAGITALVEFLEPFEARKAFRTLAYTKYKHLPLYLEWAPDNSFTTPASKNN 588

Query: 181 GKEKE--KNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE-PEPDTTLYIKNLNF 237
             E      +  + +E K E T +E N     E + N  ++E+ E PE DTTL++KN+NF
Sbjct: 589 TIENNVTTKKSADLKEVKDEVTIKEFN-----ENKNNTHKEEDNEPPESDTTLFVKNINF 643

Query: 238 NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           ++TE+ ++ +F KCGP+  +T+A K DP++P + LSM
Sbjct: 644 STTEEQLKDYFGKCGPLHYITIATKMDPENPAKKLSM 680

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	274
ZFIN|ZDB-GENE-031125-3	927	rbm19 "RNA binding motif prote	0.627	0.185	0.542	8.4e-53
UNIPROTKB|F1P1R2	621	RBM19 "Uncharacterized protein	0.616	0.272	0.523	7.7e-52
UNIPROTKB|F1NEC5	945	RBM19 "Uncharacterized protein	0.616	0.178	0.523	7.8e-50
UNIPROTKB|E2RRF5	968	RBM19 "Uncharacterized protein	0.613	0.173	0.508	2.8e-48
MGI|MGI:1921361	952	Rbm19 "RNA binding motif prote	0.609	0.175	0.505	4.3e-48
UNIPROTKB|Q9Y4C8	960	RBM19 "Probable RNA-binding pr	0.605	0.172	0.514	1.9e-47
UNIPROTKB|F1RKD1	965	RBM19 "Uncharacterized protein	0.605	0.172	0.491	3.1e-46
FB|FBgn0036018	918	CG3335 [Drosophila melanogaste	0.532	0.159	0.493	6e-46
POMBASE|SPBP22H7.02c	833	SPBP22H7.02c "RNA-binding prot	0.547	0.180	0.428	1.3e-38
DICTYBASE|DDB_G0284663	895	mrd1 "RNA-binding region RNP-1	0.624	0.191	0.390	6.1e-37

ZFIN|ZDB-GENE-031125-3 rbm19 "RNA binding motif protein 19" [Danio rerio (taxid:7955)]

 Score = 467 (169.5 bits), Expect = 8.4e-53, Sum P(2) = 8.4e-53
 Identities = 95/175 (54%), Positives = 120/175 (68%)

Query:     1 PGIDEGSSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLT--GSGA 58
             P     SSY           +G  H WN+LFLGT+A+A+A+AE YN TK++VL     G+
Sbjct:   486 PDAPGSSSYKRKKDAKDKAASGSSHNWNTLFLGTSAVADAIAEKYNTTKSQVLDHESDGS 545

Query:    59 -ATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALF 117
              A R+A+GET+IV++TR FL +NGV LD+F+Q    RSK +ILVKNLP      DL+ALF
Sbjct:   546 LAVRMALGETQIVQETRQFLLDNGVSLDSFSQASGERSKCVILVKNLPSGVQVADLEALF 605

Query:   118 EPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
              P G LGRVL+PP G+T +VEFL+  +AK AF  LAYTKF+ VPLYLEWAP  VF
Sbjct:   606 SPHGSLGRVLLPPSGLTAIVEFLEPTEAKRAFMKLAYTKFQHVPLYLEWAPVAVF 660

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0048546 "digestive tract morphogenesis" evidence=IMP

UNIPROTKB|F1P1R2 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 446 (162.1 bits), Expect = 7.7e-52, Sum P(2) = 7.7e-52
 Identities = 90/172 (52%), Positives = 118/172 (68%)

Query:     4 DEGSSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAAT 60
             +E SSY           +   H WN+LF+GTNA+A+A+A+ YNA+K++VL   +    A 
Sbjct:   167 EESSSYKKQKEAKDKANSASSHNWNTLFVGTNAVADAIAQKYNASKSQVLDHESKDSVAV 226

Query:    61 RLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPF 120
             R+A+GETE+V++ R FL ENGV LD+F+Q    RSK +ILVKNLP  T   +L+A+F   
Sbjct:   227 RVALGETELVQEIRRFLIENGVSLDSFSQAAGERSKTVILVKNLPATTSTAELEAVFGKH 286

Query:   121 GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             G LGRVL+P  GIT +VEFL+  +AK AF  LAY+KF  VPLYLEWAP GVF
Sbjct:   287 GSLGRVLLPTGGITAIVEFLEPIEAKQAFTKLAYSKFHSVPLYLEWAPMGVF 338

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

UNIPROTKB|F1NEC5 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 446 (162.1 bits), Expect = 7.8e-50, Sum P(2) = 7.8e-50
 Identities = 90/172 (52%), Positives = 118/172 (68%)

Query:     4 DEGSSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAAT 60
             +E SSY           +   H WN+LF+GTNA+A+A+A+ YNA+K++VL   +    A 
Sbjct:   491 EESSSYKKQKEAKDKANSASSHNWNTLFVGTNAVADAIAQKYNASKSQVLDHESKDSVAV 550

Query:    61 RLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPF 120
             R+A+GETE+V++ R FL ENGV LD+F+Q    RSK +ILVKNLP  T   +L+A+F   
Sbjct:   551 RVALGETELVQEIRRFLIENGVSLDSFSQAAGERSKTVILVKNLPATTSTAELEAVFGKH 610

Query:   121 GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             G LGRVL+P  GIT +VEFL+  +AK AF  LAY+KF  VPLYLEWAP GVF
Sbjct:   611 GSLGRVLLPTGGITAIVEFLEPIEAKQAFTKLAYSKFHSVPLYLEWAPMGVF 662

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

UNIPROTKB|E2RRF5 RBM19 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 437 (158.9 bits), Expect = 2.8e-48, Sum P(2) = 2.8e-48
 Identities = 87/171 (50%), Positives = 115/171 (67%)

Query:     5 EGSSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATR 61
             +GSSY           +   H WN+LF+G NA+A+A+A+ YNATK++V    T    A R
Sbjct:   494 QGSSYKKKKESKDKANSSSSHNWNTLFMGPNAVADAIAQKYNATKSQVFDHETKGSVAVR 553

Query:    62 LAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG 121
             +A+GET++V++ R FL +NGV LD+F+Q    RSK +ILVKNLP  TL  +L+  F  FG
Sbjct:   554 VALGETQLVQEVRRFLLDNGVSLDSFSQAAAERSKTVILVKNLPAGTLVAELQETFGRFG 613

Query:   122 DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
              LGRVL+P  GIT +VEFL+  +A+ AF  LAY+KF   PLYLEWAP GVF
Sbjct:   614 SLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHTPLYLEWAPVGVF 664

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1921361 Rbm19 "RNA binding motif protein 19" [Mus musculus (taxid:10090)]

 Score = 434 (157.8 bits), Expect = 4.3e-48, Sum P(2) = 4.3e-48
 Identities = 86/170 (50%), Positives = 115/170 (67%)

Query:     6 GSSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRL 62
             GSSY           +   H WN+LF+G NA+A+A+A+ YNATK++V    T    A R+
Sbjct:   490 GSSYKKKKEAMDKANSSSSHNWNTLFMGPNAVADAIAQKYNATKSQVFDHETRGSVAVRV 549

Query:    63 AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
             A+GET++V++ R+FL +NGV LD+F+Q    RSK +IL KNLP  TL  +++  F  FG 
Sbjct:   550 ALGETQLVQEVRSFLIDNGVCLDSFSQAAAERSKTVILAKNLPAGTLAAEIQETFSRFGS 609

Query:   123 LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             LGRVL+P  GIT +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF
Sbjct:   610 LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF 659

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IMP

UNIPROTKB|Q9Y4C8 RBM19 "Probable RNA-binding protein 19" [Homo sapiens (taxid:9606)]

 Score = 432 (157.1 bits), Expect = 1.9e-47, Sum P(2) = 1.9e-47
 Identities = 87/169 (51%), Positives = 113/169 (66%)

Query:     7 SSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRLA 63
             SSY           +   H WN+LF+G NA+A+A+A+ YNATK++V    T    A R+A
Sbjct:   494 SSYKKKKEAQDKANSASSHNWNTLFMGPNAVADAIAQKYNATKSQVFDHETKGSVAVRVA 553

Query:    64 MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
             +GET++V++ R FL +NGV LD+F+Q    RSK +ILVKNLP  TL   L+  F  FG L
Sbjct:   554 LGETQLVQEVRRFLIDNGVSLDSFSQAAAERSKTVILVKNLPAGTLAAQLQETFGHFGSL 613

Query:   124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             GRVL+P  GIT +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF
Sbjct:   614 GRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPVGVF 662

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS;IDA

GO:0005737 "cytoplasm" evidence=ISS;IDA

GO:0040019 "positive regulation of embryonic development" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|F1RKD1 RBM19 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 421 (153.3 bits), Expect = 3.1e-46, Sum P(2) = 3.1e-46
 Identities = 83/169 (49%), Positives = 112/169 (66%)

Query:     7 SSYXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL---TGSGAATRLA 63
             SSY           +   H WN+LF+G NA+A+A+A+ YN+TK++V    T    A R+A
Sbjct:   495 SSYKKKKESKDKASSSSSHNWNTLFMGPNAVADAIAQKYNSTKSQVFDHETKGSVAVRVA 554

Query:    64 MGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL 123
             +GET++V++ R FL +NGV LD+F+Q    RSK +IL KNLP  T   +L+  F  FG L
Sbjct:   555 LGETQLVQEVRRFLLDNGVSLDSFSQAAAERSKTVILAKNLPAGTQAAELQETFGRFGSL 614

Query:   124 GRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             GRVL+P  G+T +VEFL+  +A+ AF  LAY+KF  VPLYLEWAP GVF
Sbjct:   615 GRVLLPEGGVTAIVEFLEALEARKAFRHLAYSKFHHVPLYLEWAPMGVF 663

GO:0040019 "positive regulation of embryonic development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0036018 CG3335 [Drosophila melanogaster (taxid:7227)]

 Score = 394 (143.8 bits), Expect = 6.0e-46, Sum P(2) = 6.0e-46
 Identities = 74/150 (49%), Positives = 105/150 (70%)

Query:    27 WNSLFLGTNAIAEAMAETYNATKAEVLT----GSGAATRLAMGETEIVEKTRAFLEENGV 82
             WN+LFLG NA+AE +A+ +  +K  +L     GS AA RLA+GET++V + + FLEE GV
Sbjct:   478 WNTLFLGANAVAEILAKQFKTSKERILDTSDGGSSAAVRLALGETQVVIEMKRFLEEEGV 537

Query:    83 QLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQK 142
             +LDAF++  + RS  +IL KNLP  T  +++  +F  FG +GR+++PP G+T L+E+   
Sbjct:   538 RLDAFDEPAKKRSNTVILAKNLPAATEISEITPIFSRFGPIGRIVLPPSGVTALIEYCDP 597

Query:   143 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
              +A+ AF  LAY+KFK  PLYLEWAPE VF
Sbjct:   598 LEARQAFKKLAYSKFKNAPLYLEWAPEQVF 627

GO:0004386 "helicase activity" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

POMBASE|SPBP22H7.02c SPBP22H7.02c "RNA-binding protein Mrd1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 339 (124.4 bits), Expect = 1.3e-38, Sum P(2) = 1.3e-38
 Identities = 66/154 (42%), Positives = 96/154 (62%)

Query:    21 AGHVHTWNSLFLGTNAIAEAMAETYNATKAEVL--TGSGAATRLAMGETEIVEKTRAFLE 78
             A    +WNSL++  +A+  ++A      K ++L  T S +A + A+ ET ++++T+ F E
Sbjct:   430 ASSTFSWNSLYMNADAVVTSLASRLGVKKTDILDPTSSDSAVKQALTETHVIQETKNFFE 489

Query:    79 ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVE 138
             E+GV LDAF     ARS  ++LVKN PY T   +L +LF PFG+LGR+L+PP G   ++E
Sbjct:   490 EHGVDLDAFKNA--ARSDNVLLVKNFPYGTSAEELTSLFSPFGELGRILIPPAGTIAIIE 547

Query:   139 FLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
             FL     + AF+ LAYT+ K   LYLE AP  VF
Sbjct:   548 FLNAPDCRQAFSKLAYTRIKSSILYLEKAPRDVF 581

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0006364 "rRNA processing" evidence=ISO

GO:0030686 "90S preribosome" evidence=ISO

GO:0034462 "small-subunit processome assembly" evidence=ISO

DICTYBASE|DDB_G0284663 mrd1 "RNA-binding region RNP-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 350 (128.3 bits), Expect = 6.1e-37, Sum P(2) = 6.1e-37
 Identities = 68/174 (39%), Positives = 104/174 (59%)

Query:     2 GIDEGSS-YXXXXXXXXXXIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLTGS--GA 58
             G + GSS +           +G  H WN+LF+ ++AI  ++AE Y  T+ ++L  +    
Sbjct:   455 GAEGGSSSFKAEKEQKQKTTSGSTHNWNALFMRSDAIVSSLAERYKMTQGQLLDPNQMDL 514

Query:    59 ATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFE 118
             A R+ + ET ++ +T+ FLE+ GV +         RS  ++LVKN+P++T   +L  LF 
Sbjct:   515 AVRMTLMETHVINETKKFLEDQGVIIQDIGNKGSKRSNTVLLVKNIPFKTQEHELHELFS 574

Query:   119 PFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
              FG+L RV++ P     L+E++  N+AK  F +LAY+KF  VPLYLEWAPEGVF
Sbjct:   575 KFGELSRVVLSPARTIALIEYIHPNEAKVGFKNLAYSKFHHVPLYLEWAPEGVF 628

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0030515 "snoRNA binding" evidence=ISS

GO:0006364 "rRNA processing" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	274
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	5e-34
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	6e-31
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	9e-25
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-19
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-08
smart00360	73	smart00360, RRM, RNA recognition motif	4e-08
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-07
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	4e-07
smart00360	73	smart00360, RRM, RNA recognition motif	9e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	8e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	0.001
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.002
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.002
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	0.003
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.003
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.004
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.004
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.004
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.004
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.004

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score =  117 bits (296), Expect = 5e-34
 Identities = 47/71 (66%), Positives = 56/71 (78%)

Query: 98  IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
           +ILVKNLP  TL  +L+ LF  FG LGRVL+PP GIT +VEFL+ ++AK AF  LAY+KF
Sbjct: 2   VILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGITAIVEFLEPSEAKLAFRKLAYSKF 61

Query: 158 KEVPLYLEWAP 168
           K VPLYLEWAP
Sbjct: 62  KHVPLYLEWAP 72

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>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 =  109 bits (275), Expect = 6e-31
 Identities = 43/72 (59%), Positives = 53/72 (73%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
            +ILVKNLP+ T   +L+ LFE FG LGR+L+PP     LVEFL+ + A+ AF SLAY +
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60

Query: 157 FKEVPLYLEWAP 168
           FK VPLYLEWAP
Sbjct: 61  FKHVPLYLEWAP 72

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|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 93.6 bits (233), Expect = 9e-25
 Identities = 38/70 (54%), Positives = 46/70 (65%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           ILVKN PY T   +L+ LFEP G L RVL+PP G   +VEF    QA+ AF +LAY +FK
Sbjct: 3   ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRRFK 62

Query: 159 EVPLYLEWAP 168
           +  LYLE  P
Sbjct: 63  DSILYLEKGP 72

This subgroup corresponds to the RRM3 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 = 72

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

 Score = 80.3 bits (199), Expect = 2e-19
 Identities = 29/47 (61%), Positives = 42/47 (89%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           TTL++KNLNF +TE+++++HF+KCG + SVT+A+KKDPK PG+ LSM
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSM 47

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-------GLVEFLQKNQAKAAFNS 151
           ILV+N+P+     +L+ LF  FG+L  V +P            G V+F+ K  AK AF +
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 152 LAY-TKFKEVPLYLEWA 167
           L + T      L LEWA
Sbjct: 63  LCHSTHLYGRRLVLEWA 79

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           TL++ NL  ++TE+ +R  F K G + SV + R K+    
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKS 40

Length = 73

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNSLA 153
           ++V+N+P+     +L+ LF PFG +  V +P    G       VEF+ K +A+ A  +L 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 154 YTKFKEVPLYLEWA 167
            T      L LE+A
Sbjct: 63  STHLYGRHLVLEYA 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           L++ NL  ++TE+ +R  F K G I SV + R KD KS G
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG 40

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

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 21/46 (45%), Positives = 26/46 (56%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           TL++KNLNF++T   +   FK         V  K DPK PGQ LSM
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSM 47

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

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

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V NLP  T   +L+ LF  FG +  V +     TG       VEF  +  A+ A  +L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 153 AYTKFKEVPLYL 164
              +    PL +
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 14/41 (34%), Positives = 27/41 (65%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           TL++ NL++++ +D +   FK+CG +  V +A+  D +S G
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKG 41

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

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 153
           + V NLP  T   DL+ LF  FG++  V +             VEF     A+ A  +L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 154 YTKFKEVPLYLE 165
             +     L + 
Sbjct: 61  GKELDGRKLKVS 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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 47.6 bits (112), Expect = 2e-06
 Identities = 25/112 (22%), Positives = 47/112 (41%), Gaps = 8/112 (7%)

Query: 165 EWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEERE- 223
           E   E    + + +     K++    E +EE +    E+++ +     E   E     E 
Sbjct: 45  ELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSES 104

Query: 224 -------PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
                   E + TL++ NL ++ TE+ +R  FKK GP+  V + R ++    
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKS 156

Length = 306

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

 Score = 43.7 bits (104), Expect = 3e-06
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           L++ NL  ++TE+ ++  F K GPI S+ + R +  +S G
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG 40

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +Y++NL+F   ED +R  F K G + S+ + +K+D K 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQ 40

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

 Score = 42.8 bits (101), Expect = 7e-06
 Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
           + V+NLPY     DL+ LF  FG+L  V V          G    V FL    A  A+  
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGF-AYVLFLDPEDAVKAYKE 63

Query: 152 LAYTKFK 158
           L    F+
Sbjct: 64  LDGKVFQ 70

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNSLA 153
           + V NLP  T   DLK LF  FG +  + +             VEF  +  A+ A  +L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 154 YTKFK 158
             +  
Sbjct: 61  GKELG 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           LY++NL  + TE+ +R  F   G +  V + R KD   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPR 38

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

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFNS 151
           + ++NL Y     DL+ LF  +G L  V +P       P G    V ++    A  AF  
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF-AFVTYMIPEHAVKAFAE 63

Query: 152 LAYTKFK 158
           L  T F+
Sbjct: 64  LDGTVFQ 70

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

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 2/39 (5%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           ++++ NL F+  E+ +R+HF+ CG + +V + R  D K+
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVR--DRKT 37

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 10/40 (25%), Positives = 22/40 (55%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           T++I+NL F++TE+ ++  F + G +    + + K     
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHS 41

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI----TGLVEFLQKNQAKAAFNSLAY 154
           + V+NLP      DL+  F P+G +  V +            VEF     A+AA   L  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 155 TKFK 158
               
Sbjct: 61  LVLD 64

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

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT----GLVEFLQKNQAKAAFNSL 152
           V NL YRT P DL+ +FE +G++G V +P   Y         V F  K  A+ A +++
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

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

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

 Score = 43.0 bits (100), Expect = 7e-05
 Identities = 39/190 (20%), Positives = 65/190 (34%), Gaps = 33/190 (17%)

Query: 88  NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQ 141
           ++         + V NLPY     DL+ LF+ FG + RV +     TG       VEF  
Sbjct: 107 SRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFES 166

Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
           +  A+ A   L   + +  PL ++ A          +   + + +          K+ + 
Sbjct: 167 EESAEKAIEELNGKELEGRPLRVQKA----------QPASQPRSELSNNLDASFAKKLSR 216

Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
            +                     E    LY+ NL   + E+ +   FK  G I   ++  
Sbjct: 217 GKALLL-----------------EKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPP 259

Query: 262 KKDPKSPGQF 271
            KD K P   
Sbjct: 260 SKDGKIPKSR 269

Length = 306

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           L+I  L++ +T+DS++ +F + G I    V +  DP +
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMK--DPNT 37

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

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

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 27/75 (36%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAAFNSL 152
           ILVKNLP+     D++ LF  +G L  V VP        G    VEF    +A  A N+L
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGF-AFVEFSTAKEALNAMNAL 61

Query: 153 AYTKFKEVPLYLEWA 167
             T      L L++A
Sbjct: 62  KDTHLLGRRLVLQYA 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           T+++ NL+++  ED +R+ F KCG I  V + +    KS G
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKG 41

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|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 = 38.8 bits (91), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 112 DLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW 166
           +L++LF PFG++  V +PP    G V+F+ +  A+AA   L  T      + L W
Sbjct: 17  ELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGIT---GLVEFLQKNQAKAAFNS 151
           R+I V+NLP++    DLK LF PFG +  V +P  P G       V+F  K  A+ A   
Sbjct: 1   RLI-VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 152 LAYTKFKEVPLYLEWA 167
           +   K K  P+ ++WA
Sbjct: 60  VNGKKIKGRPVAVDWA 75

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|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 = 38.4 bits (90), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
           + V+NLP+ T   +L+ LFE FG++  V +P    T        V F+    A  A++ L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 153 AYTKFK 158
             + F+
Sbjct: 62  DGSIFQ 67

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 11/38 (28%), Positives = 22/38 (57%)

Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           ++ N+++ +T + ++ HFK CG I  +T+   K    P
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQP 40

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

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           LY+KNL+ +  ++ +R  F   G I S  V   +  +S G
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKG 43

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           L++ NL+F +TED +R HF + G I  V +   +D
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFED 35

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

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 48/211 (22%), Positives = 78/211 (36%), Gaps = 44/211 (20%)

Query: 75  AFLEENGVQLDAFNQVVE---ARSKRI---------ILVKNLPYRTLPTDLKALFEPFGD 122
           A  + NG+ L+     V     + +R          + VKNL        L+ LF  FG 
Sbjct: 145 AIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFG- 203

Query: 123 LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGK 182
                     IT        +     F  + + K            E   A+A E+  GK
Sbjct: 204 ---------EITSAAVMKDGSGRSRGFAFVNFEK-----------HEDA-AKAVEEMNGK 242

Query: 183 EKEKNEEGE----GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN 238
           +    +EG+    G  +K+     E  ++     EE  +E + +    +  LY+KNL+  
Sbjct: 243 KIGLAKEGKKLYVGRAQKRAEREAELRRK----FEELQQERKMKAQGVN--LYVKNLDDT 296

Query: 239 STEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
            T++ +R  F +CG I S  V   +   S G
Sbjct: 297 VTDEKLRELFSECGEITSAKVMLDEKGVSRG 327

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|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 = 37.3 bits (87), Expect = 6e-04
 Identities = 13/39 (33%), Positives = 23/39 (58%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           L+++NL F +TE+ +R  F+  G I+ V +   K+ K  
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRS 40

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 14/42 (33%), Positives = 23/42 (54%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           T +Y+KNL  +  ++ ++  F K G I S  V +  + KS G
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKG 43

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

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

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           LY+ NL+F +TE+ I   F +CG I  + +   +  K+P  F
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGF 42

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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
           T LY+ NLN   TE+ + + F + GP+ASV
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASV 31

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>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 = 37.1 bits (86), Expect = 8e-04
 Identities = 12/37 (32%), Positives = 23/37 (62%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
           L+I  L+F++ E S+ + F K G I+ V V + ++ +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQ 39

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
            L++ NL +++T + +  HFK  G   SV +   K     
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKS 41

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 36.3 bits (85), Expect = 0.001
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 113 LKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
           L  LF PFG++ ++ +         VEF  +  A+ A   L    F   PL ++++
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|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG----QFLSM 274
           L ++NL F  TE  +++ F   G +  VT+ RK D K  G    QF S 
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSK 50

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|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 17/57 (29%), Positives = 23/57 (40%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
            ++ V+ LP      DL      FG +  V + P     LVEF   + AKA  N   
Sbjct: 3   PVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNHAQ 59

This subfamily corresponds to the RRM1 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). . Length = 80

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 15/40 (37%), Positives = 25/40 (62%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           TL++  LN+++TE  +RR F++ GPI  + + R K    P
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKP 42

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 98  IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNS 151
            I V NL       DL+ LF PFG + RV +     TG       V F  +  A+ A   
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 152 LAYTKFKEVPLYLEWA 167
           L    +  + L +EWA
Sbjct: 61  LNGFGYDNLILSVEWA 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 2/38 (5%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           L+I  L+F +T+DS+R HF+K G +    V R  DP++
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMR--DPQT 40

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

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKK 263
           P  TL ++ L+  +TE+ I +        PI  V + R K
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDK 40

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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTT 229
           A+ +E  K  ++E  E  E +EE+KE    ED +      +E+ E +EE E E + +
Sbjct: 46  ADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEES 102

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           L++ NL+F++ EDSI   F + G I+SV +    D   P  F
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGF 42

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

>gnl|CDD|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 = 35.3 bits (82), Expect = 0.004
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           TT+Y+ NL    TE+ ++R F   G I  V V + K
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK 36

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 11/32 (34%), Positives = 18/32 (56%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           LY+ +L+ + TE  +   F   GP+ S+ V R
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCR 33

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

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +++ NL F   E+ + R F KCG I  V + R  DPK+
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVR--DPKT 37

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	274
KOG0110|consensus	725		100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.91
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.88
KOG0127|consensus	678		99.88
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.88
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.86
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.86
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.85
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.85
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.84
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.83
KOG0148|consensus	321		99.82
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.8
KOG0131|consensus	203		99.79
KOG0145|consensus	360		99.79
KOG0123|consensus	369		99.78
KOG0117|consensus	506		99.77
KOG0127|consensus	678		99.76
KOG0109|consensus	346		99.76
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.75
KOG0144|consensus	510		99.75
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.73
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.71
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.69
KOG0123|consensus	369		99.69
KOG0124|consensus	544		99.69
KOG0110|consensus	725		99.68
KOG0145|consensus	360		99.65
KOG0105|consensus	241		99.65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.56
KOG0121|consensus	153		99.56
KOG4206|consensus	221		99.55
PLN03120	260	nucleic acid binding protein; Provisional	99.5
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.49
KOG0148|consensus	321		99.48
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.48
KOG0107|consensus	195		99.47
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.46
KOG0114|consensus	124		99.46
KOG4205|consensus	311		99.44
KOG0122|consensus	270		99.41
PLN03121	243	nucleic acid binding protein; Provisional	99.41
PLN03213	759	repressor of silencing 3; Provisional	99.38
smart00362	72	RRM_2 RNA recognition motif.	99.38
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.37
KOG0125|consensus	376		99.37
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.35
KOG1457|consensus	284		99.34
KOG4207|consensus	256		99.28
KOG0144|consensus	510		99.28
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.27
KOG0147|consensus	549		99.27
KOG0126|consensus	219		99.27
KOG0113|consensus	335		99.26
KOG0117|consensus	506		99.25
KOG0149|consensus	247		99.23
KOG0146|consensus	371		99.21
smart00360	71	RRM RNA recognition motif.	99.19
KOG0130|consensus	170		99.18
KOG0111|consensus	298		99.15
KOG1190|consensus	492		99.14
KOG4212|consensus	608		99.12
KOG0106|consensus	216		99.1
KOG0108|consensus	435		99.06
KOG1190|consensus	492		99.06
KOG4211|consensus	510		99.04
KOG0109|consensus	346		99.03
KOG0147|consensus	549		99.03
KOG0132|consensus	894		98.97
KOG0153|consensus	377		98.96
KOG0415|consensus	479		98.92
KOG1548|consensus	382		98.92
smart00361	70	RRM_1 RNA recognition motif.	98.89
KOG4208|consensus	214		98.79
KOG4454|consensus	267		98.77
KOG0146|consensus	371		98.67
KOG4661|consensus	940		98.66
KOG0131|consensus	203		98.63
KOG0129|consensus	520		98.61
KOG0124|consensus	544		98.59
KOG0151|consensus	877		98.59
KOG4212|consensus	608		98.54
KOG0116|consensus	419		98.51
KOG4660|consensus	549		98.49
KOG0533|consensus	243		98.48
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.45
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.45
KOG0128|consensus	881		98.44
KOG1456|consensus	494		98.36
KOG0121|consensus	153		98.27
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.25
KOG4209|consensus	231		98.23
KOG0120|consensus	500		98.23
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.18
KOG4205|consensus	311		98.1
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.08
KOG0114|consensus	124		98.03
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.03
KOG4676|consensus	479		98.0
smart00362	72	RRM_2 RNA recognition motif.	97.95
KOG1457|consensus	284		97.92
KOG0112|consensus	975		97.9
KOG1456|consensus	494		97.89
KOG2193|consensus	584		97.88
KOG0126|consensus	219		97.85
KOG4206|consensus	221		97.82
KOG0120|consensus	500		97.8
KOG4210|consensus	285		97.78
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.73
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.7
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.66
KOG4211|consensus	510		97.66
KOG0106|consensus	216		97.66
KOG0113|consensus	335		97.61
KOG3152|consensus	278		97.58
KOG0226|consensus	290		97.55
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.45
smart00360	71	RRM RNA recognition motif.	97.42
KOG0122|consensus	270		97.3
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.29
KOG1365|consensus	508		97.29
KOG4307|consensus	944		97.26
KOG0115|consensus	275		97.23
KOG1548|consensus	382		97.22
KOG0125|consensus	376		97.18
KOG4210|consensus	285		97.02
KOG1365|consensus	508		97.0
KOG0153|consensus	377		96.88
KOG0533|consensus	243		96.82
KOG2314|consensus	698		96.8
KOG0108|consensus	435		96.8
KOG2202|consensus	260		96.72
KOG4207|consensus	256		96.61
KOG1855|consensus	484		96.57
KOG0415|consensus	479		96.52
KOG0116|consensus	419		96.42
KOG1995|consensus	351		96.38
KOG0105|consensus	241		96.38
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.32
KOG0112|consensus	975		96.24
KOG0151|consensus	877		96.15
KOG0130|consensus	170		96.03
KOG1996|consensus	378		95.95
KOG4307|consensus	944		95.88
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.79
KOG0132|consensus	894		95.75
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.71
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.67
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.6
KOG2416|consensus	718		94.96
KOG0129|consensus	520		94.84
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.68
KOG4660|consensus	549		94.44
KOG4285|consensus	350		94.22
KOG4661|consensus	940		94.19
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.19
KOG4849|consensus	498		94.01
KOG2135|consensus	526		93.52
KOG2591|consensus	684		93.22
KOG1855|consensus	484		93.08
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.0
KOG0115|consensus	275		92.07
KOG4209|consensus	231		91.97
KOG0128|consensus	881		91.87
KOG0226|consensus	290		91.78
KOG2318|consensus	650		91.38
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	90.87
KOG4574|consensus	1007		90.71
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.48
KOG3152|consensus	278		90.47
KOG2068|consensus	327		90.29
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	90.07
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	88.5
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	86.83
KOG0804|consensus	493		85.88
smart00361	70	RRM_1 RNA recognition motif.	85.83
KOG4208|consensus	214		83.01
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	82.95

>KOG0110|consensus

Probab=100.00  E-value=1.7e-35  Score=276.42  Aligned_cols=256  Identities=42%  Similarity=0.724  Sum_probs=204.5

Q ss_pred             CCchHHHHHHHHHHhCCCccccccccChhHHHHHHHHHhCCCcccccC---CchhHHHhhhhhhhHHHHHHHHHHHCCCC
Q psy3343           7 SSYKTKKAKELKKIAGHVHTWNSLFLGTNAIAEAMAETYNATKAEVLT---GSGAATRLAMGETEIVEKTRAFLEENGVQ   83 (274)
Q Consensus         7 ~~~k~~~~~~~~~~~~~~~~wn~lf~~~~~v~~~~~~~~~~~~~~l~~---~~~~avr~al~e~~~~~~~~~~l~~~g~~   83 (274)
                      ++||++|+.+++..+...++||+|||+.++|+..++.++||++.+++|   +.+ +||+|++|++++.+++.++.++|+.
T Consensus       296 ~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gs-avr~al~etr~~~e~~~~~ee~gV~  374 (725)
T KOG0110|consen  296 SDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGS-AVRLALGETRVVQEVRRFFEENGVK  374 (725)
T ss_pred             CcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcch-HHHHHHHHhhhchhhhhhHHhhCcc
Confidence            569999999999977777999999999999999999999999999999   445 9999999999999999999999999


Q ss_pred             ccccchhhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          84 LDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        84 ~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      +++|++  ..++.+.|+|+|||..+..++|..+|..||.|.++.||+.+..++|+|.++.+|..|++.|++..+...++|
T Consensus       375 l~~F~~--~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~ply  452 (725)
T KOG0110|consen  375 LDAFSQ--AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSAPLY  452 (725)
T ss_pred             cccchh--hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhhccCccc
Confidence            999998  889999999999999999999999999999999999998877899999999999999999999999999999


Q ss_pred             EEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcc--cc--c-cccc-ccCCCCCCceEEEeCCCC
Q psy3343         164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEV--EE--N-VEED-EEREPEPDTTLYIKNLNF  237 (274)
Q Consensus       164 v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~-~~~~-~~~~~~~~~~lfV~NL~~  237 (274)
                      ++|+|..+|... ++............ ++.+     .+..........  ..  + .... ........++|||+||+|
T Consensus       453 le~aP~dvf~~~-pka~~~~~e~~~~~-ee~~-----~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf  525 (725)
T KOG0110|consen  453 LEWAPEDVFTED-PKADDLSAESRSKM-EENP-----SERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNF  525 (725)
T ss_pred             cccChhhhccCC-cccccccccccccc-ccCc-----ceecccccccccccCCccccccchhhhhccccchhhhhhcCCc
Confidence            999999988854 22111111100000 0000     000000000000  00  0 0000 011112233499999999


Q ss_pred             CCCHHHHHHHhhhcCCeeEEEEecCCCCCCCCCCCCC
Q psy3343         238 NSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM  274 (274)
Q Consensus       238 ~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g~~ls~  274 (274)
                      ++|.++|..+|.+.|.|.+|.|.++++++.  +.|||
T Consensus       526 ~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~--k~lSm  560 (725)
T KOG0110|consen  526 DTTLEDLEDLFSKQGTVLSIEISKKKDPAN--KYLSM  560 (725)
T ss_pred             ccchhHHHHHHHhcCeEEEEEEeccccccc--ccccc
Confidence            999999999999999999999999999876  88888

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.91  E-value=1.5e-23  Score=190.00  Aligned_cols=121  Identities=26%  Similarity=0.333  Sum_probs=107.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||+++|+++|+++|+.||.|.+|+|+.+      ++||||+|.+.++|..|+..|++..+.+++|.|.|
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            446799999999999999999999999999999998753      48999999999999999999999999999999999


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +...       .                                            .....++|||.|||+.+|+++|++
T Consensus       184 a~p~-------~--------------------------------------------~~~~~~~lfV~nLp~~vtee~L~~  212 (346)
T TIGR01659       184 ARPG-------G--------------------------------------------ESIKDTNLYVTNLPRTITDDQLDT  212 (346)
T ss_pred             cccc-------c--------------------------------------------cccccceeEEeCCCCcccHHHHHH
Confidence            7422       0                                            011246899999999999999999


Q ss_pred             HhhhcCCeeEEEEecCCC
Q psy3343         247 HFKKCGPIASVTVARKKD  264 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~~  264 (274)
                      +|++||.|..|+|++++.
T Consensus       213 ~F~~fG~V~~v~i~~d~~  230 (346)
T TIGR01659       213 IFGKYGQIVQKNILRDKL  230 (346)
T ss_pred             HHHhcCCEEEEEEeecCC
Confidence            999999999999998863

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.88  E-value=4.5e-22  Score=181.52  Aligned_cols=119  Identities=19%  Similarity=0.330  Sum_probs=106.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+.+++++|+++|++||+|.+|+|.++      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            4689999999999999999999999999999999753      4899999999999999999999999999999999984


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ..       .                                            ....+++|||+|||..+++++|+++|
T Consensus        82 ~~-------~--------------------------------------------~~~~~~~l~v~~l~~~~~~~~l~~~f  110 (352)
T TIGR01661        82 PS-------S--------------------------------------------DSIKGANLYVSGLPKTMTQHELESIF  110 (352)
T ss_pred             cc-------c--------------------------------------------cccccceEEECCccccCCHHHHHHHH
Confidence            32       0                                            11234689999999999999999999


Q ss_pred             hhcCCeeEEEEecCCC
Q psy3343         249 KKCGPIASVTVARKKD  264 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~~  264 (274)
                      ++||.|..++++.+..
T Consensus       111 ~~~G~i~~~~~~~~~~  126 (352)
T TIGR01661       111 SPFGQIITSRILSDNV  126 (352)
T ss_pred             hccCCEEEEEEEecCC
Confidence            9999999999998763

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

>KOG0127|consensus

Probab=99.88  E-value=6.1e-22  Score=180.90  Aligned_cols=171  Identities=25%  Similarity=0.524  Sum_probs=114.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC--C---eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY--G---ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~--~---~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..+|+|+|||+.+...+|+.+|+.||.|..|.||+.  +   |||||.|.+..+|..|++.+|+..|.||+|.|+||..+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            689999999999999999999999999999999972  2   79999999999999999999999999999999999755


Q ss_pred             -CCcccccccc-----ccccccccc-ccchhh-hhcc----chhhcccCCC--------Cccc-ccc---cc----c---
Q psy3343         171 -VFAEAKEKSK-----GKEKEKNEE-GEGEEE-KKEN----TAEEDNQQGV--------PEVE-ENV---EE----D---  219 (274)
Q Consensus       171 -~f~~~~~~~~-----~~~~~~~~~-~~~~~~-~~~~----~~~~~~~~~~--------~~~~-~~~---~~----~---  219 (274)
                       .|........     .....+..+ .+++.. .++.    ..+.+.....        .++. ..+   ..    .   
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence             2222111000     000000000 000000 0000    0000000000        0000 000   00    0   


Q ss_pred             --------ccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         220 --------EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       220 --------~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                              .......+.+|||+||||++|+++|.++|++||+|.++.|+.+++..
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~  331 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTG  331 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCC
Confidence                    01223345799999999999999999999999999999999999764

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

Probab=99.88  E-value=1.2e-21  Score=186.98  Aligned_cols=132  Identities=14%  Similarity=0.208  Sum_probs=107.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|+.      ++|||||+|.+.++|..|++.|+|..+.|+.|.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            3458999999999999999999999999999999865      4689999999999999999999999999999999864


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      ...      .....    ...              .                ........++|||+|||+++++++|+++
T Consensus       185 ~~~------p~a~~----~~~--------------~----------------~~~~~~~~~rLfVgnLp~~vteedLk~l  224 (612)
T TIGR01645       185 SNM------PQAQP----IID--------------M----------------VQEEAKKFNRIYVASVHPDLSETDIKSV  224 (612)
T ss_pred             ccc------ccccc----ccc--------------c----------------ccccccccceEEeecCCCCCCHHHHHHH
Confidence            321      00000    000              0                0001123469999999999999999999


Q ss_pred             hhhcCCeeEEEEecCCCC
Q psy3343         248 FKKCGPIASVTVARKKDP  265 (274)
Q Consensus       248 F~~fG~I~~v~v~~~~~~  265 (274)
                      |+.||.|.+|+|++++.+
T Consensus       225 Fs~FG~I~svrl~~D~~t  242 (612)
T TIGR01645       225 FEAFGEIVKCQLARAPTG  242 (612)
T ss_pred             HhhcCCeeEEEEEecCCC
Confidence            999999999999998764

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=99.86  E-value=5.3e-21  Score=174.45  Aligned_cols=234  Identities=15%  Similarity=0.227  Sum_probs=140.2

Q ss_pred             cccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh--------hhhhhh----HHHHHHHHHH-HCCCCccc---
Q psy3343          28 NSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL--------AMGETE----IVEKTRAFLE-ENGVQLDA---   86 (274)
Q Consensus        28 n~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~--------al~e~~----~~~~~~~~l~-~~g~~~~~---   86 (274)
                      +.|||+...        ..+++.+|.+     |....|++        +.|++.    -.+++...+. .+|..+..   
T Consensus         4 ~~l~V~nLp--------~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i   75 (352)
T TIGR01661         4 TNLIVNYLP--------QTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI   75 (352)
T ss_pred             cEEEEeCCC--------CCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeE
Confidence            567888874        7788888866     54444444        233443    2456666553 45554321   


Q ss_pred             ---cchhh-hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCe
Q psy3343          87 ---FNQVV-EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTK  156 (274)
Q Consensus        87 ---~~~~~-~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~  156 (274)
                         +..+. .....++|||+|||+.+++++|+.+|++||.|..+.++.      .+|||||+|.+.++|..|++.|+|..
T Consensus        76 ~v~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~  155 (352)
T TIGR01661        76 KVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT  155 (352)
T ss_pred             EEEeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCc
Confidence               11111 122457899999999999999999999999999988865      35899999999999999999999999


Q ss_pred             eCC--eEEEEEEecCCCCcccccccc--ccc-cccccc------------------ccchhh--hhccchh--h--cccC
Q psy3343         157 FKE--VPLYLEWAPEGVFAEAKEKSK--GKE-KEKNEE------------------GEGEEE--KKENTAE--E--DNQQ  207 (274)
Q Consensus       157 ~~g--~~l~v~~a~~~~f~~~~~~~~--~~~-~~~~~~------------------~~~~~~--~~~~~~~--~--~~~~  207 (274)
                      +.|  .+|.|.|+.............  ... ......                  .....+  ...+...  .  ....
T Consensus       156 ~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (352)
T TIGR01661       156 PSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAV  235 (352)
T ss_pred             cCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccc
Confidence            877  678888875332110000000  000 000000                  000000  0000000  0  0000


Q ss_pred             CC---Ccccccc-----------cccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         208 GV---PEVEENV-----------EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       208 ~~---~~~~~~~-----------~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      ..   .......           ..........+.+|||+|||+.+++++|+++|++||.|.+|+|++++ .+.+.|
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG  312 (352)
T TIGR01661       236 AQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKG  312 (352)
T ss_pred             ccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccc
Confidence            00   0000000           00001113345589999999999999999999999999999999998 444444

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

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

Probab=99.86  E-value=3.4e-21  Score=186.29  Aligned_cols=124  Identities=24%  Similarity=0.363  Sum_probs=108.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .+|||+|||+++|+++|+++|++||.|.+|++.++      .|||||+|.+.++|.+|+..|++..+.|++|+|.|+...
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            37999999999999999999999999999999763      479999999999999999999999999999999997432


Q ss_pred             CCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhh
Q psy3343         171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  250 (274)
Q Consensus       171 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~  250 (274)
                      .      .        .                                   ......+|||+|||.++++++|+++|+.
T Consensus        81 ~------~--------~-----------------------------------~~~~~~~vfV~nLp~~~~~~~L~~~F~~  111 (562)
T TIGR01628        81 P------S--------L-----------------------------------RRSGVGNIFVKNLDKSVDNKALFDTFSK  111 (562)
T ss_pred             c------c--------c-----------------------------------cccCCCceEEcCCCccCCHHHHHHHHHh
Confidence            0      0        0                                   0112358999999999999999999999


Q ss_pred             cCCeeEEEEecCCCCCCCC
Q psy3343         251 CGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       251 fG~I~~v~v~~~~~~~~~g  269 (274)
                      ||.|.+|+|+++.++++.|
T Consensus       112 ~G~i~~~~i~~~~~g~skg  130 (562)
T TIGR01628       112 FGNILSCKVATDENGKSRG  130 (562)
T ss_pred             cCCcceeEeeecCCCCccc
Confidence            9999999999998876655

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

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

Probab=99.85  E-value=6.3e-21  Score=184.40  Aligned_cols=187  Identities=26%  Similarity=0.304  Sum_probs=138.4

Q ss_pred             ccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh--------hhhhhh----HHHHHHHHHHH-CCCCcc-----
Q psy3343          29 SLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL--------AMGETE----IVEKTRAFLEE-NGVQLD-----   85 (274)
Q Consensus        29 ~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~--------al~e~~----~~~~~~~~l~~-~g~~~~-----   85 (274)
                      ||||+...        .++++++|.+     |....||+        ++|+++    -.+++.+.+.. ++..+.     
T Consensus         2 sl~VgnLp--------~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~   73 (562)
T TIGR01628         2 SLYVGDLD--------PDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIR   73 (562)
T ss_pred             eEEEeCCC--------CCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEE
Confidence            78888873        7788888866     44444544        334443    34555565543 333211     


Q ss_pred             -ccch--hhh-cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCe
Q psy3343          86 -AFNQ--VVE-ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTK  156 (274)
Q Consensus        86 -~~~~--~~~-~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~  156 (274)
                       .+..  +.. ....++|||+|||.++++++|+++|+.||.|.+|.+..     ++|||||+|.+.++|..|++.|+|..
T Consensus        74 i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~  153 (562)
T TIGR01628        74 IMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGML  153 (562)
T ss_pred             eecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccE
Confidence             1111  111 12347899999999999999999999999999998875     35899999999999999999999999


Q ss_pred             eCCeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCC
Q psy3343         157 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLN  236 (274)
Q Consensus       157 ~~g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~  236 (274)
                      +.|+.|+|.+.....      .    +.                                    .......++|||+|||
T Consensus       154 ~~~~~i~v~~~~~~~------~----~~------------------------------------~~~~~~~~~l~V~nl~  187 (562)
T TIGR01628       154 LNDKEVYVGRFIKKH------E----RE------------------------------------AAPLKKFTNLYVKNLD  187 (562)
T ss_pred             ecCceEEEecccccc------c----cc------------------------------------cccccCCCeEEEeCCC
Confidence            999999998754220      0    00                                    0012235789999999


Q ss_pred             CCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         237 FNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       237 ~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +++|+++|+++|++||.|.++.|+++.+++..|
T Consensus       188 ~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G  220 (562)
T TIGR01628       188 PSVNEDKLRELFAKFGEITSAAVMKDGSGRSRG  220 (562)
T ss_pred             CcCCHHHHHHHHHhcCCEEEEEEEECCCCCccc
Confidence            999999999999999999999999998776654

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

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

Probab=99.85  E-value=1.5e-20  Score=178.38  Aligned_cols=130  Identities=21%  Similarity=0.341  Sum_probs=106.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh--CCCeeCCeEEEEEEecCCCCc
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL--AYTKFKEVPLYLEWAPEGVFA  173 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l--~~~~~~g~~l~v~~a~~~~f~  173 (274)
                      +++|||+|||+.+++++|+++|++||.|.+|.++++++||||+|.+.++|..|+..+  ++..+.|++|+|.|+......
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~   81 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIK   81 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccc
Confidence            579999999999999999999999999999999999999999999999999999874  789999999999998543100


Q ss_pred             ccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCC
Q psy3343         174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP  253 (274)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~  253 (274)
                      ....          .              .               ..........+|||+||++.+|+++|+++|++||.
T Consensus        82 ~~~~----------~--------------~---------------~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~  122 (481)
T TIGR01649        82 RDGN----------S--------------D---------------FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGK  122 (481)
T ss_pred             cCCC----------C--------------c---------------ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCC
Confidence            0000          0              0               00001112358999999999999999999999999


Q ss_pred             eeEEEEecCCC
Q psy3343         254 IASVTVARKKD  264 (274)
Q Consensus       254 I~~v~v~~~~~  264 (274)
                      |.+|.|+++.+
T Consensus       123 V~~v~i~~~~~  133 (481)
T TIGR01649       123 VLRIVTFTKNN  133 (481)
T ss_pred             EEEEEEEecCC
Confidence            99999988654

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

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

Probab=99.84  E-value=6.6e-20  Score=172.99  Aligned_cols=133  Identities=22%  Similarity=0.328  Sum_probs=107.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      .+..++|||+|||+.+++++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            45678999999999999999999999999999999976      35899999999999999996 999999999999987


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +....       .........                                ........++|||+|||+.+|+++|++
T Consensus       165 ~~~~~-------~~~~~~~~~--------------------------------~~~~~p~~~~l~v~nl~~~~te~~l~~  205 (457)
T TIGR01622       165 SQAEK-------NRAAKAATH--------------------------------QPGDIPNFLKLYVGNLHFNITEQELRQ  205 (457)
T ss_pred             cchhh-------hhhhhcccc--------------------------------cCCCCCCCCEEEEcCCCCCCCHHHHHH
Confidence            64220       000000000                                000112367999999999999999999


Q ss_pred             HhhhcCCeeEEEEecCCCC
Q psy3343         247 HFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~~~  265 (274)
                      +|++||.|.+|.|++++++
T Consensus       206 ~f~~~G~i~~v~~~~d~~~  224 (457)
T TIGR01622       206 IFEPFGDIEDVQLHRDPET  224 (457)
T ss_pred             HHHhcCCeEEEEEEEcCCC
Confidence            9999999999999998764

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.

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

Probab=99.83  E-value=2e-19  Score=170.74  Aligned_cols=157  Identities=18%  Similarity=0.242  Sum_probs=109.3

Q ss_pred             CCCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Q psy3343          94 RSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  171 (274)
Q Consensus        94 ~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~  171 (274)
                      ..+++|||+|||+ .+|+++|+++|+.||.|.+|.++++ +|||||+|.+.++|..|+..|+|..|.|++|+|.++....
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~  352 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQN  352 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccccc
Confidence            3568999999998 6999999999999999999999875 5899999999999999999999999999999999975431


Q ss_pred             Ccccccccccccccccccccchhhhhccchhh-cccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhh
Q psy3343         172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEE-DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  250 (274)
Q Consensus       172 f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~  250 (274)
                      .......       .....    ......+.. ...+...   .. ......-..++.+|||+|||+.+|+++|+++|++
T Consensus       353 ~~~~~~~-------~~~~~----~~~~~d~~~~~~~r~~~---~~-~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~  417 (481)
T TIGR01649       353 VQPPREG-------QLDDG----LTSYKDYSSSRNHRFKK---PG-SANKNNIQPPSATLHLSNIPLSVSEEDLKELFAE  417 (481)
T ss_pred             ccCCCCC-------cCcCC----CcccccccCCccccCCC---cc-cccccccCCCCcEEEEecCCCCCCHHHHHHHHHh
Confidence            1110000       00000    000000000 0000000   00 0000011246789999999999999999999999


Q ss_pred             cCC--eeEEEEecCCCC
Q psy3343         251 CGP--IASVTVARKKDP  265 (274)
Q Consensus       251 fG~--I~~v~v~~~~~~  265 (274)
                      ||.  |.+|++..++++
T Consensus       418 ~G~~~i~~ik~~~~~~~  434 (481)
T TIGR01649       418 NGVHKVKKFKFFPKDNE  434 (481)
T ss_pred             cCCccceEEEEecCCCC
Confidence            998  888988765543

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).

>KOG0148|consensus

Probab=99.82  E-value=9.8e-20  Score=153.98  Aligned_cols=134  Identities=24%  Similarity=0.348  Sum_probs=110.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .--+||+-|...++-++|++.|.+||+|..+++.+      ++|||||.|.+.++|+.||..|||..|.+|.|+..||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            46799999999999999999999999999999877      579999999999999999999999999999999999976


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      +.         .+....           ...++.-               -.......|+|||+||+..+||+.|+++|+
T Consensus       142 Kp---------~e~n~~-----------~ltfdeV---------------~NQssp~NtsVY~G~I~~~lte~~mr~~Fs  186 (321)
T KOG0148|consen  142 KP---------SEMNGK-----------PLTFDEV---------------YNQSSPDNTSVYVGNIASGLTEDLMRQTFS  186 (321)
T ss_pred             Cc---------cccCCC-----------CccHHHH---------------hccCCCCCceEEeCCcCccccHHHHHHhcc
Confidence            62         000000           0001110               022345678999999999999999999999


Q ss_pred             hcCCeeEEEEecCCC
Q psy3343         250 KCGPIASVTVARKKD  264 (274)
Q Consensus       250 ~fG~I~~v~v~~~~~  264 (274)
                      +||.|..|||.+++.
T Consensus       187 ~fG~I~EVRvFk~qG  201 (321)
T KOG0148|consen  187 PFGPIQEVRVFKDQG  201 (321)
T ss_pred             cCCcceEEEEecccc
Confidence            999999999998763

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

Probab=99.80  E-value=1e-18  Score=167.01  Aligned_cols=150  Identities=14%  Similarity=0.208  Sum_probs=106.1

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccC------------CCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPF------------GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~------------G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      ..+..++|||+|||+.+|+++|.++|..|            +.|..+.+..++|||||+|.+.++|..|+. |+|..|.|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~-l~g~~~~g  249 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA-LDSIIYSN  249 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc-CCCeEeeC
Confidence            45566899999999999999999999874            456777787889999999999999999994 99999999


Q ss_pred             eEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCC
Q psy3343         160 VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNS  239 (274)
Q Consensus       160 ~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~  239 (274)
                      ++|.|.+....  .+...... ..  ...     .+.      ...      ...+............++|||+|||+.+
T Consensus       250 ~~l~v~r~~~~--~~~~~~~~-~~--~~~-----~~~------~~~------~~~~~~~~~~~~~~~~~~l~v~nlp~~~  307 (509)
T TIGR01642       250 VFLKIRRPHDY--IPVPQITP-EV--SQK-----NPD------DNA------KNVEKLVNSTTVLDSKDRIYIGNLPLYL  307 (509)
T ss_pred             ceeEecCcccc--CCccccCC-CC--CCC-----CCc------ccc------cccccccccccCCCCCCEEEEeCCCCCC
Confidence            99999754321  10000000 00  000     000      000      0000000001122346799999999999


Q ss_pred             CHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         240 TEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       240 tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      |+++|+++|++||.|..+.|++++.
T Consensus       308 ~~~~l~~~f~~~G~i~~~~~~~~~~  332 (509)
T TIGR01642       308 GEDQIKELLESFGDLKAFNLIKDIA  332 (509)
T ss_pred             CHHHHHHHHHhcCCeeEEEEEecCC
Confidence            9999999999999999999998864

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

>KOG0131|consensus

Probab=99.79  E-value=3e-19  Score=143.10  Aligned_cols=123  Identities=21%  Similarity=0.278  Sum_probs=107.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .+..+|||+||+..++++.|.++|-+.|+|.++.+|++      +||||++|.+.++|.-|++-||..++.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            34689999999999999999999999999999999984      589999999999999999999999999999999987


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      ...       +                                           .....+.+|||+||.+.+++..|.+.
T Consensus        87 s~~-------~-------------------------------------------~nl~vganlfvgNLd~~vDe~~L~dt  116 (203)
T KOG0131|consen   87 SAH-------Q-------------------------------------------KNLDVGANLFVGNLDPEVDEKLLYDT  116 (203)
T ss_pred             ccc-------c-------------------------------------------ccccccccccccccCcchhHHHHHHH
Confidence            411       0                                           01224579999999999999999999


Q ss_pred             hhhcCCeeE-EEEecCCCCC
Q psy3343         248 FKKCGPIAS-VTVARKKDPK  266 (274)
Q Consensus       248 F~~fG~I~~-v~v~~~~~~~  266 (274)
                      |+.||.+.+ -.|++++++.
T Consensus       117 FsafG~l~~~P~i~rd~~tg  136 (203)
T KOG0131|consen  117 FSAFGVLISPPKIMRDPDTG  136 (203)
T ss_pred             HHhccccccCCcccccccCC
Confidence            999999877 4788888843

>KOG0145|consensus

Probab=99.79  E-value=5.3e-19  Score=148.82  Aligned_cols=120  Identities=20%  Similarity=0.360  Sum_probs=109.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC------eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~------~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|.|.-||.++|+++|+.+|+..|+|++|++.+++      ||+||.|.++++|++|+..|||.++..+.|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            5567999999999999999999999999999999999965      7999999999999999999999999999999999


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      |.+.                                                   .+...+.+|||.+||..+|..+|.+
T Consensus       118 ARPS---------------------------------------------------s~~Ik~aNLYvSGlPktMtqkelE~  146 (360)
T KOG0145|consen  118 ARPS---------------------------------------------------SDSIKDANLYVSGLPKTMTQKELEQ  146 (360)
T ss_pred             ccCC---------------------------------------------------hhhhcccceEEecCCccchHHHHHH
Confidence            9533                                                   0223467999999999999999999


Q ss_pred             HhhhcCCeeEEEEecCC
Q psy3343         247 HFKKCGPIASVTVARKK  263 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~  263 (274)
                      +|++||.|..-+|..|.
T Consensus       147 iFs~fGrIItSRiL~dq  163 (360)
T KOG0145|consen  147 IFSPFGRIITSRILVDQ  163 (360)
T ss_pred             HHHHhhhhhhhhhhhhc
Confidence            99999999998888775

>KOG0123|consensus

Probab=99.78  E-value=1e-18  Score=159.38  Aligned_cols=188  Identities=23%  Similarity=0.317  Sum_probs=139.6

Q ss_pred             cccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh-----hhhhhhH----HHHHHHHHHHCCCC-cc--ccchh
Q psy3343          28 NSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL-----AMGETEI----VEKTRAFLEENGVQ-LD--AFNQV   90 (274)
Q Consensus        28 n~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~-----al~e~~~----~~~~~~~l~~~g~~-~~--~~~~~   90 (274)
                      .+||++           ..|+.++|++     +..+.||+     +|||+++    -+++.+++..-... +.  .+.-.
T Consensus         2 ~sl~vg-----------~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim   70 (369)
T KOG0123|consen    2 ASLYVG-----------PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIM   70 (369)
T ss_pred             CceecC-----------CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEee
Confidence            578888           4567777766     44444444     6777765    24455555443322 11  01111


Q ss_pred             hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...+..+.|||+||++.++..+|.++|+.||.|.+|++..    ++|| ||+|.+.+.|++|+..+||..+.|+.|+|..
T Consensus        71 ~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~  149 (369)
T KOG0123|consen   71 WSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGL  149 (369)
T ss_pred             hhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEee
Confidence            1345556699999999999999999999999999999987    4588 9999999999999999999999999999998


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +..+          .++.....                                . ....-+++||+|++.+++++.|..
T Consensus       150 ~~~~----------~er~~~~~--------------------------------~-~~~~~t~v~vk~~~~~~~~~~l~~  186 (369)
T KOG0123|consen  150 FERK----------EEREAPLG--------------------------------E-YKKRFTNVYVKNLEEDSTDEELKD  186 (369)
T ss_pred             ccch----------hhhccccc--------------------------------c-hhhhhhhhheeccccccchHHHHH
Confidence            7543          01100000                                0 122357999999999999999999


Q ss_pred             HhhhcCCeeEEEEecCCCCCCCCC
Q psy3343         247 HFKKCGPIASVTVARKKDPKSPGQ  270 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~~~~~~g~  270 (274)
                      +|++||.|.++.|+.+..++++|-
T Consensus       187 ~f~~~g~i~s~~v~~~~~g~~~~~  210 (369)
T KOG0123|consen  187 LFSAYGSITSVAVMRDSIGKSKGF  210 (369)
T ss_pred             hhcccCcceEEEEeecCCCCCCCc
Confidence            999999999999999999876653

>KOG0117|consensus

Probab=99.77  E-value=2.7e-18  Score=153.95  Aligned_cols=169  Identities=21%  Similarity=0.270  Sum_probs=113.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~  166 (274)
                      ...+-|||+.||.++.|++|..+|++.|.|-.++|+.      ++|||||.|.+.+.|++|++.||+.+|. |+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4569999999999999999999999999999999877      3689999999999999999999999986 88888876


Q ss_pred             ecC--CCCccccccccccc--ccccccc-cch-------hhhhcc-----c-----------hhhcc-cCCC-----C--
Q psy3343         167 APE--GVFAEAKEKSKGKE--KEKNEEG-EGE-------EEKKEN-----T-----------AEEDN-QQGV-----P--  210 (274)
Q Consensus       167 a~~--~~f~~~~~~~~~~~--~~~~~~~-~~~-------~~~~~~-----~-----------~~~~~-~~~~-----~--  210 (274)
                      +..  .+|..+.+..+.+.  ..+.... +..       .+.+.+     .           +.++. ...+     .  
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            544  47777766544211  0000000 000       000000     0           00000 0000     0  


Q ss_pred             -ccccccccccc-CCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         211 -EVEENVEEDEE-REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       211 -~~~~~~~~~~~-~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                       -+..+.+++-+ .....-..|||+||+-+||+|.|+++|++||.|..|+.++|
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD  294 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD  294 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc
Confidence             00001111111 12223358999999999999999999999999999998865

>KOG0127|consensus

Probab=99.76  E-value=4.2e-18  Score=155.95  Aligned_cols=150  Identities=23%  Similarity=0.362  Sum_probs=114.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ++.+|||++||+.++.++|.++|+.+|+|..+.+..      .+|||||.|.-.++++.|+..+.+..|.|+.|.|+.|.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            348999999999999999999999999999999876      35899999999999999999999999999999999986


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ...    ..+..........         +...+...            ........+-..|.|+||||.|.+.+|+.+|
T Consensus        84 ~R~----r~e~~~~~e~~~v---------eK~~~q~~------------~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vF  138 (678)
T KOG0127|consen   84 KRA----RSEEVEKGENKAV---------EKPIEQKR------------PTKAKVDLPKWRLIIRNLPFKCKKPDLKNVF  138 (678)
T ss_pred             ccc----cchhcccccchhh---------hcccccCC------------cchhhccCccceEEeecCCcccCcHHHHHHH
Confidence            541    0000000000000         00000000            0001112346799999999999999999999


Q ss_pred             hhcCCeeEEEEecCCCCCCCC
Q psy3343         249 KKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +.||.|..|.|+++++|+-.|
T Consensus       139 s~~G~V~Ei~IP~k~dgklcG  159 (678)
T KOG0127|consen  139 SNFGKVVEIVIPRKKDGKLCG  159 (678)
T ss_pred             hhcceEEEEEcccCCCCCccc
Confidence            999999999999999988765

>KOG0109|consensus

Probab=99.76  E-value=1.4e-18  Score=148.28  Aligned_cols=111  Identities=23%  Similarity=0.388  Sum_probs=101.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCcccc
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAK  176 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~~~~  176 (274)
                      ..|||+|||.++++.+|+.+|++||.|.+|.|.+  +||||+.++...|..|+..|+|.+|+|..|.|+-+..+      
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK------   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK------   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--ccceEEeecccccHHHHhhcccceecceEEEEEecccc------
Confidence            4689999999999999999999999999999985  49999999999999999999999999999999976422      


Q ss_pred             cccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE
Q psy3343         177 EKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS  256 (274)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~  256 (274)
                                                                     ....++|+|+||.+.++..+|+..|++||+|..
T Consensus        75 -----------------------------------------------sk~stkl~vgNis~tctn~ElRa~fe~ygpvie  107 (346)
T KOG0109|consen   75 -----------------------------------------------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIE  107 (346)
T ss_pred             -----------------------------------------------CCCccccccCCCCccccCHHHhhhhcccCCcee
Confidence                                                           124579999999999999999999999999999


Q ss_pred             EEEecC
Q psy3343         257 VTVARK  262 (274)
Q Consensus       257 v~v~~~  262 (274)
                      |.|+++
T Consensus       108 cdivkd  113 (346)
T KOG0109|consen  108 CDIVKD  113 (346)
T ss_pred             eeeecc
Confidence            999876

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

Probab=99.75  E-value=2.4e-17  Score=157.29  Aligned_cols=110  Identities=20%  Similarity=0.226  Sum_probs=94.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a  167 (274)
                      ...++|||+|||+++++++|+++|++||.|..|+|+.     ++|||||+|.+.++|.+|++.|++..+. |+.|.|.++
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            3459999999999999999999999999999999875     4689999999999999999999999885 677666554


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      .                                                         ..++|||+|||.++|+++|.+.
T Consensus       136 ~---------------------------------------------------------~~~rLFVgNLP~~~TeeeL~ee  158 (578)
T TIGR01648       136 V---------------------------------------------------------DNCRLFVGGIPKNKKREEILEE  158 (578)
T ss_pred             c---------------------------------------------------------cCceeEeecCCcchhhHHHHHH
Confidence            1                                                         1368999999999999999999


Q ss_pred             hhhcCC-eeEEEEe
Q psy3343         248 FKKCGP-IASVTVA  260 (274)
Q Consensus       248 F~~fG~-I~~v~v~  260 (274)
                      |++++. +..+.+.
T Consensus       159 Fskv~egvv~vIv~  172 (578)
T TIGR01648       159 FSKVTEGVVDVIVY  172 (578)
T ss_pred             hhcccCCceEEEEe
Confidence            999974 5555444

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.

>KOG0144|consensus

Probab=99.75  E-value=2.2e-18  Score=153.93  Aligned_cols=126  Identities=23%  Similarity=0.378  Sum_probs=108.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCe-eCC--eEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTK-FKE--VPLYL  164 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~-~~g--~~l~v  164 (274)
                      .+...+||+-+|..++|.||+++|++||.|.+|.|++|      +|||||.|.+.++|.+|+.+|+... |-|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            44588999999999999999999999999999999885      4899999999999999999998854 544  67888


Q ss_pred             EEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHH
Q psy3343         165 EWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSI  244 (274)
Q Consensus       165 ~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L  244 (274)
                      .||...                                .+                  .......|||+-|+..+||.++
T Consensus       112 k~Ad~E--------------------------------~e------------------r~~~e~KLFvg~lsK~~te~ev  141 (510)
T KOG0144|consen  112 KYADGE--------------------------------RE------------------RIVEERKLFVGMLSKQCTENEV  141 (510)
T ss_pred             cccchh--------------------------------hh------------------ccccchhhhhhhccccccHHHH
Confidence            887322                                00                  0112368999999999999999


Q ss_pred             HHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         245 RRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       245 ~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +++|++||.|..|.|+++.++.++|
T Consensus       142 r~iFs~fG~Ied~~ilrd~~~~sRG  166 (510)
T KOG0144|consen  142 REIFSRFGHIEDCYILRDPDGLSRG  166 (510)
T ss_pred             HHHHHhhCccchhhheecccccccc
Confidence            9999999999999999999998887

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

Probab=99.73  E-value=3.6e-17  Score=156.05  Aligned_cols=181  Identities=19%  Similarity=0.239  Sum_probs=123.5

Q ss_pred             cccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh-------hhhhhh----HHHHHHHHHHH-CCCCccc--cc
Q psy3343          28 NSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL-------AMGETE----IVEKTRAFLEE-NGVQLDA--FN   88 (274)
Q Consensus        28 n~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~-------al~e~~----~~~~~~~~l~~-~g~~~~~--~~   88 (274)
                      .+|||+...        ..+++.+|.+     +....+|+       +.++..    -.+.+...+.. ++..+..  .-
T Consensus        59 ~~lFVgnLp--------~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l  130 (578)
T TIGR01648        59 CEVFVGKIP--------RDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL  130 (578)
T ss_pred             CEEEeCCCC--------CCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccc
Confidence            478998874        6777777755     43344443       223322    23344444432 3333210  00


Q ss_pred             hhhhcCCCcEEEEeCCCCCCCHHHHHHccccCCC-eeEEEee-C------CCeEEEEEecCHHHHHHHHHHhCC--CeeC
Q psy3343          89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD-LGRVLVP-P------YGITGLVEFLQKNQAKAAFNSLAY--TKFK  158 (274)
Q Consensus        89 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~l~-~------~~~~afV~F~~~~~A~~A~~~l~~--~~~~  158 (274)
                      ........++|||+|||+++++++|.+.|++++. +..+.+. .      +++||||+|.+.++|..|++.|..  ..+.
T Consensus       131 ~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~  210 (578)
T TIGR01648       131 GVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLW  210 (578)
T ss_pred             cccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEec
Confidence            0112234689999999999999999999999864 4444442 1      368999999999999999998864  4678


Q ss_pred             CeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCC
Q psy3343         159 EVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN  238 (274)
Q Consensus       159 g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~  238 (274)
                      |+.|.|.|+....      ..        .                                ........+|||+||+++
T Consensus       211 Gr~I~VdwA~p~~------~~--------d--------------------------------~~~~~~~k~LfVgNL~~~  244 (578)
T TIGR01648       211 GHVIAVDWAEPEE------EV--------D--------------------------------EDVMAKVKILYVRNLMTT  244 (578)
T ss_pred             CceEEEEeecccc------cc--------c--------------------------------ccccccccEEEEeCCCCC
Confidence            9999999985330      00        0                                001123468999999999


Q ss_pred             CCHHHHHHHhhhc--CCeeEEEEecC
Q psy3343         239 STEDSIRRHFKKC--GPIASVTVARK  262 (274)
Q Consensus       239 ~tee~L~~~F~~f--G~I~~v~v~~~  262 (274)
                      +|+++|+++|++|  |.|.+|+++++
T Consensus       245 ~tee~L~~~F~~f~~G~I~rV~~~rg  270 (578)
T TIGR01648       245 TTEEIIEKSFSEFKPGKVERVKKIRD  270 (578)
T ss_pred             CCHHHHHHHHHhcCCCceEEEEeecC
Confidence            9999999999999  99999988753

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.

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

Probab=99.71  E-value=2.4e-16  Score=150.66  Aligned_cols=146  Identities=20%  Similarity=0.233  Sum_probs=103.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+.+++++|+++|+.||.|..+.|..      ++|||||+|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            347999999999999999999999999999998865      35899999999999999999999999999999999985


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCC---------
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNS---------  239 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~---------  239 (274)
                      ...-.......  ..  ...-.  ..      ....          . .........++.+|+|.||.+.-         
T Consensus       374 ~~~~~~~~~~~--~~--~~~~~--~~------~~~~----------~-~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~  430 (509)
T TIGR01642       374 VGANQATIDTS--NG--MAPVT--LL------AKAL----------S-QSILQIGGKPTKVVQLTNLVTGDDLMDDEEYE  430 (509)
T ss_pred             cCCCCCCcccc--cc--ccccc--cc------cccc----------h-hhhccccCCCceEEEeccCCchhHhcCcchHH
Confidence            43110000000  00  00000  00      0000          0 00001123456799999996421         


Q ss_pred             -CHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         240 -TEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       240 -tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                       ..++|+++|++||.|.+|.|++..
T Consensus       431 ~~~edl~~~f~~~G~v~~v~i~~~~  455 (509)
T TIGR01642       431 EIYEDVKTEFSKYGPLINIVIPRPN  455 (509)
T ss_pred             HHHHHHHHHHHhcCCeeEEEeeccC
Confidence             236899999999999999999863

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

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

Probab=99.69  E-value=4.7e-16  Score=146.78  Aligned_cols=134  Identities=22%  Similarity=0.258  Sum_probs=99.5

Q ss_pred             ccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh------------hhhhhhHHHHHHHHHHHCCCCccccc-
Q psy3343          27 WNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL------------AMGETEIVEKTRAFLEENGVQLDAFN-   88 (274)
Q Consensus        27 wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~------------al~e~~~~~~~~~~l~~~g~~~~~~~-   88 (274)
                      -.+|||+...        +.++..+|.+     |....|++            |..+..-.+.+.+++..+|..+..-. 
T Consensus        89 ~~~l~V~nlp--------~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i  160 (457)
T TIGR01622        89 DRTVFVLQLA--------LKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPI  160 (457)
T ss_pred             CcEEEEeCCC--------CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeee
Confidence            4578888774        5666666644     33333333            33344456777777877765432100 


Q ss_pred             -----h-------------hhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHH
Q psy3343          89 -----Q-------------VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQ  144 (274)
Q Consensus        89 -----~-------------~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~  144 (274)
                           .             .......++|||+|||+.+++++|+++|++||.|..|.++.      .+|||||+|.+.++
T Consensus       161 ~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~  240 (457)
T TIGR01622       161 IVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE  240 (457)
T ss_pred             EEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH
Confidence                 0             00112258999999999999999999999999999999875      35899999999999


Q ss_pred             HHHHHHHhCCCeeCCeEEEEEEec
Q psy3343         145 AKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus       145 A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      |..|+..|+|..|.|++|.|.|+.
T Consensus       241 A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       241 AKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             HHHHHHhcCCcEECCEEEEEEEcc
Confidence            999999999999999999999976

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.

>KOG0123|consensus

Probab=99.69  E-value=1.6e-16  Score=145.09  Aligned_cols=110  Identities=23%  Similarity=0.311  Sum_probs=101.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCc
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFA  173 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~  173 (274)
                      ..|||+   +++|+..|.++|+++|++.++++.++   =|||||.|.++.+|.+|+.++|...++|+++++.|....   
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd---   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD---   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC---
Confidence            468998   89999999999999999999999774   379999999999999999999999999999999998422   


Q ss_pred             ccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCC
Q psy3343         174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP  253 (274)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~  253 (274)
                                                                           .+.|||+||+.+++...|.++|+.||+
T Consensus        76 -----------------------------------------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~  102 (369)
T KOG0123|consen   76 -----------------------------------------------------PSLVFIKNLDESIDNKSLYDTFSEFGN  102 (369)
T ss_pred             -----------------------------------------------------CceeeecCCCcccCcHHHHHHHHhhcC
Confidence                                                                 123999999999999999999999999


Q ss_pred             eeEEEEecCCCC
Q psy3343         254 IASVTVARKKDP  265 (274)
Q Consensus       254 I~~v~v~~~~~~  265 (274)
                      |.||+|+++.+|
T Consensus       103 ilS~kv~~~~~g  114 (369)
T KOG0123|consen  103 ILSCKVATDENG  114 (369)
T ss_pred             eeEEEEEEcCCC
Confidence            999999999998

>KOG0124|consensus

Probab=99.69  E-value=4.5e-17  Score=142.96  Aligned_cols=130  Identities=14%  Similarity=0.232  Sum_probs=106.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ++|||+.|.+.+.|+.|+..|.+||+|.+|.|.-      .+|||||+|+-++.|..|++.|||..+.||.|+|.+...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            8999999999999999999999999999998843      4699999999999999999999999999999999864211


Q ss_pred             CCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhh
Q psy3343         171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  250 (274)
Q Consensus       171 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~  250 (274)
                            ++..              +--++-.                    .+.....+|||..+.++.++++|+.+|+.
T Consensus       194 ------pQAQ--------------piID~vq--------------------eeAk~fnRiYVaSvHpDLSe~DiKSVFEA  233 (544)
T KOG0124|consen  194 ------PQAQ--------------PIIDMVQ--------------------EEAKKFNRIYVASVHPDLSETDIKSVFEA  233 (544)
T ss_pred             ------cccc--------------hHHHHHH--------------------HHHHhhheEEeeecCCCccHHHHHHHHHh
Confidence                  1110              0000000                    01223569999999999999999999999


Q ss_pred             cCCeeEEEEecCCCCC
Q psy3343         251 CGPIASVTVARKKDPK  266 (274)
Q Consensus       251 fG~I~~v~v~~~~~~~  266 (274)
                      ||+|.+|.+.+.+.+.
T Consensus       234 FG~I~~C~LAr~pt~~  249 (544)
T KOG0124|consen  234 FGEIVKCQLARAPTGR  249 (544)
T ss_pred             hcceeeEEeeccCCCC
Confidence            9999999999998754

>KOG0110|consensus

Probab=99.68  E-value=1.5e-16  Score=149.96  Aligned_cols=124  Identities=26%  Similarity=0.376  Sum_probs=104.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--C-------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--Y-------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~-------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ++|||+||++.+|.++|..+|..+|.|.++.|..  +       .|||||+|.++++|+.|++.|+|+.++|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            4599999999999999999999999999998865  2       289999999999999999999999999999999998


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      ...      +....                     +.               .......++.|.|+||||..+-.+++++
T Consensus       596 ~~k------~~~~~---------------------gK---------------~~~~kk~~tKIlVRNipFeAt~rEVr~L  633 (725)
T KOG0110|consen  596 ENK------PASTV---------------------GK---------------KKSKKKKGTKILVRNIPFEATKREVRKL  633 (725)
T ss_pred             cCc------ccccc---------------------cc---------------ccccccccceeeeeccchHHHHHHHHHH
Confidence            622      00000                     00               0011223679999999999999999999


Q ss_pred             hhhcCCeeEEEEecC
Q psy3343         248 FKKCGPIASVTVARK  262 (274)
Q Consensus       248 F~~fG~I~~v~v~~~  262 (274)
                      |..||.|.+|+|+++
T Consensus       634 F~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  634 FTAFGQLKSVRLPKK  648 (725)
T ss_pred             Hhcccceeeeccchh
Confidence            999999999999988

>KOG0145|consensus

Probab=99.65  E-value=7e-16  Score=130.11  Aligned_cols=197  Identities=15%  Similarity=0.237  Sum_probs=123.2

Q ss_pred             hhhhhhhHH----HHHHH-HHHHCCCCcc------ccchh-hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEee
Q psy3343          62 LAMGETEIV----EKTRA-FLEENGVQLD------AFNQV-VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP  129 (274)
Q Consensus        62 ~al~e~~~~----~~~~~-~l~~~g~~~~------~~~~~-~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~  129 (274)
                      .+|||..+-    +++.+ .-..||..+.      ++..| .......+|||.+||..+|..||..+|++||.|..-+|.
T Consensus        81 qSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL  160 (360)
T KOG0145|consen   81 QSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRIL  160 (360)
T ss_pred             cccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhh
Confidence            367776442    23322 2345676654      22222 234456899999999999999999999999998655554


Q ss_pred             C------CCeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCCCCccccccccccc------cccccc--cc-c
Q psy3343         130 P------YGITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEGVFAEAKEKSKGKE------KEKNEE--GE-G  192 (274)
Q Consensus       130 ~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~~f~~~~~~~~~~~------~~~~~~--~~-~  192 (274)
                      .      ++|.|||.|....+|+.|++.|||..--|  .+|.|.|+...      .++....      ....+.  +. -
T Consensus       161 ~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP------sq~t~~a~ls~ly~sp~rr~~Gp~h  234 (360)
T KOG0145|consen  161 VDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP------SQKTNQALLSQLYQSPARRYGGPMH  234 (360)
T ss_pred             hhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc------ccccchhhhHHhhcCccccCCCccc
Confidence            3      57899999999999999999999988776  47999988532      1111000      000000  00 0


Q ss_pred             hhhhhccchhhcccCC---CCccccc-------ccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         193 EEEKKENTAEEDNQQG---VPEVEEN-------VEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       193 ~~~~~~~~~~~~~~~~---~~~~~~~-------~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      -++.+-. .+....+.   .-...+.       ....-......+.+|||.||.++++|.-|+++|.+||.|..|+|++|
T Consensus       235 h~~~r~r-~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD  313 (360)
T KOG0145|consen  235 HQAQRFR-LDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRD  313 (360)
T ss_pred             chhhhhc-cccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEec
Confidence            0000000 00000000   0000000       00111334556789999999999999999999999999999999999


Q ss_pred             CCC
Q psy3343         263 KDP  265 (274)
Q Consensus       263 ~~~  265 (274)
                      .+.
T Consensus       314 ~tt  316 (360)
T KOG0145|consen  314 FTT  316 (360)
T ss_pred             CCc
Confidence            864

>KOG0105|consensus

Probab=99.65  E-value=2.2e-15  Score=121.25  Aligned_cols=147  Identities=17%  Similarity=0.236  Sum_probs=107.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .+..++|||+|||.++.+.+|.++|.+||.|..|.|..   .-.||||+|+++.+|+.||..-+|..++|..|.|+++..
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            35679999999999999999999999999999998754   236999999999999999999999999999999999865


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      ..-...........   -...  .         +           -......+..-....|.|..||.+-+|++|+++..
T Consensus        83 gr~s~~~~G~y~gg---grgG--g---------g-----------~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmR  137 (241)
T KOG0105|consen   83 GRSSSDRRGSYSGG---GRGG--G---------G-----------GGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMR  137 (241)
T ss_pred             CCcccccccccCCC---CCCC--C---------C-----------CCcccCCcccccceeEEEecCCCCCchHHHHHHHH
Confidence            52000000000000   0000  0         0           00000011222335899999999999999999999


Q ss_pred             hcCCeeEEEEecCCC
Q psy3343         250 KCGPIASVTVARKKD  264 (274)
Q Consensus       250 ~fG~I~~v~v~~~~~  264 (274)
                      ..|.|..+.|.+|--
T Consensus       138 eaGdvCfadv~rDg~  152 (241)
T KOG0105|consen  138 EAGDVCFADVQRDGV  152 (241)
T ss_pred             hhCCeeeeeeecccc
Confidence            999999999988753

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

Probab=99.64  E-value=1.5e-15  Score=121.50  Aligned_cols=78  Identities=19%  Similarity=0.221  Sum_probs=71.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|.+|.++.      .++||||+|.+.++|+.|++.|++..|.|++|+|.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999999875      368999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       111 a~~~  114 (144)
T PLN03134        111 ANDR  114 (144)
T ss_pred             CCcC
Confidence            8644

>PF00076 RRM_1: RNA recognition motif

Probab=99.56  E-value=1.3e-14  Score=100.88  Aligned_cols=65  Identities=25%  Similarity=0.357  Sum_probs=61.2

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      |||+|||+++|+++|+++|++||.|..+.+.++     +++|||+|.+.++|..|+..|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999988773     47999999999999999999999999999875

(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 ....

>KOG0121|consensus

Probab=99.56  E-value=5.7e-15  Score=112.14  Aligned_cols=77  Identities=22%  Similarity=0.440  Sum_probs=71.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC------eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~------~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ..+.+++|||+||++.++|++|.++|+++|.|.+|.|-.++      |||||+|.+.++|..|++.++|..++.++|.++
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            45678999999999999999999999999999999886543      799999999999999999999999999999999


Q ss_pred             Eec
Q psy3343         166 WAP  168 (274)
Q Consensus       166 ~a~  168 (274)
                      |..
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            975

>KOG4206|consensus

Probab=99.55  E-value=1.1e-13  Score=115.14  Aligned_cols=160  Identities=16%  Similarity=0.208  Sum_probs=108.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHH----ccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          96 KRIILVKNLPYRTLPTDLKA----LFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~----~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.+|||.||+..+..++|+.    +|++||.|..|....   -+|-|||.|.+.+.|..|+..|+|..|.|++++++||.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            45999999999999999988    999999999988765   46899999999999999999999999999999999997


Q ss_pred             CC--CCcccccccccccccccccccchhhhhccchhhcccCCCCcc---cccc-cccccCCCCCCceEEEeCCCCCCCHH
Q psy3343         169 EG--VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEV---EENV-EEDEEREPEPDTTLYIKNLNFNSTED  242 (274)
Q Consensus       169 ~~--~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~lfV~NL~~~~tee  242 (274)
                      .+  ++..... .-.++....... ....     ........+...   .... .........+...||+.|||..++.+
T Consensus        89 s~sdii~~~~~-~~v~~~~k~~~~-~~~~-----~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e  161 (221)
T KOG4206|consen   89 SDSDIIAQAPG-TFVEKEKKINGE-ILAR-----IKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESE  161 (221)
T ss_pred             CccchhhccCc-eeccccCccccc-cccc-----cCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHH
Confidence            55  1111000 000000000000 0000     000000000000   0000 00012335677899999999999999


Q ss_pred             HHHHHhhhcCCeeEEEEecC
Q psy3343         243 SIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       243 ~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .|..+|.+|+....++++.-
T Consensus       162 ~l~~lf~qf~g~keir~i~~  181 (221)
T KOG4206|consen  162 MLSDLFEQFPGFKEIRLIPP  181 (221)
T ss_pred             HHHHHHhhCcccceeEeccC
Confidence            99999999999999988753

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.50  E-value=1e-13  Score=119.06  Aligned_cols=73  Identities=21%  Similarity=0.256  Sum_probs=68.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+   +|||||+|.++++|..|+. |+|..|.|++|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            479999999999999999999999999999999874   5899999999999999995 999999999999999863

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

Probab=99.49  E-value=5.8e-13  Score=115.21  Aligned_cols=143  Identities=24%  Similarity=0.373  Sum_probs=107.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..+|||+|||+.+++++|+++|..||.|..+.+..+      +|||||+|.+.++|..|+..++|..|.|++|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            599999999999999999999999999999988764      48999999999999999999999999999999999753


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      .  ................              ..           ..............+++.|++..++...+...|.
T Consensus       195 ~--~~~~~~~~~~~~~~~~--------------~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (306)
T COG0724         195 A--SQPRSELSNNLDASFA--------------KK-----------LSRGKALLLEKSDNLYVGNLPLKTAEEELADLFK  247 (306)
T ss_pred             c--cccccccccccchhhh--------------cc-----------ccccccccccccceeeccccccccchhHHHHhcc
Confidence            0  0000000000000000              00           0000112334567999999999999999999999


Q ss_pred             hcCCeeEEEEecCCCC
Q psy3343         250 KCGPIASVTVARKKDP  265 (274)
Q Consensus       250 ~fG~I~~v~v~~~~~~  265 (274)
                      .+|.+..+.+......
T Consensus       248 ~~~~~~~~~~~~~~~~  263 (306)
T COG0724         248 SRGDIVRASLPPSKDG  263 (306)
T ss_pred             ccccceeeeccCCCCC
Confidence            9999987777766554

>KOG0148|consensus

Probab=99.48  E-value=1.4e-13  Score=116.90  Aligned_cols=135  Identities=20%  Similarity=0.260  Sum_probs=99.3

Q ss_pred             HHHHHHHHHhCCCcccccC----------CchhHHHhhhhhhhHHHHHHHHHHHCCCCcc--------------ccch--
Q psy3343          36 AIAEAMAETYNATKAEVLT----------GSGAATRLAMGETEIVEKTRAFLEENGVQLD--------------AFNQ--   89 (274)
Q Consensus        36 ~v~~~~~~~~~~~~~~l~~----------~~~~avr~al~e~~~~~~~~~~l~~~g~~~~--------------~~~~--   89 (274)
                      .+-++++.--.|+...++-          +-.-..+-..+|..+.+..-+||-.+.|.-.              .|+.  
T Consensus        78 ~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~  157 (321)
T KOG0148|consen   78 KLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVY  157 (321)
T ss_pred             HHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHh
Confidence            3444555444556555542          1122334455555555555566655444311              1111  


Q ss_pred             hhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          90 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        90 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .....++++|||+|++..+|+++|++.|++||+|.+|++-+++||+||.|.+.|+|..||..+|+..+.|..++|.|...
T Consensus       158 NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  158 NQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             ccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            12456779999999999999999999999999999999999999999999999999999999999999999999999864


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus       238 ~  238 (321)
T KOG0148|consen  238 G  238 (321)
T ss_pred             C
Confidence            4

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.48  E-value=9.3e-14  Score=126.18  Aligned_cols=136  Identities=18%  Similarity=0.250  Sum_probs=97.0

Q ss_pred             ccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh------------hhhhhhHHHHHHHHHH-HCCCCccc--
Q psy3343          27 WNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL------------AMGETEIVEKTRAFLE-ENGVQLDA--   86 (274)
Q Consensus        27 wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~------------al~e~~~~~~~~~~l~-~~g~~~~~--   86 (274)
                      =.+|||+...        +.+++++|.+     +....|++            |..+..-.+++..++. .+|..+..  
T Consensus       107 ~~~LfVgnLp--------~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~  178 (346)
T TIGR01659       107 GTNLIVNYLP--------QDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKR  178 (346)
T ss_pred             CcEEEEeCCC--------CCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCce
Confidence            3468888763        6777777755     44434433            2222223445555553 35554321  


Q ss_pred             ----cchh-hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCC
Q psy3343          87 ----FNQV-VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYT  155 (274)
Q Consensus        87 ----~~~~-~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~  155 (274)
                          +..+ ......++|||+|||+.+|+++|+++|++||.|..|.|+++      ++||||+|.+.++|.+|++.|++.
T Consensus       179 i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  258 (346)
T TIGR01659       179 LKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV  258 (346)
T ss_pred             eeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence                1111 12234688999999999999999999999999999998864      379999999999999999999999


Q ss_pred             eeCC--eEEEEEEecCC
Q psy3343         156 KFKE--VPLYLEWAPEG  170 (274)
Q Consensus       156 ~~~g--~~l~v~~a~~~  170 (274)
                      .+.+  ++|.|.|+...
T Consensus       259 ~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       259 IPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             ccCCCceeEEEEECCcc
Confidence            8876  78999998643

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).

>KOG0107|consensus

Probab=99.47  E-value=1.1e-13  Score=110.68  Aligned_cols=75  Identities=23%  Similarity=0.240  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..+.|||+||+..+++.||...|..||.|..|.|.. ..|||||+|+++.+|..|+..|+|..|.|..|.|+....
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            369999999999999999999999999999998877 458999999999999999999999999999999998753

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.46  E-value=3.4e-13  Score=94.14  Aligned_cols=65  Identities=28%  Similarity=0.375  Sum_probs=59.3

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      |||+|||+++++++|+++|+.||.|..+.+..+     +++|||+|.+.++|..|+..+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999875     48999999999999999999999999999874

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 ....

>KOG0114|consensus

Probab=99.46  E-value=3.7e-13  Score=98.68  Aligned_cols=74  Identities=20%  Similarity=0.338  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      -++.|||+|||+++|.++..++|.+||.|..|++-.   .+|.|||.|++..+|++|++.|+|..+.++.|.|-|-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            358999999999999999999999999999999965   56899999999999999999999999999999998764

>KOG4205|consensus

Probab=99.44  E-value=3.7e-13  Score=119.40  Aligned_cols=126  Identities=17%  Similarity=0.259  Sum_probs=103.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..+.|||++|++.++++.|++.|++||.|..|.+++      .++|+||+|.+++....++. ..-..|.|+.|-+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            568999999999999999999999999999999877      35899999999999988885 35567889988887775


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ........                                             ........|||+.||.++++++|++.|
T Consensus        84 ~r~~~~~~---------------------------------------------~~~~~tkkiFvGG~~~~~~e~~~r~yf  118 (311)
T KOG4205|consen   84 SREDQTKV---------------------------------------------GRHLRTKKIFVGGLPPDTTEEDFKDYF  118 (311)
T ss_pred             Cccccccc---------------------------------------------ccccceeEEEecCcCCCCchHHHhhhh
Confidence            43110000                                             011134689999999999999999999


Q ss_pred             hhcCCeeEEEEecCCCCC
Q psy3343         249 KKCGPIASVTVARKKDPK  266 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~~~~  266 (274)
                      .+||.|..+.++.|.+..
T Consensus       119 e~~g~v~~~~~~~d~~~~  136 (311)
T KOG4205|consen  119 EQFGKVADVVIMYDKTTS  136 (311)
T ss_pred             hccceeEeeEEeeccccc
Confidence            999999999999998654

>KOG0122|consensus

Probab=99.41  E-value=7.1e-13  Score=111.14  Aligned_cols=76  Identities=26%  Similarity=0.420  Sum_probs=70.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|-|.|||.++++.+|++||.+||.|.+|.|.+      ++|||||.|.+.++|.+||..|+|.-+++-.|.|+|+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            458899999999999999999999999999999987      35899999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            43

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.41  E-value=1.2e-12  Score=110.90  Aligned_cols=73  Identities=16%  Similarity=0.140  Sum_probs=67.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...+|||+||++.+|+++|+++|+.||.|.+|.|+++   +++|||+|.++++|..|+. |+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4579999999999999999999999999999999884   4799999999999999995 99999999999998764

>PLN03213 repressor of silencing 3; Provisional

Probab=99.38  E-value=1.4e-12  Score=118.91  Aligned_cols=77  Identities=22%  Similarity=0.181  Sum_probs=70.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--CCeEEEEEecCH--HHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQK--NQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~--~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ....+||||||++.+++++|+.+|+.||.|.+|.|++  .+|||||+|...  .++.+||..|+|..++|+.|+|..|.+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            3458999999999999999999999999999999998  468999999987  789999999999999999999999864


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus        88 ~   88 (759)
T PLN03213         88 H   88 (759)
T ss_pred             H
Confidence            3

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=3e-12  Score=88.23  Aligned_cols=67  Identities=34%  Similarity=0.474  Sum_probs=63.1

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC----eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG----ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~----~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      +|||+|||..++.++|+++|.+||.|..+.+..+.    ++|||+|.+.++|..|+..+++..+.|++|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            48999999999999999999999999999988765    89999999999999999999999999999876

>PF13893 RRM_5: RNA recognition motif

Probab=99.37  E-value=4.3e-12  Score=84.83  Aligned_cols=55  Identities=27%  Similarity=0.420  Sum_probs=51.6

Q ss_pred             HHHccccCCCeeEEEeeCCC-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343         113 LKALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus       113 l~~~F~~~G~i~~v~l~~~~-~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      |+++|++||.|.++.+.+.+ ++|||+|.+.++|..|+..|+|..+.|++|.|.|+
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            67899999999999999877 99999999999999999999999999999999986

(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 ....

>KOG0125|consensus

Probab=99.37  E-value=1.2e-12  Score=113.87  Aligned_cols=79  Identities=25%  Similarity=0.272  Sum_probs=72.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +...++|+|.|||+...+-||+.+|.+||.|.+|.|.-    +||||||+|+++++|++|-.+|+|..+.||.|.|..|.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            34458999999999999999999999999999998865    67999999999999999999999999999999999987


Q ss_pred             CCC
Q psy3343         169 EGV  171 (274)
Q Consensus       169 ~~~  171 (274)
                      ..+
T Consensus       173 arV  175 (376)
T KOG0125|consen  173 ARV  175 (376)
T ss_pred             hhh
Confidence            553

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

Probab=99.35  E-value=2.9e-12  Score=123.00  Aligned_cols=75  Identities=19%  Similarity=0.216  Sum_probs=69.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|.+      .+|||||+|.+.++|.+|+..||+..++|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            347999999999999999999999999999999976      35899999999999999999999999999999999986


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            3

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.

>KOG1457|consensus

Probab=99.34  E-value=1.8e-11  Score=101.54  Aligned_cols=74  Identities=26%  Similarity=0.352  Sum_probs=64.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CC------eEEEEEecCHHHHHHHHHHhCCCeeC---CeEEEEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YG------ITGLVEFLQKNQAKAAFNSLAYTKFK---EVPLYLEW  166 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~------~~afV~F~~~~~A~~A~~~l~~~~~~---g~~l~v~~  166 (274)
                      ++|||.+||.++...+|..+|..|-..+.+.|.. ++      .+|||.|.+...|..|+..|||.+|+   +..|++++
T Consensus        35 RTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiEl  114 (284)
T KOG1457|consen   35 RTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIEL  114 (284)
T ss_pred             ceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeee
Confidence            8999999999999999999999986666666644 22      48999999999999999999999997   68899999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      |..+
T Consensus       115 AKSN  118 (284)
T KOG1457|consen  115 AKSN  118 (284)
T ss_pred             hhcC
Confidence            9755

>KOG4207|consensus

Probab=99.28  E-value=4e-12  Score=104.21  Aligned_cols=75  Identities=31%  Similarity=0.484  Sum_probs=70.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      -+.|.|-||.+-++.++|+.+|++||.|-.|.|+.+      +|||||.|....+|+.|+++|+|..++|+.|.|+.|..
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            488999999999999999999999999999999984      58999999999999999999999999999999998854


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus        93 g   93 (256)
T KOG4207|consen   93 G   93 (256)
T ss_pred             C
Confidence            3

>KOG0144|consensus

Probab=99.28  E-value=2.6e-12  Score=115.40  Aligned_cols=118  Identities=21%  Similarity=0.272  Sum_probs=90.8

Q ss_pred             cccChhHHHHHHHHHhCCCcccccC--CchhHHHhhhhhhhHHHHHHHHHHHCCCCccccchhhhcCCCcEEEEeCCCCC
Q psy3343          30 LFLGTNAIAEAMAETYNATKAEVLT--GSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYR  107 (274)
Q Consensus        30 lf~~~~~v~~~~~~~~~~~~~~l~~--~~~~avr~al~e~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~l~V~nLp~~  107 (274)
                      .||..-+..++......+...-.|-  ...+.||.|.+|.+.+                       ...+.|||+-|+..
T Consensus        79 CFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~-----------------------~~e~KLFvg~lsK~  135 (510)
T KOG0144|consen   79 CFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERI-----------------------VEERKLFVGMLSKQ  135 (510)
T ss_pred             EEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhcc-----------------------ccchhhhhhhcccc
Confidence            4555555555555554555444554  3466777777766443                       12478999999999


Q ss_pred             CCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCC-eeCC--eEEEEEEecCC
Q psy3343         108 TLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYT-KFKE--VPLYLEWAPEG  170 (274)
Q Consensus       108 ~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~-~~~g--~~l~v~~a~~~  170 (274)
                      +||.+++++|++||.|++|.|.+     ++|||||.|.+.+.|..|++.|||. ++.|  .+|.|.||..+
T Consensus       136 ~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq  206 (510)
T KOG0144|consen  136 CTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ  206 (510)
T ss_pred             ccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence            99999999999999999999987     5799999999999999999999995 4665  68999999644

>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=99.27  E-value=3.4e-11  Score=83.34  Aligned_cols=69  Identities=29%  Similarity=0.434  Sum_probs=64.3

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      +|+|+|||+.+++++|+++|..||.|..+.+..+     .++|||+|.+.++|..|+..+++..+.|+.+.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999998874     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).

>KOG0147|consensus

Probab=99.27  E-value=1.7e-12  Score=119.78  Aligned_cols=140  Identities=26%  Similarity=0.411  Sum_probs=108.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ..+..+++|+--|+-.+++-+|.++|+.+|.|..|++..      ++|.|||+|.+.+....|+ .|.|..+.|.+|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            355668899999999999999999999999999999876      4589999999999999999 599999999999998


Q ss_pred             EecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHH
Q psy3343         166 WAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIR  245 (274)
Q Consensus       166 ~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~  245 (274)
                      .....       .+........             ..+                 ..-..+...|||+||+|++++++|+
T Consensus       254 ~sEae-------knr~a~~s~a-------------~~~-----------------k~~~~p~~rl~vgnLHfNite~~lr  296 (549)
T KOG0147|consen  254 LSEAE-------KNRAANASPA-------------LQG-----------------KGFTGPMRRLYVGNLHFNITEDMLR  296 (549)
T ss_pred             ccHHH-------HHHHHhcccc-------------ccc-----------------cccccchhhhhhcccccCchHHHHh
Confidence            65311       0000000000             000                 0011233449999999999999999


Q ss_pred             HHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         246 RHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       246 ~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      .+|++||.|..|.+++|. .|...|
T Consensus       297 ~ifepfg~Ie~v~l~~d~~tG~skg  321 (549)
T KOG0147|consen  297 GIFEPFGKIENVQLTKDSETGRSKG  321 (549)
T ss_pred             hhccCcccceeeeeccccccccccC
Confidence            999999999999999997 666655

>KOG0126|consensus

Probab=99.27  E-value=2.5e-12  Score=103.47  Aligned_cols=80  Identities=14%  Similarity=0.207  Sum_probs=73.3

Q ss_pred             hhhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy3343          89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPL  162 (274)
Q Consensus        89 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l  162 (274)
                      ....-..+.-|||+|||+..||.||..+|++||.|..|.|.+      ++||||+.|++..+...|+..|||..|.||.|
T Consensus        28 WH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRti  107 (219)
T KOG0126|consen   28 WHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTI  107 (219)
T ss_pred             hhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeE
Confidence            345566789999999999999999999999999999999988      35899999999999999999999999999999


Q ss_pred             EEEEec
Q psy3343         163 YLEWAP  168 (274)
Q Consensus       163 ~v~~a~  168 (274)
                      +|+...
T Consensus       108 rVDHv~  113 (219)
T KOG0126|consen  108 RVDHVS  113 (219)
T ss_pred             Eeeecc
Confidence            998764

>KOG0113|consensus

Probab=99.26  E-value=1.7e-11  Score=105.61  Aligned_cols=76  Identities=18%  Similarity=0.308  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+-++|||.-|+++++|..|+..|+.||.|..|.|..      ++|||||+|.+..+...|++...|..|+|+.|.|++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            45569999999999999999999999999999999987      358999999999999999999999999999999977


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      -.
T Consensus       178 ER  179 (335)
T KOG0113|consen  178 ER  179 (335)
T ss_pred             cc
Confidence            54

>KOG0117|consensus

Probab=99.25  E-value=1.3e-11  Score=111.33  Aligned_cols=72  Identities=26%  Similarity=0.391  Sum_probs=68.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..|||+||+.++|++.|+++|+.||.|.+|..+++  ||||+|.+.++|.+|++.+||..|.|.+|.|..|.+.
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecccc--eeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            78999999999999999999999999999999877  9999999999999999999999999999999998643

>KOG0149|consensus

Probab=99.23  E-value=1.3e-11  Score=103.20  Aligned_cols=74  Identities=22%  Similarity=0.241  Sum_probs=65.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .-++|||++|+|.++.+.|+++|++||+|.+..+..      ++|||||+|.+.++|.+|++. ..-.|+||.-.|..|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            348999999999999999999999999998888765      468999999999999999973 4567899998888875


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      .
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

>KOG0146|consensus

Probab=99.21  E-value=6.7e-11  Score=100.58  Aligned_cols=74  Identities=26%  Similarity=0.398  Sum_probs=66.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCe-eCC--eEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTK-FKE--VPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~-~~g--~~l~v~~  166 (274)
                      ..++|||+-|...-.|+|++.+|..||.|.+|.+.+     ++|+|||.|.+.-+|..||..|+|.. +-|  ..|.|.|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            458999999999999999999999999999998876     57999999999999999999999954 444  5688888


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus        98 AD   99 (371)
T KOG0146|consen   98 AD   99 (371)
T ss_pred             cc
Confidence            85

>smart00360 RRM RNA recognition motif

Probab=99.19  E-value=7.7e-11  Score=80.72  Aligned_cols=64  Identities=28%  Similarity=0.400  Sum_probs=59.2

Q ss_pred             EeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343         101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus       101 V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      |+|||..+++++|+.+|++||.|..+.+...      +++|||+|.+.++|..|+..+++..+.|+.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5799999999999999999999999988763      479999999999999999999999999999876

>KOG0130|consensus

Probab=99.18  E-value=3.7e-11  Score=92.32  Aligned_cols=76  Identities=18%  Similarity=0.283  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ....|||.++...+++++|.+.|..||.|..+.|..+      +|||+|+|.+.++|+.|+..+||..+.|.+|.|+|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            4578999999999999999999999999999988763      5899999999999999999999999999999999985


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus       151 v~  152 (170)
T KOG0130|consen  151 VK  152 (170)
T ss_pred             ec
Confidence            33

>KOG0111|consensus

Probab=99.15  E-value=3.3e-11  Score=99.79  Aligned_cols=76  Identities=26%  Similarity=0.367  Sum_probs=71.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||++|..++++.-|...|-+||.|..|.+|.      .+|||||+|...++|..|+..||+..+.||.|+|.+|.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            458999999999999999999999999999999987      36899999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      +.
T Consensus        89 P~   90 (298)
T KOG0111|consen   89 PE   90 (298)
T ss_pred             Cc
Confidence            54

>KOG1190|consensus

Probab=99.14  E-value=7.9e-10  Score=99.01  Aligned_cols=152  Identities=19%  Similarity=0.213  Sum_probs=104.1

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCCC-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCc
Q psy3343          96 KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFA  173 (274)
Q Consensus        96 ~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~~-~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~  173 (274)
                      +++|.|.||.. .+|.+-|..+|+-||.|.+|.|...+ --|+|+|.+...|..|+..|+|..+.|++|+|.+.......
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq  376 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ  376 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc
Confidence            68999999975 48999999999999999999998854 58999999999999999999999999999999987533111


Q ss_pred             ccccccccccccccccccchhhhhccchhhcc-cCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcC
Q psy3343         174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDN-QQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCG  252 (274)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG  252 (274)
                      -+.....+ +.- ++           ++.... .+.    +......--.--+++.+|...|+|.++++|+|+.+|..-|
T Consensus       377 lp~egq~d-~gl-T~-----------dy~~spLhrf----kkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g  439 (492)
T KOG1190|consen  377 LPREGQED-QGL-TK-----------DYGNSPLHRF----KKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPG  439 (492)
T ss_pred             CCCCCCcc-ccc-cc-----------cCCCCchhhc----cCcccccccccCCchhheeeccCCcccchhHHHHhhhcCC
Confidence            11110000 000 00           000000 000    0000000001224677999999999999999999999998


Q ss_pred             CeeEEEEecCCC
Q psy3343         253 PIASVTVARKKD  264 (274)
Q Consensus       253 ~I~~v~v~~~~~  264 (274)
                      ...+....--++
T Consensus       440 ~~vkafkff~kd  451 (492)
T KOG1190|consen  440 GQVKAFKFFQKD  451 (492)
T ss_pred             ceEEeeeecCCC
Confidence            887766554333

>KOG4212|consensus

Probab=99.12  E-value=1.1e-09  Score=98.88  Aligned_cols=173  Identities=17%  Similarity=0.255  Sum_probs=112.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccc-cCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFE-PFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..+.+||.|||+++...+|+++|. +.|.|..|.|.-     .+++|.|+|.+++.+++|++.||...+.||+|.|.-.+
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            346799999999999999999996 689999998865     46899999999999999999999999999999997665


Q ss_pred             CC--------------CCcccccccccccccccccccchhhhhccc----hhhcccCCCCccccccc-------------
Q psy3343         169 EG--------------VFAEAKEKSKGKEKEKNEEGEGEEEKKENT----AEEDNQQGVPEVEENVE-------------  217 (274)
Q Consensus       169 ~~--------------~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~-------------  217 (274)
                      ..              .|.....-+.-  ...+...-.-.-.....    .+........+...+..             
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G--~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGG--NGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecc--cccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            42              01100000000  00000000000000000    00000000000011000             


Q ss_pred             -c----cccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         218 -E----DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       218 -~----~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                       .    .....++....+||.||.+.+....|++.|.-.|.|.++.+..++.+.+.|
T Consensus       201 ~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G  257 (608)
T KOG4212|consen  201 ASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRG  257 (608)
T ss_pred             hhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCC
Confidence             0    011234445689999999999999999999999999999999999987766

>KOG0106|consensus

Probab=99.10  E-value=1.2e-10  Score=97.73  Aligned_cols=129  Identities=19%  Similarity=0.324  Sum_probs=96.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCcccc
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAK  176 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~~~~  176 (274)
                      ..+||++||+.+.+.+|..+|..||.|..+.|..  ||+||+|.+..+|.-|+..|++..|.|-.+.|+|+...-.....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~   79 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGR   79 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--ccceeccCchhhhhcccchhcCceecceeeeeecccccccccCC
Confidence            4689999999999999999999999999998853  68999999999999999999999999988999998532000000


Q ss_pred             cccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE
Q psy3343         177 EKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS  256 (274)
Q Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~  256 (274)
                      +... .+..-.               .               .-.......+.++|.|++-.+.+.+|.++|.++|.+.+
T Consensus        80 ~~~g-~r~~~~---------------~---------------~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~  128 (216)
T KOG0106|consen   80 PRGG-DRRSDS---------------R---------------RYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTY  128 (216)
T ss_pred             CCCC-Cccchh---------------h---------------ccCCcccccceeeeccchhhhhHHHHhhhhcccCCCch
Confidence            0000 000000               0               00011234578999999999999999999999999955


Q ss_pred             EE
Q psy3343         257 VT  258 (274)
Q Consensus       257 v~  258 (274)
                      ..
T Consensus       129 ~~  130 (216)
T KOG0106|consen  129 VD  130 (216)
T ss_pred             hh
Confidence            43

>KOG0108|consensus

Probab=99.06  E-value=3.4e-10  Score=104.87  Aligned_cols=74  Identities=22%  Similarity=0.316  Sum_probs=69.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +.|||||+|+++++++|..+|+..|.|.++++..+      +||||++|.+.++|..|++.|||..+.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999763      489999999999999999999999999999999999644

>KOG1190|consensus

Probab=99.06  E-value=2.9e-10  Score=101.80  Aligned_cols=159  Identities=16%  Similarity=0.256  Sum_probs=106.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~a~~~  170 (274)
                      ..+.++|.++|||++++|+||..++.+||.|..+.+...+..||++|.+.++|...+.....  -.+.|++|+|+|....
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn~~  104 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSNHS  104 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccchhhhhhhcchhhhhheeecccccCccccCcceeehhhhHH
Confidence            33679999999999999999999999999999999998888999999999998875543333  3478999999997544


Q ss_pred             CCcccccccccccccccccccchhhhhccchh-hcccCCCCcccccccccccCCCCCC--ceEEEeCCCCCCCHHHHHHH
Q psy3343         171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAE-EDNQQGVPEVEENVEEDEEREPEPD--TTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       171 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~--~~lfV~NL~~~~tee~L~~~  247 (274)
                      .+.+....... +....             +. ....+..................++  -+++|.|+-+.+|-+-|..+
T Consensus       105 ~lkt~s~p~q~-r~~~v-------------y~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqv  170 (492)
T KOG1190|consen  105 ELKTDSQPNQI-RGQAV-------------YQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQV  170 (492)
T ss_pred             HHhccCchhhh-hhhhH-------------HhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHH
Confidence            33333222100 00000             00 0000000000000000001112222  37889999999999999999


Q ss_pred             hhhcCCeeEEEEecCCCC
Q psy3343         248 FKKCGPIASVTVARKKDP  265 (274)
Q Consensus       248 F~~fG~I~~v~v~~~~~~  265 (274)
                      |++||.|..+.-..+.++
T Consensus       171 FS~fG~VlKIiTF~Knn~  188 (492)
T KOG1190|consen  171 FSKFGFVLKIITFTKNNG  188 (492)
T ss_pred             HhhcceeEEEEEEecccc
Confidence            999999999887777665

>KOG4211|consensus

Probab=99.04  E-value=2.8e-09  Score=97.66  Aligned_cols=135  Identities=13%  Similarity=0.217  Sum_probs=99.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..-.|-+++|||++|++||.++|+-++ |.++.+++.    .|-|||+|.+.+++++|++ .+...+..|-|.|--+...
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            346778899999999999999999987 778888773    3689999999999999998 5667777777777544211


Q ss_pred             CCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhh
Q psy3343         171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  250 (274)
Q Consensus       171 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~  250 (274)
                             +    .....+              .               .........-.|-++.|||.||+++|.++|+.
T Consensus        87 -------e----~d~~~~--------------~---------------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaG  126 (510)
T KOG4211|consen   87 -------E----ADWVMR--------------P---------------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAG  126 (510)
T ss_pred             -------c----cccccc--------------C---------------CCCCCCCCCceEEecCCCccCcHHHHHHHhcC
Confidence                   0    000000              0               00001123458999999999999999999998


Q ss_pred             cCCeeE-EEEecCCCCCCCCCC
Q psy3343         251 CGPIAS-VTVARKKDPKSPGQF  271 (274)
Q Consensus       251 fG~I~~-v~v~~~~~~~~~g~~  271 (274)
                      .--|.. +.++.++.+++.|+.
T Consensus       127 L~Iv~~gi~l~~d~rgR~tGEA  148 (510)
T KOG4211|consen  127 LEIVPDGILLPMDQRGRPTGEA  148 (510)
T ss_pred             CcccccceeeeccCCCCcccce
Confidence            866666 667888888887764

>KOG0109|consensus

Probab=99.03  E-value=2.8e-10  Score=97.89  Aligned_cols=77  Identities=18%  Similarity=0.259  Sum_probs=70.9

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .....++|+|+||.+.++..+|+..|.+||++.+|.|.+  +|+||.|...++|..|++.|++..|.|+++.|+.....
T Consensus        74 Ksk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   74 KSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             cCCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--ceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            344569999999999999999999999999999999975  49999999999999999999999999999999987654

>KOG0147|consensus

Probab=99.03  E-value=2.6e-10  Score=105.48  Aligned_cols=73  Identities=23%  Similarity=0.375  Sum_probs=67.2

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .|||+||.+++++++|+.+|++||.|..|.++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|..-...
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            399999999999999999999999999999876      3689999999999999999999999999999999866443

>KOG0132|consensus

Probab=98.97  E-value=1.1e-09  Score=104.75  Aligned_cols=75  Identities=23%  Similarity=0.480  Sum_probs=72.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +++||||.|+.++++.||..+|+.||.|.+|.+...++||||.+.+..+|.+|+..|+...+.++.|+|.|+...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            489999999999999999999999999999999999999999999999999999999999999999999999644

>KOG0153|consensus

Probab=98.96  E-value=2.9e-09  Score=93.65  Aligned_cols=80  Identities=18%  Similarity=0.295  Sum_probs=72.0

Q ss_pred             hhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC-CeeCCeEEEEEEec
Q psy3343          90 VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY-TKFKEVPLYLEWAP  168 (274)
Q Consensus        90 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~-~~~~g~~l~v~~a~  168 (274)
                      +....+-++|||++|...+++.+|+++|-+||.|.++++...+++|||+|.+.++|+.|...+-. ..|+|+.|.|.|..
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            44566779999999999999999999999999999999998889999999999999998877544 66899999999997


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      .
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            5

>KOG0415|consensus

Probab=98.92  E-value=1.5e-09  Score=95.66  Aligned_cols=79  Identities=16%  Similarity=0.251  Sum_probs=72.7

Q ss_pred             hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC------eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~------~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ...++.++|||.-|.+-+|.++|.-+|+.||.|.+|.+.++.      .||||+|.+.+++++|+-.|.+..|+++.|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            356677999999999999999999999999999999998853      49999999999999999999999999999999


Q ss_pred             EEecC
Q psy3343         165 EWAPE  169 (274)
Q Consensus       165 ~~a~~  169 (274)
                      +|++.
T Consensus       314 DFSQS  318 (479)
T KOG0415|consen  314 DFSQS  318 (479)
T ss_pred             ehhhh
Confidence            99763

>KOG1548|consensus

Probab=98.92  E-value=9e-09  Score=90.60  Aligned_cols=155  Identities=17%  Similarity=0.230  Sum_probs=97.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCee--------EEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLG--------RVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      ...++.|||.|||.++|-+++.++|+++|-|.        .|.|-++     +|=|++.|...+++..|+..|++..|.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            34568899999999999999999999999773        3444432     3679999999999999999999999999


Q ss_pred             eEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCC---
Q psy3343         160 VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLN---  236 (274)
Q Consensus       160 ~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~---  236 (274)
                      +.|+|+.|.-.   .......... ...+..    +. ....+.+.   +.-... ...+.+......++|.++|+=   
T Consensus       211 ~~~rVerAkfq---~Kge~~~~~k-~k~k~~----~~-kk~~k~q~---k~~dw~-pd~~~~sk~r~~~tVi~kn~Ftp~  277 (382)
T KOG1548|consen  211 KKLRVERAKFQ---MKGEYDASKK-EKGKCK----DK-KKLKKQQQ---KLLDWR-PDRDDPSKARADRTVILKNMFTPE  277 (382)
T ss_pred             cEEEEehhhhh---hccCcCcccc-cccccc----cH-HHHHHHHH---hhcccC-CCccccccccCCcEEEeeecCCHH
Confidence            99999998533   1100000000 000000    00 00000000   000000 001112234456799999982   


Q ss_pred             -CCCC-------HHHHHHHhhhcCCeeEEEEe
Q psy3343         237 -FNST-------EDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       237 -~~~t-------ee~L~~~F~~fG~I~~v~v~  260 (274)
                       +..+       .++|++-+++||.|.+|.|.
T Consensus       278 ~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~  309 (382)
T KOG1548|consen  278 DFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY  309 (382)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHhCCcceEEEe
Confidence             3444       46677779999999999877

>smart00361 RRM_1 RNA recognition motif

Probab=98.89  E-value=7.7e-09  Score=72.31  Aligned_cols=55  Identities=18%  Similarity=0.249  Sum_probs=48.2

Q ss_pred             HHHHHHccc----cCCCeeEEE---eeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343         110 PTDLKALFE----PFGDLGRVL---VPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus       110 e~~l~~~F~----~~G~i~~v~---l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      +++|+++|+    +||.|.+|.   +++      .+|||||+|.+.++|..|+..|+|..+.|+.|.+
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            578888998    999998884   332      3689999999999999999999999999999876

>KOG4208|consensus

Probab=98.79  E-value=1.7e-08  Score=83.09  Aligned_cols=79  Identities=22%  Similarity=0.270  Sum_probs=71.2

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccC-CCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPF-GDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      .......+||..+|....+.++..+|.+| |.+.++++.+      ++|||||+|++++.|.-|-+.||+..|.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34456899999999999999999999998 7888999866      4589999999999999999999999999999999


Q ss_pred             EEecCC
Q psy3343         165 EWAPEG  170 (274)
Q Consensus       165 ~~a~~~  170 (274)
                      .+-|+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            998765

>KOG4454|consensus

Probab=98.77  E-value=1.8e-09  Score=89.57  Aligned_cols=72  Identities=21%  Similarity=0.108  Sum_probs=65.8

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC----eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG----ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~----~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .++|||+|+...++++-|.++|-+-|+|..|.|+..+    .||||.|.+.-+..-|+..+||..+.++++.+.+-
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            5899999999999999999999999999999998732    49999999999999999999999999988777654

>KOG0146|consensus

Probab=98.67  E-value=2.1e-08  Score=85.55  Aligned_cols=77  Identities=21%  Similarity=0.231  Sum_probs=68.7

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ....+|+|||-.||.+....||..+|-+||.|.+.++-.      +++||||.|.++.+|+.||..|||..|.-++|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            345679999999999999999999999999997766533      57899999999999999999999999999999998


Q ss_pred             Eec
Q psy3343         166 WAP  168 (274)
Q Consensus       166 ~a~  168 (274)
                      ...
T Consensus       361 LKR  363 (371)
T KOG0146|consen  361 LKR  363 (371)
T ss_pred             hcC
Confidence            754

>KOG4661|consensus

Probab=98.66  E-value=3.6e-08  Score=91.80  Aligned_cols=76  Identities=25%  Similarity=0.264  Sum_probs=68.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||.+|+..+...+|+.+|++||.|.-..+..      .++|+||++.+..+|.+||..|+.+.++|+.|.|+.+.
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            448999999999999999999999999997776654      35899999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            44

>KOG0131|consensus

Probab=98.63  E-value=4.5e-08  Score=79.18  Aligned_cols=77  Identities=18%  Similarity=0.141  Sum_probs=66.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEE-EeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.+|||+||.+.+++..|.+.|+.||.|.+. .+.+      .++||||.|.+.+.+.+|+..++|..+..+++.|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            445899999999999999999999999987542 2222      347999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus       174 a~k~  177 (203)
T KOG0131|consen  174 AFKK  177 (203)
T ss_pred             EEec
Confidence            9644

>KOG0129|consensus

Probab=98.61  E-value=7.8e-07  Score=82.35  Aligned_cols=139  Identities=15%  Similarity=0.205  Sum_probs=90.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---------CCe---EEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---------YGI---TGLVEFLQKNQAKAAFNSLAYTKFKEV  160 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---------~~~---~afV~F~~~~~A~~A~~~l~~~~~~g~  160 (274)
                      .+..+.|||++||++++|++|...|..||.+ .|..+.         .+|   |+|+.|+++.+...-+.+..   ....
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~---~~~~  331 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS---EGEG  331 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh---hccc
Confidence            4456899999999999999999999999976 344441         234   99999999988877554432   2444


Q ss_pred             EEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCC
Q psy3343         161 PLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST  240 (274)
Q Consensus       161 ~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~t  240 (274)
                      .+++....... ....-+   .+.-.+.                     +++   --.+....-.+..||||+.||-.++
T Consensus       332 ~~yf~vss~~~-k~k~VQ---IrPW~la---------------------Ds~---fv~d~sq~lDprrTVFVGgvprpl~  383 (520)
T KOG0129|consen  332 NYYFKVSSPTI-KDKEVQ---IRPWVLA---------------------DSD---FVLDHNQPIDPRRTVFVGGLPRPLT  383 (520)
T ss_pred             ceEEEEecCcc-ccccee---EEeeEec---------------------cch---hhhccCcccCccceEEecCCCCcch
Confidence            44444332110 000000   0000000                     000   0000112334668999999999999


Q ss_pred             HHHHHHHhh-hcCCeeEEEEecCC
Q psy3343         241 EDSIRRHFK-KCGPIASVTVARKK  263 (274)
Q Consensus       241 ee~L~~~F~-~fG~I~~v~v~~~~  263 (274)
                      -++|..+|+ -||.|.+|-|=+|+
T Consensus       384 A~eLA~imd~lyGgV~yaGIDtD~  407 (520)
T KOG0129|consen  384 AEELAMIMEDLFGGVLYVGIDTDP  407 (520)
T ss_pred             HHHHHHHHHHhcCceEEEEeccCc
Confidence            999999998 89999999999883

>KOG0124|consensus

Probab=98.59  E-value=1.2e-07  Score=84.24  Aligned_cols=76  Identities=20%  Similarity=0.235  Sum_probs=70.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      .+...+|||..+.++.+++||+..|+.||+|..|.+.+      .+||||++|.+..+-..|+..||-..+.|.-|+|..
T Consensus       207 Ak~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  207 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             HHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            45668999999999999999999999999999999976      358999999999999999999999999999999987


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus       287 ~v  288 (544)
T KOG0124|consen  287 CV  288 (544)
T ss_pred             cc
Confidence            63

>KOG0151|consensus

Probab=98.59  E-value=7.9e-08  Score=91.53  Aligned_cols=76  Identities=24%  Similarity=0.259  Sum_probs=69.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      ....++|||+||++.++++.|...|..||+|.+|+|+-         .+.+|||-|-+..+|+.|++.|+|+.+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45669999999999999999999999999998888753         246999999999999999999999999999999


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      +.|+.
T Consensus       251 ~gWgk  255 (877)
T KOG0151|consen  251 LGWGK  255 (877)
T ss_pred             ecccc
Confidence            99984

>KOG4212|consensus

Probab=98.54  E-value=1.4e-07  Score=85.51  Aligned_cols=76  Identities=18%  Similarity=0.271  Sum_probs=67.7

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..+..+.|||+|||++.|...|++-|..||.|....|+.. +.-+.|.|.++++|+.|+..|+|.++.|+.|.|.|+
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            4566789999999999999999999999999988888542 234699999999999999999999999999999874

>KOG0116|consensus

Probab=98.51  E-value=1.7e-07  Score=86.61  Aligned_cols=73  Identities=25%  Similarity=0.299  Sum_probs=62.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----C--CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----Y--GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~--~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ....|||+|||++++..+|+++|..||.|....|..    .  .+||||+|.+.++++.|+.+ +-..++++.|.|+--.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            345699999999999999999999999998777754    2  27999999999999999985 6788899999998643

>KOG4660|consensus

Probab=98.49  E-value=6.8e-08  Score=89.89  Aligned_cols=71  Identities=20%  Similarity=0.296  Sum_probs=65.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .....+|+|-|||..+++++|+.+|+.||+|..|+..+ ..+..||+|.+..+|+.|+++|++.++.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            34558999999999999999999999999999998877 458999999999999999999999999999887

>KOG0533|consensus

Probab=98.48  E-value=4.8e-07  Score=77.76  Aligned_cols=76  Identities=30%  Similarity=0.389  Sum_probs=68.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..+.|+|.|||+.++.+||+++|..||.+..+.+..+     .|.|-|.|...++|..|++.++|..++|+++.+.....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            3488999999999999999999999999998888763     27999999999999999999999999999999987654


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus       162 ~  162 (243)
T KOG0533|consen  162 P  162 (243)
T ss_pred             c
Confidence            4

>PF00076 RRM_1: RNA recognition motif

Probab=98.45  E-value=1.7e-07  Score=64.56  Aligned_cols=36  Identities=36%  Similarity=0.599  Sum_probs=33.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      |||+|||.++|+++|+++|++||.|..+.++.+..+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~   36 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSG   36 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTS
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccc
Confidence            799999999999999999999999999999998443

(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 ....

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

Probab=98.45  E-value=3.8e-07  Score=72.94  Aligned_cols=40  Identities=23%  Similarity=0.454  Sum_probs=37.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+++|||+|||+.+|+++|+++|++||.|.+|.|++++.
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~   71 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRE   71 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC
Confidence            4567999999999999999999999999999999999874

>KOG0128|consensus

Probab=98.44  E-value=1.4e-08  Score=98.34  Aligned_cols=110  Identities=25%  Similarity=0.318  Sum_probs=93.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +...++||+||++.+.+.+|...|..+|.+..+++.-      -+|+||++|.+++++.+|+.. ....+.|        
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f-~d~~~~g--------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF-RDSCFFG--------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh-hhhhhhh--------
Confidence            4457899999999999999999999999887766641      358999999999999999973 3222222        


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                                                                                 ...|||.|+||..|.+.|+.+
T Consensus       736 -----------------------------------------------------------K~~v~i~g~pf~gt~e~~k~l  756 (881)
T KOG0128|consen  736 -----------------------------------------------------------KISVAISGPPFQGTKEELKSL  756 (881)
T ss_pred             -----------------------------------------------------------hhhhheeCCCCCCchHHHHhh
Confidence                                                                       137999999999999999999


Q ss_pred             hhhcCCeeEEEEecCCCCCCCCCC
Q psy3343         248 FKKCGPIASVTVARKKDPKSPGQF  271 (274)
Q Consensus       248 F~~fG~I~~v~v~~~~~~~~~g~~  271 (274)
                      |+.+|.+.+.+++..++|++.|+.
T Consensus       757 ~~~~gn~~~~~~vt~r~gkpkg~a  780 (881)
T KOG0128|consen  757 ASKTGNVTSLRLVTVRAGKPKGKA  780 (881)
T ss_pred             ccccCCccccchhhhhccccccce
Confidence            999999999999999999988874

>KOG1456|consensus

Probab=98.36  E-value=1.7e-05  Score=70.91  Aligned_cols=159  Identities=16%  Similarity=0.079  Sum_probs=105.5

Q ss_pred             hcCCCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCC-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          92 EARSKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~-~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...+.+++.|-+|... ++.+-|..+|..||.|.+|.+++.+ |.|.|++.+....++|+..||+..+.|..|.|..+..
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence            4456799999999875 7889999999999999999999865 7999999999999999999999999999998887643


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccc--cCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDE--EREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      ........---.+....-+           .+..++.     +.....+..  ..-..++++|..-|.|..+||+.|.++
T Consensus       363 ~~v~~~~pflLpDgSpSfK-----------dys~SkN-----nRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i  426 (494)
T KOG1456|consen  363 NFVSPVQPFLLPDGSPSFK-----------DYSGSKN-----NRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGI  426 (494)
T ss_pred             cccccCCceecCCCCcchh-----------hcccccc-----cccCChhHhhcccccCCcceeEEecCCCccCHHHHHHH
Confidence            3211110000000000000           0000000     000000000  012346789999999999999999999


Q ss_pred             hhhcCC-eeEEEEecCCCCC
Q psy3343         248 FKKCGP-IASVTVARKKDPK  266 (274)
Q Consensus       248 F~~fG~-I~~v~v~~~~~~~  266 (274)
                      |..-+. ..+++|.--+.-+
T Consensus       427 ~nek~v~~~svkvFp~kser  446 (494)
T KOG1456|consen  427 CNEKDVPPTSVKVFPLKSER  446 (494)
T ss_pred             hhhcCCCcceEEeecccccc
Confidence            975432 5667776555433

>KOG0121|consensus

Probab=98.27  E-value=7.9e-07  Score=68.09  Aligned_cols=44  Identities=34%  Similarity=0.630  Sum_probs=39.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ..+++|||+||++.|+||+|.++|+.+|+|..|.+-.|+..+.|
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktp   77 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTP   77 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCc
Confidence            45789999999999999999999999999999988888887654

>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=98.25  E-value=2.7e-06  Score=60.49  Aligned_cols=70  Identities=21%  Similarity=0.335  Sum_probs=48.7

Q ss_pred             cEEEEeCCCCCCCHHHHH----HccccCC-CeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLK----ALFEPFG-DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~----~~F~~~G-~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +.|+|.|||.+.+...|+    +++.-+| .|..|    .++.|+|.|.+++.|.+|.+.|+|-.+.|..|.|.|.+..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            579999999998877655    5666664 56666    4689999999999999999999999999999999998644

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209|consensus

Probab=98.23  E-value=2.5e-06  Score=73.27  Aligned_cols=78  Identities=19%  Similarity=0.241  Sum_probs=70.1

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....+.+||+|+.+.+|.+++...|+.||.|..+.++++      ++|+||+|.+.+.+..|+. |+|..|.|+.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            3456799999999999999999999999999998888773      5799999999999999998 99999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      +...+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87544

>KOG0120|consensus

Probab=98.23  E-value=1.1e-06  Score=82.35  Aligned_cols=78  Identities=21%  Similarity=0.250  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+...+||++||...++.++.++...||.+....+..      ++||||.+|.++.....|+..|||..+.+..|.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            44668999999999999999999999999997777654      468999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      |..+
T Consensus       366 A~~g  369 (500)
T KOG0120|consen  366 AIVG  369 (500)
T ss_pred             hhcc
Confidence            8655

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.18  E-value=1.8e-06  Score=59.80  Aligned_cols=38  Identities=37%  Similarity=0.704  Sum_probs=33.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      |||+|||+++++++|+++|+.||.|..+++..++++..
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~   38 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQS   38 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeecccc
Confidence            79999999999999999999999999999999877543

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 ....

>KOG4205|consensus

Probab=98.10  E-value=4e-06  Score=74.81  Aligned_cols=74  Identities=23%  Similarity=0.304  Sum_probs=66.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...|||++||.+++++++++.|.+||.|..+.++.+      ++|+||.|.+.+++.+++. .....|.++.+.|..|.+
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccc
Confidence            459999999999999999999999999988887763      5899999999999999986 678899999999999875


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      +
T Consensus       176 k  176 (311)
T KOG4205|consen  176 K  176 (311)
T ss_pred             h
Confidence            5

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.08  E-value=2.3e-05  Score=58.07  Aligned_cols=73  Identities=14%  Similarity=0.219  Sum_probs=60.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccC--CCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeC----CeEEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPF--GDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFK----EVPLYL  164 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~----g~~l~v  164 (274)
                      ++|-|+|||...|.++|.+++...  |...-+.||-      +.|||||.|.+++.|..-.+.++|....    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            789999999999999999887653  6667777765      3589999999999999999999998875    456777


Q ss_pred             EEecC
Q psy3343         165 EWAPE  169 (274)
Q Consensus       165 ~~a~~  169 (274)
                      .||..
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88753

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0114|consensus

Probab=98.03  E-value=8e-06  Score=60.36  Aligned_cols=41  Identities=32%  Similarity=0.574  Sum_probs=36.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..++.|||+|||+++|.|+.-++|.+||.|.-++|--.++.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T   56 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET   56 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc
Confidence            34679999999999999999999999999999999776664

>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=98.03  E-value=1.4e-05  Score=60.39  Aligned_cols=69  Identities=28%  Similarity=0.324  Sum_probs=44.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCC-----eeCCeEEEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT-----KFKEVPLYLE  165 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~-----~~~g~~l~v~  165 (274)
                      +.|.|.+++..++.++|++.|+.||.|..|.+.+.-..|||.|.+++.|+.|+..+.-.     .+.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57889999999999999999999999999999887679999999999999999877544     4455544443

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

>KOG4676|consensus

Probab=98.00  E-value=7.6e-06  Score=73.48  Aligned_cols=167  Identities=15%  Similarity=0.143  Sum_probs=99.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC---------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY---------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~---------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...|.|.||.+++|.++++.||.-.|.|..+.|.++         ...|||-|.+...+..|.. |..+.|-++.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            458999999999999999999999999999988762         2489999999999998886 788888888877765


Q ss_pred             ecCCCCcccccc---cccccccccccccchhh-hhccchhhcccCCCCcccccccccccCCCC--CCceEEEeCCCCCCC
Q psy3343         167 APEGVFAEAKEK---SKGKEKEKNEEGEGEEE-KKENTAEEDNQQGVPEVEENVEEDEEREPE--PDTTLYIKNLNFNST  240 (274)
Q Consensus       167 a~~~~f~~~~~~---~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~lfV~NL~~~~t  240 (274)
                      ...........-   ......+.+...+..-+ +..+...+.. ....-...+..-+.+....  --.+++|.+|+..+-
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~-p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~  164 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHS-PNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAI  164 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCC-ccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhc
Confidence            543311111000   00000000000000000 0000000000 0000000000000000011  125899999999999


Q ss_pred             HHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         241 EDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       241 ee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++-++|..+|+|.++++.-+.+
T Consensus       165 l~e~~e~f~r~Gev~ya~~ask~~  188 (479)
T KOG4676|consen  165 LPESGESFERKGEVSYAHTASKSR  188 (479)
T ss_pred             chhhhhhhhhcchhhhhhhhccCC
Confidence            999999999999999998876655

>smart00362 RRM_2 RNA recognition motif

Probab=97.95  E-value=1.8e-05  Score=53.71  Aligned_cols=35  Identities=37%  Similarity=0.679  Sum_probs=33.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +|||+|||..+++++|+++|++||.|..+.+..++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~   35 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT   35 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC
Confidence            58999999999999999999999999999999876

>KOG1457|consensus

Probab=97.92  E-value=9.1e-06  Score=68.00  Aligned_cols=65  Identities=20%  Similarity=0.283  Sum_probs=55.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC--eEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--ITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~--~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      +-..+|||-||.++++|++|+.+|+.|-....++|...+  ..||++|++.+.|..|+..|+|..+.
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            344799999999999999999999999877777776533  47999999999999999999997653

>KOG0112|consensus

Probab=97.90  E-value=5.2e-06  Score=81.33  Aligned_cols=116  Identities=17%  Similarity=0.241  Sum_probs=96.7

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.+.+||++||+..+++.+|+..|..+|.|.+|.|...     -.||||.|.+...+..|.-.+.+..|..-.+.+.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            4567799999999999999999999999999999988652     25999999999999999998998877655555544


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      ...                                                     ...+.+.++|+.|+..+....|..
T Consensus       448 G~~-----------------------------------------------------kst~ttr~~sgglg~w~p~~~l~r  474 (975)
T KOG0112|consen  448 GQP-----------------------------------------------------KSTPTTRLQSGGLGPWSPVSRLNR  474 (975)
T ss_pred             ccc-----------------------------------------------------ccccceeeccCCCCCCChHHHHHH
Confidence            311                                                     123567899999999999999999


Q ss_pred             HhhhcCCeeEEEEe
Q psy3343         247 HFKKCGPIASVTVA  260 (274)
Q Consensus       247 ~F~~fG~I~~v~v~  260 (274)
                      .|..||.|..|.+-
T Consensus       475 ~fd~fGpir~Idy~  488 (975)
T KOG0112|consen  475 EFDRFGPIRIIDYR  488 (975)
T ss_pred             HhhccCcceeeecc
Confidence            99999999987653

>KOG1456|consensus

Probab=97.89  E-value=8.1e-05  Score=66.69  Aligned_cols=128  Identities=19%  Similarity=0.259  Sum_probs=95.0

Q ss_pred             hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEEec
Q psy3343          91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAP  168 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~a~  168 (274)
                      .....+.+|.|++|-..+++.+|-+..+.||.|..+...+.+..|.|+|++.+.|+.++..-..  ..+.|+.-.+.|+.
T Consensus        26 hk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NySt  105 (494)
T KOG1456|consen   26 HKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYST  105 (494)
T ss_pred             CCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccch
Confidence            3445568999999999999999999999999999999988888999999999999998864322  34556665555543


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEE--EeCCCCCCCHHHHHH
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLY--IKNLNFNSTEDSIRR  246 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf--V~NL~~~~tee~L~~  246 (274)
                      .++....                                            .++...+...|.  |-|--+.+|-+-|..
T Consensus       106 sq~i~R~--------------------------------------------g~es~~pN~VLl~TIlNp~YpItvDVly~  141 (494)
T KOG1456|consen  106 SQCIERP--------------------------------------------GDESATPNKVLLFTILNPQYPITVDVLYT  141 (494)
T ss_pred             hhhhccC--------------------------------------------CCCCCCCCeEEEEEeecCccccchhhhhh
Confidence            2211000                                            011122334444  455557889999999


Q ss_pred             HhhhcCCeeEEEEecC
Q psy3343         247 HFKKCGPIASVTVARK  262 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~  262 (274)
                      ++.+.|+|.+|.|+++
T Consensus       142 Icnp~GkVlRIvIfkk  157 (494)
T KOG1456|consen  142 ICNPQGKVLRIVIFKK  157 (494)
T ss_pred             hcCCCCceEEEEEEec
Confidence            9999999999999987

>KOG2193|consensus

Probab=97.88  E-value=4.2e-06  Score=75.77  Aligned_cols=111  Identities=14%  Similarity=0.155  Sum_probs=87.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC-CeeCCeEEEEEEecCCCCccc
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY-TKFKEVPLYLEWAPEGVFAEA  175 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~-~~~~g~~l~v~~a~~~~f~~~  175 (274)
                      ..+|++||.+.++..+|..+|...---.+-.+....||+||.+.+...|.+|++.++| ..+.|.++.+++...+     
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k-----   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK-----   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH-----
Confidence            4689999999999999999997541111111111347999999999999999999999 5688999888876432     


Q ss_pred             ccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCee
Q psy3343         176 KEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA  255 (274)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~  255 (274)
                       .                                               ...+.+-|+|+|+..-++.|..+..+||.+.
T Consensus        77 -k-----------------------------------------------qrsrk~Qirnippql~wevld~Ll~qyg~ve  108 (584)
T KOG2193|consen   77 -K-----------------------------------------------QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVE  108 (584)
T ss_pred             -H-----------------------------------------------HHhhhhhHhcCCHHHHHHHHHHHHhccCCHh
Confidence             0                                               0124588999999999999999999999999


Q ss_pred             EEEEe
Q psy3343         256 SVTVA  260 (274)
Q Consensus       256 ~v~v~  260 (274)
                      .|..+
T Consensus       109 ~~eqv  113 (584)
T KOG2193|consen  109 NCEQV  113 (584)
T ss_pred             Hhhhh
Confidence            98763

>KOG0126|consensus

Probab=97.85  E-value=3.8e-06  Score=68.13  Aligned_cols=40  Identities=28%  Similarity=0.468  Sum_probs=37.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .++-|||+|||+..|+-+|.-+|++||.|+.|.+++|++.
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~T   73 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKT   73 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCC
Confidence            3568999999999999999999999999999999999753

>KOG4206|consensus

Probab=97.82  E-value=6.8e-05  Score=62.95  Aligned_cols=75  Identities=28%  Similarity=0.402  Sum_probs=67.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a  167 (274)
                      .+++..+|+.|||..++.+.+..+|.+|.....|++.+ -++.|||+|.+...|..|...|.+..+. ...+.|.++
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            45678999999999999999999999999999999887 5689999999999999999999998887 677777765

>KOG0120|consensus

Probab=97.80  E-value=5e-05  Score=71.43  Aligned_cols=149  Identities=17%  Similarity=0.264  Sum_probs=105.2

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccC-----------CC-eeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPF-----------GD-LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~-----------G~-i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      ..+....++|+++|+.++++..-.+|..-           |+ +..+.+...++|||++|.+.+.|..|+. +++.-+.|
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~-~~~~~f~g  249 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMA-LDGIIFEG  249 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhc-ccchhhCC
Confidence            45667899999999999999999988763           32 7788888888999999999999999996 89999999


Q ss_pred             eEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCC
Q psy3343         160 VPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNS  239 (274)
Q Consensus       160 ~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~  239 (274)
                      +++.+..-....-.+.....-..    +.           .+...             ..-.........+||+|||...
T Consensus       250 ~~~~~~r~~d~~~~p~~~~~~~~----~~-----------~~~~~-------------~~~t~~~~~~~ki~v~~lp~~l  301 (500)
T KOG0120|consen  250 RPLKIRRPHDYQPVPGITLSPSQ----LG-----------KVGLL-------------PASTDVPDSPNKIFVGGLPLYL  301 (500)
T ss_pred             CCceecccccccCCccchhhhcc----cc-----------ccCCc-------------ccccCcccccchhhhccCcCcc
Confidence            98877543222000000000000    00           00000             0001123345689999999999


Q ss_pred             CHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         240 TEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       240 tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ++.+++++...||.+...+++.+.+ |.+.|
T Consensus       302 ~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg  332 (500)
T KOG0120|consen  302 TEDQVKELLDSFGPLKAFRLVKDSATGNSKG  332 (500)
T ss_pred             CHHHHHHHHHhcccchhheeecccccccccc
Confidence            9999999999999999999999976 34444

>KOG4210|consensus

Probab=97.78  E-value=3.1e-05  Score=68.71  Aligned_cols=130  Identities=18%  Similarity=0.170  Sum_probs=91.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCC-eeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYT-KFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~-~~~g~~l~v~~  166 (274)
                      ...+++|++++...+.+.+...++..+|......+..      .++++.+.|...+.+..|+. +.+. .+.++.+....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~-~s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALE-ESGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHH-hhhccccccccccCcc
Confidence            4679999999999999999999999999765555433      56899999999999999997 4553 44454443333


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceE-EEeCCCCCCCHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTL-YIKNLNFNSTEDSIR  245 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-fV~NL~~~~tee~L~  245 (274)
                      .....   .....      ...                                .....+..++ +|+||++.+++++|+
T Consensus       165 ~~~~~---~~~~n------~~~--------------------------------~~~~~~s~~~~~~~~~~f~~~~d~~~  203 (285)
T KOG4210|consen  165 NTRRG---LRPKN------KLS--------------------------------RLSSGPSDTIFFVGELDFSLTRDDLK  203 (285)
T ss_pred             ccccc---ccccc------hhc--------------------------------ccccCccccceeecccccccchHHHh
Confidence            22110   00000      000                                0011223344 499999999999999


Q ss_pred             HHhhhcCCeeEEEEecCCCC
Q psy3343         246 RHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       246 ~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .+|.++|.|..++++.++..
T Consensus       204 ~~~~~~~~i~~~r~~~~~~s  223 (285)
T KOG4210|consen  204 EHFVSSGEITSVRLPTDEES  223 (285)
T ss_pred             hhccCcCcceeeccCCCCCc
Confidence            99999999999999988753

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

Probab=97.73  E-value=5.3e-05  Score=65.07  Aligned_cols=43  Identities=40%  Similarity=0.749  Sum_probs=38.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      .++|||+|||+.+|+++|.++|.+||.|..++|..++ .++..|
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g  158 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRG  158 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCc
Confidence            6899999999999999999999999999999999996 455444

>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=97.70  E-value=8.4e-05  Score=50.61  Aligned_cols=37  Identities=41%  Similarity=0.663  Sum_probs=34.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~   37 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT   37 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC
Confidence            4899999999999999999999999999999988765

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).

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

Probab=97.66  E-value=9.9e-05  Score=48.50  Aligned_cols=52  Identities=19%  Similarity=0.318  Sum_probs=44.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHH
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAF  149 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~  149 (274)
                      +.|-|.+.|++..+ .+...|..||.|..+.++....+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            56788999977654 55558999999999999977789999999999999985

>KOG4211|consensus

Probab=97.66  E-value=0.00044  Score=64.10  Aligned_cols=73  Identities=14%  Similarity=0.241  Sum_probs=56.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeE-EEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...+|-+++||+.+|++||.++|+..-.+.. |.++.     ..|-|||+|++.+.|++|+.. +...|..|-|.|-.+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            4588999999999999999999997654433 43443     236899999999999999974 6666777777776553

>KOG0106|consensus

Probab=97.66  E-value=3e-05  Score=65.40  Aligned_cols=73  Identities=29%  Similarity=0.351  Sum_probs=65.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..+.+++.|.|++..+...+|.+.|.++|.+....+  ..+++||+|...++|..|+..|++..+.++.|.+...
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            567799999999999999999999999999855555  3468999999999999999999999999999999554

>KOG0113|consensus

Probab=97.61  E-value=8.5e-05  Score=64.71  Aligned_cols=45  Identities=40%  Similarity=0.804  Sum_probs=40.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      .+-+||||.-|+++|+|..|+..|+.||+|..++|++++ .|++.|
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskG  144 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKG  144 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccc
Confidence            567899999999999999999999999999999999995 555555

>KOG3152|consensus

Probab=97.58  E-value=3.7e-05  Score=65.61  Aligned_cols=70  Identities=29%  Similarity=0.492  Sum_probs=61.7

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---C--------Ce-------EEEEEecCHHHHHHHHHHhC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---Y--------GI-------TGLVEFLQKNQAKAAFNSLA  153 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~--------~~-------~afV~F~~~~~A~~A~~~l~  153 (274)
                      ..+...+||++|||+.+...-|+++|+.||.|-+|.|-+   +        ++       -|.|+|.+...|+.+...||
T Consensus        70 kkrk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Ln  149 (278)
T KOG3152|consen   70 KKRKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLN  149 (278)
T ss_pred             hhccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhC
Confidence            445668999999999999999999999999999999976   1        11       28999999999999999999


Q ss_pred             CCeeCCeE
Q psy3343         154 YTKFKEVP  161 (274)
Q Consensus       154 ~~~~~g~~  161 (274)
                      +..|.|+.
T Consensus       150 n~~Iggkk  157 (278)
T KOG3152|consen  150 NTPIGGKK  157 (278)
T ss_pred             CCccCCCC
Confidence            99999864

>KOG0226|consensus

Probab=97.55  E-value=7.8e-05  Score=63.62  Aligned_cols=75  Identities=16%  Similarity=0.121  Sum_probs=63.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....-+||++.|..+++.+-|-..|.+|-.-....+.+      ++||+||.|.++.++..|++.|+|..++.++|.+.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            44568999999999999999999999986543333333      569999999999999999999999999999988764


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      .
T Consensus       267 S  267 (290)
T KOG0226|consen  267 S  267 (290)
T ss_pred             h
Confidence            4

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.45  E-value=0.00031  Score=62.24  Aligned_cols=74  Identities=14%  Similarity=0.288  Sum_probs=61.8

Q ss_pred             CcEEEEeCCCCCCCHHH----H--HHccccCCCeeEEEeeCC-------Ce-E-EEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3343          96 KRIILVKNLPYRTLPTD----L--KALFEPFGDLGRVLVPPY-------GI-T-GLVEFLQKNQAKAAFNSLAYTKFKEV  160 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~----l--~~~F~~~G~i~~v~l~~~-------~~-~-afV~F~~~~~A~~A~~~l~~~~~~g~  160 (274)
                      ..-+||-+||+.+..++    |  .++|.+||.|..|.+.+.       .+ + .||+|.+.++|..||...+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            46789999999876666    2  379999999999998761       12 2 39999999999999999999999999


Q ss_pred             EEEEEEecC
Q psy3343         161 PLYLEWAPE  169 (274)
Q Consensus       161 ~l~v~~a~~  169 (274)
                      .|+..|...
T Consensus       194 ~lkatYGTT  202 (480)
T COG5175         194 VLKATYGTT  202 (480)
T ss_pred             eEeeecCch
Confidence            999988753

>smart00360 RRM RNA recognition motif

Probab=97.42  E-value=0.00022  Score=47.93  Aligned_cols=33  Identities=42%  Similarity=0.619  Sum_probs=30.7

Q ss_pred             EeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         232 IKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       232 V~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      |+|||..+++++|+++|++||.|..+.+..++.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~   33 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKD   33 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCC
Confidence            679999999999999999999999999998764

>KOG0122|consensus

Probab=97.30  E-value=0.00032  Score=59.61  Aligned_cols=40  Identities=33%  Similarity=0.567  Sum_probs=37.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..++|-|.||+.++++++|.++|.+||.|.+|.|.+|+..
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~T  227 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKET  227 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEcccc
Confidence            4578999999999999999999999999999999999863

>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=97.29  E-value=0.0011  Score=49.41  Aligned_cols=71  Identities=17%  Similarity=0.152  Sum_probs=53.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEE-------------eeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVL-------------VPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP  161 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~-------------l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~  161 (274)
                      +.+.|.|-+.|+. ....+.+.|++||.|.+..             .+..+++..|.|.++.+|.+|+. -||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3567889999988 5667888999999998775             45566799999999999999997 6999999864


Q ss_pred             -EEEEEe
Q psy3343         162 -LYLEWA  167 (274)
Q Consensus       162 -l~v~~a  167 (274)
                       +-|.|+
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence             446665

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.

>KOG1365|consensus

Probab=97.29  E-value=0.00092  Score=60.27  Aligned_cols=151  Identities=16%  Similarity=0.225  Sum_probs=87.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccC----CCeeEEEeeC--CC---eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPF----GDLGRVLVPP--YG---ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~l~~--~~---~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...|-.++||++.++.|+.++|.+-    |....|.+..  ++   |=|||.|..+++|..|+.. +...+.-|  ||+.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqR--YIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQR--YIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHH--HHHH
Confidence            3567778999999999999999742    2333444332  32   6799999999999999974 33223222  2221


Q ss_pred             ecCCCCccccccccc--ccc--cccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHH
Q psy3343         167 APEGVFAEAKEKSKG--KEK--EKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTED  242 (274)
Q Consensus       167 a~~~~f~~~~~~~~~--~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee  242 (274)
                      .     .....+-..  .+.  ..+-..    .       ...      .-...-...........+|.+++||+..+.|
T Consensus       238 F-----RSTaaEvqqvlnr~~s~pLi~~----~-------~sp------~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvE  295 (508)
T KOG1365|consen  238 F-----RSTAAEVQQVLNREVSEPLIPG----L-------TSP------LLPGGPARLVPPTRSKDCVRLRGLPYEATVE  295 (508)
T ss_pred             H-----HHhHHHHHHHHHhhccccccCC----C-------CCC------CCCCCccccCCCCCCCCeeEecCCChhhhHH
Confidence            1     111000000  000  000000    0       000      0000000001111224589999999999999


Q ss_pred             HHHHHhhhcCC-eeE--EEEecCCCCCCCCCC
Q psy3343         243 SIRRHFKKCGP-IAS--VTVARKKDPKSPGQF  271 (274)
Q Consensus       243 ~L~~~F~~fG~-I~~--v~v~~~~~~~~~g~~  271 (274)
                      +|.++|..|.. |..  |.++.+..|+..|+.
T Consensus       296 dIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeA  327 (508)
T KOG1365|consen  296 DILDFLGDFATDIRFQGVHMVLNGQGRPSGEA  327 (508)
T ss_pred             HHHHHHHHHhhhcccceeEEEEcCCCCcChhh
Confidence            99999998865 555  889999999988874

>KOG4307|consensus

Probab=97.26  E-value=0.00088  Score=64.55  Aligned_cols=72  Identities=17%  Similarity=0.254  Sum_probs=62.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCe-eEEEeeC-CC----eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPP-YG----ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i-~~v~l~~-~~----~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..++|-|.|+|+.++-+||.++|.-|-.+ .+|++.. +.    |-|.|-|++.++|..|+..|+++.|..+.++|..
T Consensus       866 Gp~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  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            33699999999999999999999999766 5566655 22    5799999999999999999999999999998863

>KOG0115|consensus

Probab=97.23  E-value=0.00074  Score=57.81  Aligned_cols=72  Identities=22%  Similarity=0.272  Sum_probs=63.5

Q ss_pred             HHHHHHHHHhCCCeeCCeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccC
Q psy3343         143 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEER  222 (274)
Q Consensus       143 ~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  222 (274)
                      .-|..|-..|.+....++.|.|.|+..                                                     
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-----------------------------------------------------   31 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-----------------------------------------------------   31 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-----------------------------------------------------
Confidence            456777788999999999999999841                                                     


Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL  272 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g~~l  272 (274)
                           ..|||.||+.-++.+.|.+-|+.||+|.+..+..|..++..|+-+
T Consensus        32 -----a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~   76 (275)
T KOG0115|consen   32 -----AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGI   76 (275)
T ss_pred             -----ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccch
Confidence                 479999999999999999999999999999999999888777643

>KOG1548|consensus

Probab=97.22  E-value=0.002  Score=57.38  Aligned_cols=77  Identities=22%  Similarity=0.236  Sum_probs=63.1

Q ss_pred             hhcCCCcEEEEeCCCC----CCC-------HHHHHHccccCCCeeEEEee--CCCeEEEEEecCHHHHHHHHHHhCCCee
Q psy3343          91 VEARSKRIILVKNLPY----RTL-------PTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKF  157 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~----~~t-------e~~l~~~F~~~G~i~~v~l~--~~~~~afV~F~~~~~A~~A~~~l~~~~~  157 (274)
                      ...+..++|.++|+=.    ..+       .++|.+-.++||.|.+|.+.  ...|.+-|.|.+.++|..|++.|+|..|
T Consensus       260 sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  260 SKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             ccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            3456779999999843    233       45666778999999999886  3568999999999999999999999999


Q ss_pred             CCeEEEEEEe
Q psy3343         158 KEVPLYLEWA  167 (274)
Q Consensus       158 ~g~~l~v~~a  167 (274)
                      .||.|.....
T Consensus       340 dgRql~A~i~  349 (382)
T KOG1548|consen  340 DGRQLTASIW  349 (382)
T ss_pred             cceEEEEEEe
Confidence            9999887744

>KOG0125|consensus

Probab=97.18  E-value=0.00058  Score=60.39  Aligned_cols=44  Identities=18%  Similarity=0.351  Sum_probs=38.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      .....+|+|.||||...|-||+.+|++||+|.+|.|+.+..|.+
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSK  136 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSK  136 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCC
Confidence            33456999999999999999999999999999999998876643

>KOG4210|consensus

Probab=97.02  E-value=0.00043  Score=61.49  Aligned_cols=73  Identities=27%  Similarity=0.314  Sum_probs=64.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +..+|+||++.+++++|+..|..+|.|..++++..      .+||+|.|.....+..++.. +...+.++++.+++....
T Consensus       186 ~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  186 TIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             cceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            44449999999999999999999999999999872      47999999999999999986 788899999999987543

>KOG1365|consensus

Probab=97.00  E-value=0.006  Score=55.15  Aligned_cols=143  Identities=15%  Similarity=0.221  Sum_probs=94.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccC----CCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPF----GDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..++..|-.++||+..+..+|-.+|.-.    |-+.-|....  -.|.|.|.|.+++.-..|++. +...+.++.|.|-.
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYk  135 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYK  135 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeec
Confidence            3456778888999999999999999753    2222221111  236899999999999999874 55556677777766


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +....|..-......+....                                   ........|..++|||++|+.++.+
T Consensus       136 a~ge~f~~iagg~s~e~~~f-----------------------------------lsk~~qvivRmRGLPfdat~~dVv~  180 (508)
T KOG1365|consen  136 ATGEEFLKIAGGTSNEAAPF-----------------------------------LSKENQVIVRMRGLPFDATALDVVE  180 (508)
T ss_pred             cCchhheEecCCccccCCCC-----------------------------------CCcccceEEEecCCCCCcchHHHHH
Confidence            64442222111111000000                                   0111234788899999999999999


Q ss_pred             Hhhhc----CCeeEEEEecCCCCCCCCCC
Q psy3343         247 HFKKC----GPIASVTVARKKDPKSPGQF  271 (274)
Q Consensus       247 ~F~~f----G~I~~v~v~~~~~~~~~g~~  271 (274)
                      +|.+-    |....+-.++.+||+..|..
T Consensus       181 FF~~~cpv~~g~egvLFV~rpdgrpTGdA  209 (508)
T KOG1365|consen  181 FFGPPCPVTGGTEGVLFVTRPDGRPTGDA  209 (508)
T ss_pred             hcCCCCcccCCccceEEEECCCCCcccce
Confidence            99632    46678888899999988864

>KOG0153|consensus

Probab=96.88  E-value=0.0014  Score=58.44  Aligned_cols=43  Identities=37%  Similarity=0.500  Sum_probs=37.3

Q ss_pred             cCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       221 ~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .++...-++|||++|...+++.+|+++|-+||+|.++++...+
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~  264 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK  264 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc
Confidence            3344556799999999999999999999999999999998654

>KOG0533|consensus

Probab=96.82  E-value=0.0017  Score=56.03  Aligned_cols=43  Identities=21%  Similarity=0.427  Sum_probs=39.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      .+.|+|.|||+.|++++|+++|..||.+..+-|-.+++|.+.|
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~G  125 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLG  125 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCc
Confidence            3789999999999999999999999999999999999987765

>KOG2314|consensus

Probab=96.80  E-value=0.0025  Score=60.13  Aligned_cols=70  Identities=20%  Similarity=0.291  Sum_probs=56.5

Q ss_pred             CcEEEEeCCCCCC------CHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEE
Q psy3343          96 KRIILVKNLPYRT------LPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLY  163 (274)
Q Consensus        96 ~~~l~V~nLp~~~------te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~  163 (274)
                      .+.|+|-|+|---      -..-|..+|+++|+|..+.+|.     .+||.|++|.+..+|+.|++.|+|..|+ .+.+.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            4789999998521      1234667999999999999986     3589999999999999999999999887 45555


Q ss_pred             EE
Q psy3343         164 LE  165 (274)
Q Consensus       164 v~  165 (274)
                      |.
T Consensus       138 v~  139 (698)
T KOG2314|consen  138 VR  139 (698)
T ss_pred             ee
Confidence            54

>KOG0108|consensus

Probab=96.80  E-value=0.0014  Score=61.31  Aligned_cols=38  Identities=16%  Similarity=0.531  Sum_probs=36.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      +.|||+|+|+++++++|..+|+..|.|.+++++-|+.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~t   56 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRET   56 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccC
Confidence            89999999999999999999999999999999999864

>KOG2202|consensus

Probab=96.72  E-value=0.00067  Score=58.11  Aligned_cols=60  Identities=22%  Similarity=0.284  Sum_probs=50.3

Q ss_pred             HHHHHccc-cCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343         111 TDLKALFE-PFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus       111 ~~l~~~F~-~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +++...|+ +||.|..+.+..+     .|-++|.|...++|.+|+..||+..|.|++|+.++.+.-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            34445555 8999999877663     367999999999999999999999999999999998743

>KOG4207|consensus

Probab=96.61  E-value=0.0027  Score=52.86  Aligned_cols=42  Identities=29%  Similarity=0.558  Sum_probs=38.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      .-++|.|-||-+.||.++|+.+|++||.|-.|.|++|+..+.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~   53 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQ   53 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceeccccccccc
Confidence            346999999999999999999999999999999999987653

>KOG1855|consensus

Probab=96.57  E-value=0.0022  Score=58.64  Aligned_cols=62  Identities=23%  Similarity=0.289  Sum_probs=54.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-------------------CeEEEEEecCHHHHHHHHHHhC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-------------------GITGLVEFLQKNQAKAAFNSLA  153 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-------------------~~~afV~F~~~~~A~~A~~~l~  153 (274)
                      ....++|.+-|||.+-.-+-|.++|+.+|.|..|+|...                   +-+|+|+|...+.|.+|.+.|+
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346799999999999988999999999999999999652                   1379999999999999999775


Q ss_pred             C
Q psy3343         154 Y  154 (274)
Q Consensus       154 ~  154 (274)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>KOG0415|consensus

Probab=96.52  E-value=0.0027  Score=56.80  Aligned_cols=42  Identities=26%  Similarity=0.481  Sum_probs=38.7

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+|...|||=-|++-||+++|.-+|+.||.|.+|.|++|..
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~k  276 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRK  276 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEeccc
Confidence            456778999999999999999999999999999999999875

>KOG0116|consensus

Probab=96.42  E-value=0.0034  Score=58.45  Aligned_cols=37  Identities=24%  Similarity=0.451  Sum_probs=34.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+|||+|||++++..+|+++|.+||.|....|....
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~  324 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRS  324 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEec
Confidence            4469999999999999999999999999999998765

>KOG1995|consensus

Probab=96.38  E-value=0.0031  Score=56.48  Aligned_cols=78  Identities=19%  Similarity=0.155  Sum_probs=64.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--------EEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--------VLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      .....+|||-+||..+++.+|..+|.++|.|..        |.|-+      .++-|.|.|.++..|+.|+..+++..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            455689999999999999999999999997722        11211      3478999999999999999999999999


Q ss_pred             CeEEEEEEecCC
Q psy3343         159 EVPLYLEWAPEG  170 (274)
Q Consensus       159 g~~l~v~~a~~~  170 (274)
                      +.+|.|..|...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999888777533

>KOG0105|consensus

Probab=96.38  E-value=0.011  Score=48.46  Aligned_cols=75  Identities=31%  Similarity=0.367  Sum_probs=64.1

Q ss_pred             hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeC--CeEEEEEE
Q psy3343          91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK--EVPLYLEW  166 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~--g~~l~v~~  166 (274)
                      +..++.-.|.|.+||++.+-+||+++...-|.|+...+-+++ ++.|+|...++-+-|+..|....+.  |-..++..
T Consensus       110 psrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg-~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  110 PSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG-VGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             cccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc-ceeeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            456777899999999999999999999999999988887774 8999999999999999999987765  44444443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.32  E-value=0.032  Score=39.86  Aligned_cols=56  Identities=23%  Similarity=0.396  Sum_probs=42.5

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY  154 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~  154 (274)
                      ....+|. +|......||.++|+.||.|.-- .. +-..|||...+.+.|..|+..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~Vs-Wi-~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVS-WI-NDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEE-EE-CTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEE-EE-cCCcEEEEeecHHHHHHHHHHhcc
Confidence            4667776 99999999999999999987433 33 345899999999999999998864

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG0112|consensus

Probab=96.24  E-value=0.0048  Score=61.17  Aligned_cols=75  Identities=13%  Similarity=0.096  Sum_probs=68.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~  168 (274)
                      ...+.+|+++|+.++....|...|..||.|..|.+.....||+|.|.+...|+.|++.|-|..|.+  +.|.|.++.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            345899999999999999999999999999998887766799999999999999999999999986  678998885

>KOG0151|consensus

Probab=96.15  E-value=0.0052  Score=59.52  Aligned_cols=40  Identities=35%  Similarity=0.532  Sum_probs=36.7

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       222 ~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ...+.+++|||+||++.++++.|...|..||+|.+++|+.
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimw  208 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMW  208 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeec
Confidence            4456788999999999999999999999999999999985

>KOG0130|consensus

Probab=96.03  E-value=0.0077  Score=46.89  Aligned_cols=42  Identities=14%  Similarity=0.346  Sum_probs=37.6

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ....+..|||.++...+|++++.+.|..||+|..+.+-.|+.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRR  109 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRR  109 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccc
Confidence            345678999999999999999999999999999999987753

>KOG1996|consensus

Probab=95.95  E-value=0.019  Score=50.33  Aligned_cols=73  Identities=19%  Similarity=0.232  Sum_probs=55.8

Q ss_pred             CcEEEEeCCC--CCCC---HHHHHHccccCCCeeEEEeeCC------C-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          96 KRIILVKNLP--YRTL---PTDLKALFEPFGDLGRVLVPPY------G-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        96 ~~~l~V~nLp--~~~t---e~~l~~~F~~~G~i~~v~l~~~------~-~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      +.+|+++|.=  -.++   ++++.+-+.+||.|..|.|...      . .-.||+|...++|.+|+-.|||..|.||.+.
T Consensus       281 tkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  281 TKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             hHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            3445555542  2233   4578889999999999887541      1 2479999999999999999999999999988


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      ..|-.
T Consensus       361 A~Fyn  365 (378)
T KOG1996|consen  361 ACFYN  365 (378)
T ss_pred             heecc
Confidence            77653

>KOG4307|consensus

Probab=95.88  E-value=0.038  Score=53.66  Aligned_cols=163  Identities=11%  Similarity=-0.002  Sum_probs=92.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccC-CCeeEEEee---CC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPF-GDLGRVLVP---PY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~l~---~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..+.+-+++.+++....|++++|... -.-..+...   +. .|-++|.|....++.+|+.. +...+..|.+.+..+-.
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcccccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            44667778999999999999999642 221222222   22 37899999999999999974 55666777777754432


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      .-|................           ...+..... ...+.-.......-...+.+|||+.||+.+++..+.+.|.
T Consensus       389 ~~~~~a~~~~~~~~~~~~~-----------~~hg~p~~~-pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~  456 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQ-----------NNHGRPIAP-PRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFM  456 (944)
T ss_pred             cccccCccccccCCCCccc-----------ccCCCCCCC-cccccCCCCCCCCCCCccceEEeccCCccccccchhhhhh
Confidence            2111110000000000000           000000000 0000000000011223466999999999999999999998


Q ss_pred             hcCCeeE-EEEecCCCCCCCCC
Q psy3343         250 KCGPIAS-VTVARKKDPKSPGQ  270 (274)
Q Consensus       250 ~fG~I~~-v~v~~~~~~~~~g~  270 (274)
                      ..-.|+. |.|..-++++..+.
T Consensus       457 ~~~~Ved~I~lt~~P~~~~~~~  478 (944)
T KOG4307|consen  457 GAAAVEDFIELTRLPTDLLRPA  478 (944)
T ss_pred             hhhhhhheeEeccCCcccccch
Confidence            7767766 77777777665544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.79  E-value=0.022  Score=44.80  Aligned_cols=75  Identities=15%  Similarity=0.139  Sum_probs=56.9

Q ss_pred             hcCCCcEEEEeCCCCCC----CHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRT----LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~----te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...+-.+|.|+=|..++    +-..+...++.||+|.+|.+. .+..|.|.|.+..+|-+|+.++.. ..-|..+++.|-
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            34555788887665554    333455667889999999764 556899999999999999998765 667888899886


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>KOG0132|consensus

Probab=95.75  E-value=0.0084  Score=58.70  Aligned_cols=36  Identities=25%  Similarity=0.399  Sum_probs=33.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      .++||||+.|+..+++++|..+|+.||.|.+|.+.-
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~  455 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP  455 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc
Confidence            467999999999999999999999999999998753

>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=95.71  E-value=0.041  Score=45.39  Aligned_cols=79  Identities=13%  Similarity=0.177  Sum_probs=51.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHcccc-CCCe---eEEE--eeC--C----CeEEEEEecCHHHHHHHHHHhCCCeeCC--
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEP-FGDL---GRVL--VPP--Y----GITGLVEFLQKNQAKAAFNSLAYTKFKE--  159 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i---~~v~--l~~--~----~~~afV~F~~~~~A~~A~~~l~~~~~~g--  159 (274)
                      .....|.|++||+++|++++.+.++. ++.-   ..+.  ...  .    -.-|||.|.+.+++..-...++|..|.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34578999999999999999998887 6655   3333  111  0    1369999999999999999999977643  


Q ss_pred             ---eEEEEEEecCCCC
Q psy3343         160 ---VPLYLEWAPEGVF  172 (274)
Q Consensus       160 ---~~l~v~~a~~~~f  172 (274)
                         .+-.|++|+-..+
T Consensus        85 g~~~~~~VE~Apyqk~  100 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQKV  100 (176)
T ss_dssp             S-EEEEEEEE-SS---
T ss_pred             CCCcceeEEEcchhcc
Confidence               3568899976643

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.

>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=95.67  E-value=0.013  Score=44.18  Aligned_cols=36  Identities=22%  Similarity=0.377  Sum_probs=23.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      |+.|+|.+++..++.++|+++|++||.|.+|.+.+.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G   36 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG   36 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC
Confidence            468999999999999999999999999999988753

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

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.60  E-value=0.062  Score=42.66  Aligned_cols=75  Identities=17%  Similarity=0.148  Sum_probs=51.3

Q ss_pred             cCCCcEEEEeCCCC-----CCCH----HHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPY-----RTLP----TDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~-----~~te----~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .++..+|.|.=+.+     ..-.    .+|.+.|..||.+.-+++..  +.-+|+|.+-++|-+|+. ++|..+.|+.|.
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals-~dg~~v~g~~l~  100 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS-LDGIQVNGRTLK  100 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH-GCCSEETTEEEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc-cCCcEECCEEEE
Confidence            34456666664441     1222    36778899999987777764  367999999999999997 999999999999


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |..-.+.
T Consensus       101 i~LKtpd  107 (146)
T PF08952_consen  101 IRLKTPD  107 (146)
T ss_dssp             EEE----
T ss_pred             EEeCCcc
Confidence            9865433

; PDB: 1UFW_A 2DNR_A.

>KOG2416|consensus

Probab=94.96  E-value=0.021  Score=54.45  Aligned_cols=77  Identities=14%  Similarity=0.175  Sum_probs=63.5

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHcccc-CCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCee---CCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEP-FGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF---KEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~---~g~~l~v~~a  167 (274)
                      -....++|+|.||---.|.-+|+.++.+ .|.|....|.+-+..|||.|.+.++|.....+|+|...   +++.|.+.|.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeec
Confidence            3455699999999888999999999995 55566665555567899999999999999999999765   4577888887


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus       520 ~  520 (718)
T KOG2416|consen  520 R  520 (718)
T ss_pred             c
Confidence            5

>KOG0129|consensus

Probab=94.84  E-value=0.061  Score=50.59  Aligned_cols=57  Identities=23%  Similarity=0.304  Sum_probs=51.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccc-cCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHH
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFE-PFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNS  151 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~-~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~  151 (274)
                      ..+|||||+||--++.++|-.+|. -||.|..+-|..+      +|-|-|.|.+..+-.+||.+
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            458999999999999999999999 7999998888764      57899999999999999974

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.68  E-value=0.15  Score=34.50  Aligned_cols=54  Identities=20%  Similarity=0.242  Sum_probs=43.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccC----CCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPF----GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL  152 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l  152 (274)
                      ...|+|+++. +++.++|+.+|..|    + ..+|.+.-+ .-|-|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            4679999996 58999999999999    4 456666543 46889999999999999764

>KOG4660|consensus

Probab=94.44  E-value=0.036  Score=52.48  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=34.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+..+|+|-|||..+++++|+.+|+.||+|+-|+-...++
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~  112 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKR  112 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccC
Confidence            34567999999999999999999999999999977555444

>KOG4285|consensus

Probab=94.22  E-value=0.17  Score=44.69  Aligned_cols=72  Identities=14%  Similarity=0.171  Sum_probs=57.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeE-EEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP-LYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~-l~v~~a~~  169 (274)
                      ..-|-|-++|+.-. .-|..+|++||.|........+.+-+|.|.+.-+|++|+. -+|+.|.|.. |-|..+.+
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCC
Confidence            46677788988654 4566799999999999888888899999999999999997 5999988754 45555443

>KOG4661|consensus

Probab=94.19  E-value=0.077  Score=50.55  Aligned_cols=46  Identities=20%  Similarity=0.443  Sum_probs=39.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ  270 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g~  270 (274)
                      ...-+++|+|.+|...|.-.+|+.+|++||+|+-++|+++.  ++||.
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNa--RsPGa  446 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNA--RSPGA  446 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceeceeeeecC--CCCCc
Confidence            34557799999999999999999999999999999999864  45664

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.19  E-value=0.16  Score=42.19  Aligned_cols=61  Identities=18%  Similarity=0.058  Sum_probs=47.0

Q ss_pred             CHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhC--CCeeCCeEEEEEEecC
Q psy3343         109 LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA--YTKFKEVPLYLEWAPE  169 (274)
Q Consensus       109 te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~--~~~~~g~~l~v~~a~~  169 (274)
                      ....|+.+|..|+.+......++-+=..|.|.+.++|..|...|+  +..+.|..+.|.|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            357899999999999888777765668999999999999999999  9999999999998843

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.

>KOG4849|consensus

Probab=94.01  E-value=0.042  Score=49.29  Aligned_cols=70  Identities=16%  Similarity=0.065  Sum_probs=56.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCC--eeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGD--LGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~--i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .-.+||+||-|.+|.+||.+.....|-  +..+++-.      ++|||+|...+..+.++-++.|-.+.|+|..-.|-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            467899999999999999998887774  33333322      57999999999999999999999999999764443

>KOG2135|consensus

Probab=93.52  E-value=0.042  Score=51.15  Aligned_cols=75  Identities=17%  Similarity=0.314  Sum_probs=61.4

Q ss_pred             CCcEEEEeCCCCCC-CHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRT-LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~-te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..+.|-+.-.|+.. +.++|...|.+||.|..|.+...--.|.|+|.+..+|-.|.. ..+..|+++.|+|-|....
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            34555555566653 678999999999999999987654579999999999988885 7999999999999998653

>KOG2591|consensus

Probab=93.22  E-value=0.14  Score=48.61  Aligned_cols=71  Identities=18%  Similarity=0.264  Sum_probs=56.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHcccc--CCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEP--FGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLE  165 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~--~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~  165 (274)
                      ...+.|+++-||..+-.++++.||..  +-.+.+|.+..+.+ =||+|++..||+.|++.|..  ..|.|++|...
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            34588999999999999999999985  56677887765322 48999999999999988865  56777776443

>KOG1855|consensus

Probab=93.08  E-value=0.12  Score=47.65  Aligned_cols=40  Identities=23%  Similarity=0.473  Sum_probs=36.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      +..++++|.+.|||.+-.-+-|.++|+.||.|.+|+|+.-
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP  266 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP  266 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC
Confidence            3457899999999999999999999999999999999865

>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=93.00  E-value=0.78  Score=34.79  Aligned_cols=65  Identities=18%  Similarity=0.270  Sum_probs=47.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccC-CCeeEEEeeCCC----eEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPF-GDLGRVLVPPYG----ITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~l~~~~----~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      ....+.+...|+.++.++|..+.+.+ ..|..++|.+++    -.+++.|.+..+|..-...+||+.|..
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33444444555556666776666655 346788887754    378999999999999999999998864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115|consensus

Probab=92.07  E-value=0.15  Score=43.96  Aligned_cols=69  Identities=25%  Similarity=0.243  Sum_probs=54.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-C----CeEEEEEecCHHHHHHHHHHhCCCe----eCCeEEEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-Y----GITGLVEFLQKNQAKAAFNSLAYTK----FKEVPLYLE  165 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~----~~~afV~F~~~~~A~~A~~~l~~~~----~~g~~l~v~  165 (274)
                      ..|||.||+..+..+.+..-|+.||+|.+-.+.. +    .+-++|+|...-.|.+|...+.-.-    ..+++.-|+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCC
Confidence            7899999999999999999999999996655543 2    2568999999999999998774322    334554444

>KOG4209|consensus

Probab=91.97  E-value=0.13  Score=44.40  Aligned_cols=43  Identities=30%  Similarity=0.487  Sum_probs=38.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                      ......+||+|+.+.+|.+++..+|+.||.|..+.|..++...
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~  140 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRG  140 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCC
Confidence            3445799999999999999999999999999999999998753

>KOG0128|consensus

Probab=91.87  E-value=0.066  Score=53.14  Aligned_cols=71  Identities=14%  Similarity=0.139  Sum_probs=60.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...++|.|.|+..|.++++.+++.+|.+.+++++.     .+|.|+|.|.++.+|..+........++...+.|..
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccc
Confidence            57899999999999999999999999999988766     358999999999999999877777666665555544

>KOG0226|consensus

Probab=91.78  E-value=0.12  Score=44.58  Aligned_cols=127  Identities=20%  Similarity=0.188  Sum_probs=78.8

Q ss_pred             EEEEeCCCCCCCHHH-H--HHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          98 IILVKNLPYRTLPTD-L--KALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        98 ~l~V~nLp~~~te~~-l--~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..++.|+-..+..+- |  ...|+.|-.+....+.++     .+++|+.|.....-.++-..-+++.+.-+++++.-+..
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            344555544444333 2  455665554444333332     36899999887777777665566666666555443322


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      .      ..     .. +                                 .+-.....+||++.|..+++++-|-..|.
T Consensus       178 w------ed-----Ps-l---------------------------------~ew~~~DfRIfcgdlgNevnd~vl~raf~  212 (290)
T KOG0226|consen  178 W------ED-----PS-L---------------------------------AEWDEDDFRIFCGDLGNEVNDDVLARAFK  212 (290)
T ss_pred             c------CC-----cc-c---------------------------------ccCccccceeecccccccccHHHHHHHHH
Confidence            1      00     00 0                                 00112236899999999999999999999


Q ss_pred             hcCCeeEEEEecCC-CCCCCC
Q psy3343         250 KCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       250 ~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      +|.....++|++++ .+++.|
T Consensus       213 Kfpsf~~akviRdkRTgKSkg  233 (290)
T KOG0226|consen  213 KFPSFQKAKVIRDKRTGKSKG  233 (290)
T ss_pred             hccchhhcccccccccccccc
Confidence            99999999999986 444444

>KOG2318|consensus

Probab=91.38  E-value=1.1  Score=42.95  Aligned_cols=79  Identities=25%  Similarity=0.373  Sum_probs=64.1

Q ss_pred             hcCCCcEEEEeCCCCC-CCHHHHHHccccC----CCeeEEEeeCC-------------C---------------------
Q psy3343          92 EARSKRIILVKNLPYR-TLPTDLKALFEPF----GDLGRVLVPPY-------------G---------------------  132 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~-~te~~l~~~F~~~----G~i~~v~l~~~-------------~---------------------  132 (274)
                      .....++|-|-|+.|. +...+|.-+|+.|    |.|.+|.|.++             |                     
T Consensus       170 ~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee  249 (650)
T KOG2318|consen  170 LGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEE  249 (650)
T ss_pred             cccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhh
Confidence            3556689999999997 8899999998876    68999988541             0                     


Q ss_pred             -------------------eEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCC
Q psy3343         133 -------------------ITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  170 (274)
Q Consensus       133 -------------------~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~  170 (274)
                                         -||.|+|.+.+.|...+....|..|..  ..|-+.|.|..
T Consensus       250 ~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPDd  308 (650)
T KOG2318|consen  250 EEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPDD  308 (650)
T ss_pred             hhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCCC
Confidence                               179999999999999999999999974  45666677654

>PF13893 RRM_5: RNA recognition motif

Probab=90.87  E-value=0.26  Score=32.03  Aligned_cols=20  Identities=25%  Similarity=0.556  Sum_probs=17.1

Q ss_pred             HHHHhhhcCCeeEEEEecCC
Q psy3343         244 IRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       244 L~~~F~~fG~I~~v~v~~~~  263 (274)
                      |+++|++||+|..+.+..++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~   20 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK   20 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS
T ss_pred             ChHHhCCcccEEEEEEEeCC
Confidence            78999999999999998766

(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 ....

>KOG4574|consensus

Probab=90.71  E-value=0.13  Score=51.08  Aligned_cols=73  Identities=16%  Similarity=0.157  Sum_probs=62.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCee--CCeEEEEEEecC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF--KEVPLYLEWAPE  169 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~--~g~~l~v~~a~~  169 (274)
                      ...++.|.+-+.+..-|..+|+.||.+.+.+..++-..|.|+|...+.|..|.++|+|+.+  -|-|-+|.+|..
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            4455667777888999999999999999999988778999999999999999999999875  477888888753

>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=90.48  E-value=1.6  Score=30.45  Aligned_cols=59  Identities=20%  Similarity=0.186  Sum_probs=35.9

Q ss_pred             CCCCHHHHHHccccCCC-----eeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343         106 YRTLPTDLKALFEPFGD-----LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus       106 ~~~te~~l~~~F~~~G~-----i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..++..+|..++...+.     |-.|.+..  .|+||+-.. +.|..++..|++..+.|+++.|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35788888888887654     45666654  489998875 4788899999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG3152|consensus

Probab=90.47  E-value=0.36  Score=41.66  Aligned_cols=39  Identities=15%  Similarity=0.294  Sum_probs=35.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .-.||+.|||+.+....|+++|++||.|=.|.+....+.
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s  112 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDS  112 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhH
Confidence            348999999999999999999999999999998876554

>KOG2068|consensus

Probab=90.29  E-value=0.12  Score=46.27  Aligned_cols=72  Identities=11%  Similarity=0.210  Sum_probs=56.8

Q ss_pred             cEEEEeCCCCCCCHHH-HH--HccccCCCeeEEEeeCCC---------eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          97 RIILVKNLPYRTLPTD-LK--ALFEPFGDLGRVLVPPYG---------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~-l~--~~F~~~G~i~~v~l~~~~---------~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      .-+||-+||.....++ |.  +.|.+||.|..|.+..+.         .-++|+|...++|..||...+|..++|+.|..
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            5567778887754444 43  589999999999886621         24899999999999999999999999988766


Q ss_pred             EEec
Q psy3343         165 EWAP  168 (274)
Q Consensus       165 ~~a~  168 (274)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            6654

>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=90.07  E-value=1.5  Score=29.98  Aligned_cols=55  Identities=15%  Similarity=0.128  Sum_probs=44.2

Q ss_pred             CCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343         107 RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus       107 ~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      .++-++++..+..|+ ..+|+..++  --||.|.+..+|++++...+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~d~t--GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRDDRT--GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEecCC--EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            377889999999998 445554433  3589999999999999999999988877664

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=88.50  E-value=0.71  Score=30.06  Aligned_cols=32  Identities=22%  Similarity=0.357  Sum_probs=25.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      +.|-|.+.+.+..+ .+..+|.+||+|..+.+.
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~   33 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP   33 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC
Confidence            46778888877654 455599999999998887

>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=86.83  E-value=4.5  Score=29.34  Aligned_cols=81  Identities=10%  Similarity=0.139  Sum_probs=49.9

Q ss_pred             EEEEecCHHHHHHHHHHhCC-CeeCCeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCccc
Q psy3343         135 GLVEFLQKNQAKAAFNSLAY-TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVE  213 (274)
Q Consensus       135 afV~F~~~~~A~~A~~~l~~-~~~~g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  213 (274)
                      |+|+|.++.-|..-++.-.. ..+.+..+.|.-.|......   . +                    +            
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~---~-k--------------------~------------   44 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHL---Q-K--------------------F------------   44 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCc---e-E--------------------E------------
Confidence            68999999999998873222 33556666665544221000   0 0                    0            


Q ss_pred             ccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         214 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       214 ~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                            +-......++|-|.|||...++++|++.       ..+...+..|
T Consensus        45 ------qv~~~vs~rtVlvsgip~~l~ee~l~D~-------LeIhFqK~sn   82 (88)
T PF07292_consen   45 ------QVFSGVSKRTVLVSGIPDVLDEEELRDK-------LEIHFQKPSN   82 (88)
T ss_pred             ------EEEEcccCCEEEEeCCCCCCChhhheee-------EEEEEecCCC
Confidence                  0011234579999999999999999976       4445555554

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0804|consensus

Probab=85.88  E-value=1.9  Score=40.23  Aligned_cols=66  Identities=15%  Similarity=0.297  Sum_probs=57.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccC-CCeeEEEeeCCC----eEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPF-GDLGRVLVPPYG----ITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~-G~i~~v~l~~~~----~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      .+++.|+|-.+|..++-.||-.+...+ -.|..+++.+++    -..++.|.+..+|..-+..+||..|..
T Consensus        72 ~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   72 SSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            347999999999999999999998866 447888888754    368999999999999999999998874

>smart00361 RRM_1 RNA recognition motif

Probab=85.83  E-value=0.95  Score=30.98  Aligned_cols=24  Identities=13%  Similarity=0.375  Sum_probs=19.9

Q ss_pred             HHHHHHHhh----hcCCeeEEE-EecCCC
Q psy3343         241 EDSIRRHFK----KCGPIASVT-VARKKD  264 (274)
Q Consensus       241 ee~L~~~F~----~fG~I~~v~-v~~~~~  264 (274)
                      +++|+++|+    +||.|.++. |..+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~   30 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNV   30 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCC
Confidence            578999998    999999996 666654

>KOG4208|consensus

Probab=83.01  E-value=2.4  Score=35.55  Aligned_cols=47  Identities=23%  Similarity=0.432  Sum_probs=36.9

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhc-CCeeEEEEecCC-CCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKC-GPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~f-G~I~~v~v~~~~-~~~~~g  269 (274)
                      .......+||..+|+.+.+.++..+|.+| |.|..+++.|.+ .|.+.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKg   93 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKG   93 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCc
Confidence            44455689999999999999999999999 778888886654 444443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=82.95  E-value=1.6  Score=31.36  Aligned_cols=27  Identities=15%  Similarity=0.181  Sum_probs=19.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCee
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIA  255 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~  255 (274)
                      ...+|. .|..+-..+|.++|++||.|.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~   36 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY   36 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE
Confidence            366666 899999999999999999975

; 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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	274
1whx_A	111	Solution Structure Of The Second Rna Binding Domain		8e-20
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		1e-06
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		9e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		8e-04

>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From Hypothetical Protein Bab23448 Length = 111

Iteration: 1
 Score = 94.0 bits (232), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 55/77 (71%)
Query: 96  KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
           K +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ AF  LAY+
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 156 KFKEVPLYLEWAPEGVF 172
           KF  VPLYLEWAP GVF
Sbjct: 70  KFHHVPLYLEWAPIGVF 86

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 8/87 (9%)
Query: 89  QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQ 141
           QV + ++   ILV+N+P++    +++ LF  FG+L  V +P        +   G V+F+ 
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 142 KNQAKAAFNSLAY-TKFKEVPLYLEWA 167
           K  AK AFN+L + T      L LEWA
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWA 94

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
            + L+IKNLNF++TE++++  F K G I S T+++KK+    G  LSM
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK--AGVLLSM 50

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           I V NL   T  TDL+ LF PFG + R+ +     TG       + F ++  A  A   +
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 153 AYTKFKEVPLYLEWA 167
           +   +  + L +EWA
Sbjct: 78  SGFGYDHLILNVEWA 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	274
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-32
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-04
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-04
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-06
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-05
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-05
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-07
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-05
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-04
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	8e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-07
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-05
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-06
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-06
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-04
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-06
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-06
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	9e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	8e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-06
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-05
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	7e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	8e-05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	9e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-04
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-04
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	5e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-04

>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 =  114 bits (288), Expect = 1e-32
 Identities = 51/108 (47%), Positives = 67/108 (62%)

Query: 88  NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKA 147
           +     RSK +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ 
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61

Query: 148 AFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEE 195
           AF  LAY+KF  VPLYLEWAP GVF  A +K   + ++  E+ E    
Sbjct: 62  AFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPS 109

>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 = 43.6 bits (103), Expect = 5e-06
 Identities = 8/37 (21%), Positives = 14/37 (37%)

Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
            T +  KNL   +    I+  F + G +  V +    
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG 46

>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 = 75.3 bits (185), Expect = 1e-16
 Identities = 36/171 (21%), Positives = 63/171 (36%), Gaps = 18/171 (10%)

Query: 99  ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTK 156
           +LV NL P R  P  L  LF  +GD+ RV +        LV+    NQA+ A + L   K
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65

Query: 157 FKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENV 216
               P+ +  +        +E  + +   K+         K+  ++              
Sbjct: 66  LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI--------- 116

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                    P  TL++ N+  + +E+ ++  F   G +       +KD K 
Sbjct: 117 -------FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 160

>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 = 7e-16
 Identities = 36/173 (20%), Positives = 64/173 (36%), Gaps = 18/173 (10%)

Query: 97  RIILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 154
            ++LV NL P R  P  L  LF  +GD+ RV +        LV+    NQA+ A + L  
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 94

Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
            K    P+ +  +        +E  + +   K+         K+  ++            
Sbjct: 95  HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF------ 148

Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                      P  TL++ N+  + +E+ ++  F   G +       +KD K 
Sbjct: 149 ----------PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM 191

>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 = 66.7 bits (162), Expect = 2e-13
 Identities = 19/177 (10%), Positives = 46/177 (25%), Gaps = 16/177 (9%)

Query: 97  RIILVKNLPYRTL-PTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFNSLAY 154
            +++V  L    +    +  +F  +G++ +V          +VE         A   L  
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64

Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
                  + +  +              K+           E    + ++ ++        
Sbjct: 65  NFMFGQKMNVCVS--------------KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST 110

Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
             +  + R   P   L+  N     TE++      + G     +V            
Sbjct: 111 PEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSS 167

>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 = 57.3 bits (139), Expect = 5e-11
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 2/47 (4%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           + L+IKNLNF++TE++++  F K G I S T+   K     G  LSM
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSM 50

>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 = 58.5 bits (142), Expect = 1e-10
 Identities = 28/186 (15%), Positives = 53/186 (28%), Gaps = 46/186 (24%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQ 141
           A ++R+  V N+P+      +   F     LG +   P                 +EF  
Sbjct: 2   AMARRL-YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
            ++   A  +     F+   L +                             + +     
Sbjct: 61  VDETTQAM-AFDGIIFQGQSLKIRRP-------------------------HDYQPLPGM 94

Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
            E+    VP V   V       P+    L+I  L     +D ++      GP+ +  +  
Sbjct: 95  SENPSVYVPGVVSTVV------PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV- 147

Query: 262 KKDPKS 267
            KD  +
Sbjct: 148 -KDSAT 152

>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 = 41.2 bits (97), Expect = 1e-04
 Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 6/78 (7%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
           + +  LP       +K L   FG L    +     TGL       E++  N    A   L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 153 AYTKFKEVPLYLEWAPEG 170
              +  +  L ++ A  G
Sbjct: 177 NGMQLGDKKLLVQRASVG 194

>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 = 59.2 bits (144), Expect = 1e-10
 Identities = 31/187 (16%), Positives = 50/187 (26%), Gaps = 55/187 (29%)

Query: 90  VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKN 143
           V    +  ++ V NLP        + L  PFG L R  +     TG        E+++K+
Sbjct: 89  VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148

Query: 144 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
            A  A + L         LY+ W   G    A   S+                       
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR----------------------- 185

Query: 204 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARK 262
                                     L +  L     + D++ R            +A  
Sbjct: 186 -------------------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG 220

Query: 263 KDPKSPG 269
           +D +  G
Sbjct: 221 QDGQLKG 227

>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 = 48.4 bits (116), Expect = 7e-07
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
           + R++R IL++ LP      ++  L   +      +    G T  V  L   QA+AA N+
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKG-TAFVTLLNGEQAEAAINA 76

Query: 152 LAYTKFKEVPLYLEWAPEG 170
              ++ +E  L ++  P  
Sbjct: 77  FHQSRLRERELSVQLQPTD 95

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 39.2 bits (92), Expect = 8e-04
 Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 1/46 (2%)

Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           E  ER+      + I+ L  + T   +         +    V + K
Sbjct: 13  EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK 57

>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 = 58.5 bits (142), Expect = 3e-10
 Identities = 22/183 (12%), Positives = 49/183 (26%), Gaps = 51/183 (27%)

Query: 91  VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQ 144
           V   ++  + + N P      +++ L +    +   +  P            ++   K  
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED 171

Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED 204
           A+     L   K +   L  + +               EK K  +    E +        
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVS------------NPLEKSKRTDSATLEGR-------- 211

Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNST-EDSIRRHFKKCGPIASVTVARKK 263
                                    + I+NL+     E+ +R  F+  G I  + +   +
Sbjct: 212 ------------------------EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ 247

Query: 264 DPK 266
              
Sbjct: 248 KEH 250

>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 = 48.1 bits (115), Expect = 1e-06
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 190 GEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK 249
           G       +   +E +        +   E   R  E  TT+ +KNL  +  ++ + ++FK
Sbjct: 5   GHHARPDSKRPLDEGSPAAAGLTSKKANEALTRNRE-LTTVLVKNLPKSYNQNKVYKYFK 63

Query: 250 KCGPIASVTVARKKD 264
            CGPI  V VA    
Sbjct: 64  HCGPIIHVDVADSLK 78

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 43.1 bits (102), Expect = 5e-05
 Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
               + TL++ N   + T+ +IR   +    +A S+ +   +   S  
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160

>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 = 54.3 bits (131), Expect = 4e-10
 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 1/76 (1%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 152
           +     ILVKNLP  +   ++  L + +  L    V     T  V  L   QA+ A    
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 153 AYTKFKEVPLYLEWAP 168
               F+   L ++  P
Sbjct: 61  HQYSFRGKDLIVQLQP 76

>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 = 54.3 bits (131), Expect = 8e-10
 Identities = 21/106 (19%), Positives = 42/106 (39%), Gaps = 4/106 (3%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAFNSLA 153
           RI+ ++NLPY+    ++  +F  +G + ++ V     T     V +     AK A + L+
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 154 YTKFKEVPLYLEWA-PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKE 198
                   L + +      F +   K K ++ +  +E  G      
Sbjct: 69  GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPP 114

>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 = 52.4 bits (126), Expect = 4e-09
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 270
           PE +  LYI+NL +  T + +   F K GPI  + V     P++ G 
Sbjct: 5   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--GNTPETRGT 49

>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 = 54.3 bits (131), Expect = 1e-09
 Identities = 15/73 (20%), Positives = 28/73 (38%)

Query: 192 GEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC 251
                 + T  +       E        EE++     ++Y+ N+++ ST   +  HF  C
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 252 GPIASVTVARKKD 264
           G I  +T+   K 
Sbjct: 61  GSINRITILCDKF 73

>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 = 40.9 bits (96), Expect = 6e-05
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 68  EIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVL 127
               K  A     G       +  +   KR + V N+ Y +   DL+A F   G + R+ 
Sbjct: 8   TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67

Query: 128 VPPYGITGL------VEFLQKNQAKAA 148
           +     +G       +EF ++N   AA
Sbjct: 68  ILCDKFSGHPKGYAYIEFAERNSVDAA 94

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 55.4 bits (134), Expect = 2e-09
 Identities = 25/173 (14%), Positives = 51/173 (29%), Gaps = 48/173 (27%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 154
           V ++ Y      ++  F PFG +  + +    +T        VE+     A+ A   +  
Sbjct: 33  VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92

Query: 155 TKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE 214
                  + +                                 +     D          
Sbjct: 93  VMLGGRNIKVGRP--------------------------SNIGQAQPIIDQLA------- 119

Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                   E      +Y+ +++ + ++D I+  F+  G I S T+AR  DP +
Sbjct: 120 -------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR--DPTT 163

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 43.8 bits (104), Expect = 2e-05
 Identities = 10/40 (25%), Positives = 21/40 (52%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
                 + +Y+ ++ +   ED+IR+ F   GPI S+ ++ 
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW 62

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 17/51 (33%), Positives = 28/51 (54%)

Query: 218 EDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           E++E+  +   TLY+ NL+F +TE+ I   F K G I  + +   K  K+ 
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
           + V NL + T    +  LF   GD+ ++++    +         VE+  +  A+ A   +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101

Query: 153 AYTKFKEVPLYLEWAP 168
             T+  +  +  +W  
Sbjct: 102 NGTRLDDRIIRTDWDA 117

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 56.0 bits (134), Expect = 3e-09
 Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 5/107 (4%)

Query: 170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVE-----EDEEREP 224
           G+    +E    ++       E  EE+ E    E  ++   EVE  ++      D   + 
Sbjct: 40  GIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQG 99

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           +   TL++  +N+++TE  +RR F+  GPI  + +   K    P  +
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146

>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 = 52.1 bits (125), Expect = 4e-09
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
            ++ V+ L    +  DL    E FG +  V++ P+    LVEF   + AK      A   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 157 F--KEVPLYLEWA 167
                   +  ++
Sbjct: 76  VYIAGQQAFFNYS 88

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 7/41 (17%), Positives = 16/41 (39%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           +      ++++ L  +  E  +    +K G I  V +   K
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK 51

>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 = 53.4 bits (129), Expect = 5e-09
 Identities = 28/173 (16%), Positives = 46/173 (26%), Gaps = 57/173 (32%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
           E+ +   + + NL       +LK           + V     TG       V+F      
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67

Query: 146 KAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDN 205
           + A   L   K     + LE                                        
Sbjct: 68  EKALE-LTGLKVFGNEIKLEKP-------------------------------------- 88

Query: 206 QQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
                      +  + ++     TL  KNL+FN TED ++  F+    I  V+
Sbjct: 89  -----------KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 130

>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 = 50.7 bits (122), Expect = 5e-08
 Identities = 9/51 (17%), Positives = 17/51 (33%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
            E  E      L+I NLN N +   ++    +      + V   +   +  
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 55

>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 = 53.0 bits (128), Expect = 6e-09
 Identities = 32/179 (17%), Positives = 49/179 (27%), Gaps = 59/179 (32%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 148
           S   ++V  LP      +L ALF   G +    +     TG       V+F  +  ++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
              L     +   L + +A                                         
Sbjct: 62  IKVLNGITVRNKRLKVSYA----------------------------------------- 80

Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                         E   DT LY+ NL    T+D +   F K G I    + R  D  +
Sbjct: 81  ----------RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR--DKLT 127

>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 = 51.1 bits (123), Expect = 7e-09
 Identities = 12/49 (24%), Positives = 24/49 (48%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
             + E D T+++ NL     E+ +   F + GP+  VT+ + ++ K   
Sbjct: 10  PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 7/85 (8%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQA 145
           +  + R + V NL  R     L  LF   G L +V +       P    G V F      
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF-GFVCFKHPESV 70

Query: 146 KAAFNSLAYTKFKEVPLYLEWAPEG 170
             A   L   +    P+ +     G
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPSSG 95

>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 = 50.8 bits (122), Expect = 1e-08
 Identities = 15/47 (31%), Positives = 24/47 (51%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           E +    L+I  LN  + E  ++  F K GPI+ V + + +  KS G
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG 49

>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 = 50.7 bits (122), Expect = 1e-08
 Identities = 16/51 (31%), Positives = 22/51 (43%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
             E     D  L++  LN   +E+ + R F+  G I   TV R  D  S G
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG 57

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLG--RVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYT 155
           V  L  +    D+  LF+PFG +    VL  P G +     V+F    +A+AA ++L  +
Sbjct: 20  VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79

Query: 156 KFKE---VPLYLEWA 167
           +        L +++A
Sbjct: 80  QTMPGASSSLVVKFA 94

>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 = 50.0 bits (120), Expect = 2e-08
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
              +E        LY++NL  +++E+ I + F    P A   V + +D
Sbjct: 5   SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 15/73 (20%), Positives = 24/73 (32%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY 154
           S +I+ V+NL   T    ++  F          V        V F  +  A  A  +L  
Sbjct: 14  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73

Query: 155 TKFKEVPLYLEWA 167
                 P+ +  A
Sbjct: 74  KVLDGSPIEVTLA 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 8/41 (19%), Positives = 14/41 (34%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
             P   +    LN N  E  ++   +K G +  V +     
Sbjct: 3   QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR 43

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 96  KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAF 149
            + +    L      T LK +   +G++  V +  +  T        V F     AK   
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 150 NSLAYTKFKEVPLYLEWAPEG 170
            +L  T      ++ +   +G
Sbjct: 66  KNLHLTSVMGNIIHAQLDIKG 86

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 8/45 (17%), Positives = 22/45 (48%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           +  + +  + + ++N+ F + +  IR  F   G + +V + +K  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT 52

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 33/99 (33%), Positives = 50/99 (50%), Gaps = 8/99 (8%)

Query: 89  QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGL------VEFLQ 141
           QV + ++   ILV+N+P++    +++ LF  FG+L  V +P     TG       V+F+ 
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 142 KNQAKAAFNSLA-YTKFKEVPLYLEWAPEGVFAEAKEKS 179
           K  AK AFN+L   T      L LEWA   V  ++   S
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 49.6 bits (119), Expect = 3e-08
 Identities = 9/53 (16%), Positives = 18/53 (33%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           +  E  E      L+I NLN N +   ++    +      + V   +   +  
Sbjct: 7   DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 59

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 210 PEVEENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           P+V     +   R   P  TT YI N+   +TE  +   F+  G I       +K
Sbjct: 9   PQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 16/67 (23%), Positives = 26/67 (38%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
           + N+P+     DL  LF+ FG +      P      +++    QA     +LA   F+  
Sbjct: 32  IGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR 91

Query: 161 PLYLEWA 167
            L   W 
Sbjct: 92  NLRTGWG 98

>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 = 49.4 bits (118), Expect = 3e-08
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
           R++ ++ LP     T++ AL  PFG +  +L+        +E   +  A    N  +   
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75

Query: 157 --FKEVPLYLEWA 167
              +  P+Y++++
Sbjct: 76  PHLRNQPIYIQYS 88

>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 = 41.0 bits (96), Expect = 3e-05
 Identities = 8/45 (17%), Positives = 19/45 (42%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
            ++ +  P   L+I+ L    TE  +       G + ++ + + K
Sbjct: 7   GDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51

>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 = 51.1 bits (123), Expect = 4e-08
 Identities = 32/177 (18%), Positives = 48/177 (27%), Gaps = 55/177 (31%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--------VEFLQKNQAKAAFNSL 152
           V  +P      DL+ LFE +G +  + V                V F  +  A  A N+L
Sbjct: 8   VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67

Query: 153 AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEV 212
              K                                                     P +
Sbjct: 68  HNMKV----------------------------------------------LPGMHHP-I 80

Query: 213 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           +    + E+     D  L+I  ++   TE+ IR  F   G I    + R  D  S G
Sbjct: 81  QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG 137

>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 = 44.1 bits (105), Expect = 8e-06
 Identities = 7/41 (17%), Positives = 18/41 (43%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
             +++  +    +E  +R  F++ G +  + V R +    P
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPP 44

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 5/94 (5%)

Query: 168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPD 227
                 +A    K  ++  N+ G   E        +D  +     E +       + E  
Sbjct: 16  TTTEAVDAATAEKVFKQYANDNGVDGEWT-----YDDATKTFTVTEGSHHHHHHMDVEGM 70

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           T+L + NL + ++ D++RR F+K G +  V + R
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 34/126 (26%), Positives = 50/126 (39%), Gaps = 8/126 (6%)

Query: 33  GTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVE 92
           G     E   E  +A  AE +    A      GE    + T+ F    G      +  VE
Sbjct: 9   GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE 68

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAK 146
             +   + V NL YRT P  L+ +FE +G +G V +P    T        V F  K  A+
Sbjct: 69  GMTS--LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126

Query: 147 AAFNSL 152
            A +++
Sbjct: 127 DAMDAM 132

>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 = 49.2 bits (118), Expect = 4e-08
 Identities = 12/45 (26%), Positives = 23/45 (51%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
             E+     + L++ NL  + TE+ +R+ F+K G    V + + K
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51

>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 = 48.0 bits (115), Expect = 9e-08
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYT 155
           + V NLP      +++ LFE +G  G V +     +   G +    +  A+ A   L   
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF---GFIRLETRTLAEIAKVELDNM 74

Query: 156 KFKEVPLYLEWAPEG 170
             +   L + +A   
Sbjct: 75  PLRGKQLRVRFACHS 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 = 50.2 bits (121), Expect = 7e-08
 Identities = 27/179 (15%), Positives = 53/179 (29%), Gaps = 62/179 (34%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--------PYGITGLVEFLQKNQAKAA 148
           R++ V NL        LK  F+  G +  + +          Y     VE+ Q + A  A
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA---FVEYHQSHDANIA 57

Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
             +L   + +   + + WA                                         
Sbjct: 58  LQTLNGKQIENNIVKINWA----------------------------------------- 76

Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                    + ++   +    L++ +LN N  ++++R  FK      S  V    D ++
Sbjct: 77  --------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW--DMQT 125

>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 = 39.8 bits (94), Expect = 2e-04
 Identities = 14/41 (34%), Positives = 26/41 (63%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
            LY+ NL+   TED ++++F+  GPIA++ +   K+ K+  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN 42

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
            ++ ++ L    +  DL    + FG +  V+V P     LVEF     A  A N  A  +
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQ 81

Query: 157 FKEV--PLYLEWA 167
                 P ++ ++
Sbjct: 82  IYIAGHPAFVNYS 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           D+  +      ++I+ L     E  +    ++ GPI+ V V  KK
Sbjct: 13  DDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 48.2 bits (115), Expect = 8e-08
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 3/92 (3%)

Query: 86  AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFG---DLGRVLVPPYGITGLVEFLQK 142
           +   V + +  R + ++N+P       L +L   +G      +V          V +  K
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSK 64

Query: 143 NQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAE 174
           +QA+ A + L   + +   L + + P+ + A+
Sbjct: 65  DQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 5/44 (11%), Positives = 14/44 (31%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
           + +    L I+N+  +   + +     + G + S          
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET 54

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 48.7 bits (116), Expect = 8e-08
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
           R+I ++ LP      ++ +L  PFG +  +L+        +E   +  A    N      
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76

Query: 157 --FKEVPLYLEWA 167
              +  P+Y++++
Sbjct: 77  PVLRGQPIYIQFS 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 7/40 (17%), Positives = 17/40 (42%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
             P   ++I+ L  + TE  +       G + ++ + + K
Sbjct: 13  GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 48.0 bits (115), Expect = 8e-08
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           TTLY+  L    TE  +R HF + G I ++TV +++
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48

>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 = 39.2 bits (92), Expect = 1e-04
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQA-KAAFNSL 152
           ++   + V  L      TDL+  F  FG++  + V        ++F  +  A  AA  S 
Sbjct: 10  KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSF 69

Query: 153 AYTKFKEVPLYLEWA 167
                    L ++W 
Sbjct: 70  NKLIVNGRRLNVKWG 84

>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 = 49.0 bits (117), Expect = 1e-07
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                  P+P+  L +  L+  +TE  +R  F K GPIA V++    D +S
Sbjct: 36  HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY--DQQS 84

>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 = 42.0 bits (99), Expect = 3e-05
 Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 6/64 (9%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 148
               + V  L   T   DL+ +F  +G +  V +     +        V F   + AK A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 149 FNSL 152
               
Sbjct: 105 KERA 108

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 10/59 (16%), Positives = 22/59 (37%)

Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           +       +   E+   +    + T+Y   +    T+  +R+ F   G I  + V  +K
Sbjct: 3   SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61

>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 = 43.5 bits (103), Expect = 5e-06
 Identities = 14/69 (20%), Positives = 22/69 (31%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEV 160
              +        ++  F PFG +  + V P      V F     A  A  S+  T  +  
Sbjct: 30  CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGH 89

Query: 161 PLYLEWAPE 169
            +   W  E
Sbjct: 90  VVKCYWGKE 98

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 2/48 (4%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                D  +Y+ NL  +     I   F K G I  + +  K     P 
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL--KNRRGGPP 62

>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 = 40.4 bits (95), Expect = 6e-05
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 3/81 (3%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAKAAF 149
             +   I V NLP      D++ +F  +G +  + +           VEF     A+ A 
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78

Query: 150 NSLAYTKFKEVPLYLEWAPEG 170
                  +    L +E+   G
Sbjct: 79  YGRDGYDYDGYRLRVEFPRSG 99

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 6/60 (10%), Positives = 16/60 (26%)

Query: 205 NQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           +            ++   E     T++   L        +   F   G +  V +   ++
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 11/48 (22%), Positives = 23/48 (47%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
                 +     T++I+NL+F+S E+++    ++ G +  V V    D
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD 52

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
           +    + + ++NL + +    L  + + FGDL  V V  +  T         +F+ +  A
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 146 KAAFNSL 152
           +    + 
Sbjct: 71  QKCLAAA 77

>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 = 50.1 bits (120), Expect = 2e-07
 Identities = 11/47 (23%), Positives = 23/47 (48%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
            +  E+       L++ NL  + TE+  +R F++ G  + V + R +
Sbjct: 12  LKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 6/73 (8%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKF 157
           V NLP      D K LFE +G+   V +     +   G +    +  A+ A   L  T  
Sbjct: 27  VGNLPTDITEEDFKRLFERYGEPSEVFINRDRGF---GFIRLESRTLAEIAKAELDGTIL 83

Query: 158 KEVPLYLEWAPEG 170
           K  PL + +A  G
Sbjct: 84  KSRPLRIRFATHG 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 = 48.0 bits (114), Expect = 2e-07
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
           R+I ++ LP      ++ +L  PFG +  +L+        +E   +  A    N      
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91

Query: 157 --FKEVPLYLEWA 167
              +  P+Y++++
Sbjct: 92  PVLRGQPIYIQFS 104

>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 = 42.2 bits (99), Expect = 2e-05
 Identities = 8/51 (15%), Positives = 19/51 (37%)

Query: 213 EENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
             +   D      P   ++I+ L  + TE  +       G + ++ + + K
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 67

>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 = 47.1 bits (113), Expect = 2e-07
 Identities = 10/40 (25%), Positives = 21/40 (52%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
               ++Y+ N+++ +T + +  HF  CG +  VT+   K 
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF 43

>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 = 40.6 bits (96), Expect = 4e-05
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKA 147
              R I V N+ Y     +L+A F   G + RV +     +G       +EF  K   + 
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 148 A 148
           +
Sbjct: 64  S 64

>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 = 47.3 bits (113), Expect = 2e-07
 Identities = 10/48 (20%), Positives = 21/48 (43%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           +     +T+++ NL++      ++  F   G +    +   KD KS G
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG 57

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 152
           + V NL Y+     LK +F   G + R  +     G     G V F Q  +A  A +  
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 10/43 (23%), Positives = 24/43 (55%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           R  + + T+ + NL+ ++ E  ++  F+  G I+ + +A+ K 
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT 52

>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 = 45.7 bits (109), Expect = 8e-07
 Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
           I V NL   T  TDL+ LF PFG + R+ +     TG       + F ++  A  A   +
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77

Query: 153 AYTKFKEVPLYLEWA 167
           +   +  + L +EWA
Sbjct: 78  SGFGYDHLILNVEWA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 8/45 (17%), Positives = 18/45 (40%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                 T+ ++N+  ++  DSI         +A   +   KD ++
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQT 49

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 9/40 (22%), Positives = 19/40 (47%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
             P T L++  L  N++  ++ R F + G I ++   +  
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53

>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 = 40.3 bits (95), Expect = 5e-05
 Identities = 10/52 (19%), Positives = 19/52 (36%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL 152
           V  L   T    L   F+ FG +  +          +++   + A+AA   +
Sbjct: 22  VGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKM 73

>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 = 46.7 bits (111), Expect = 5e-07
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
           RS+  ++V  LP      DLK      GD+    V   G TG+VEF++K     A   L 
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 72

Query: 154 YTKFKEVPLYLEWA 167
            TKF+       + 
Sbjct: 73  NTKFRSHEGETAYI 86

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V+NL Y +   DL+ LF  +G L  +  P   +T        V F+    A  A+  +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

>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 = 44.1 bits (105), Expect = 2e-06
 Identities = 8/44 (18%), Positives = 20/44 (45%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
                    L+++NL++ S+E+ + + F   GP++ +       
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL 45

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 7/45 (15%), Positives = 16/45 (35%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
               +     +T L+++    +  E  +   F   GP+  V +  
Sbjct: 21  MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 65

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           + V+  P     ++L  +F PFG +  V +   G    VEF +   A  A   +    F 
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-G-FAFVEFEEAESAAKAIEEVHGKSFA 91

Query: 159 EVPLYLEWA 167
             PL + ++
Sbjct: 92  NQPLEVVYS 100

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 4/84 (4%)

Query: 88  NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL----VEFLQKN 143
             + +    R + V NL        +  LF   G      +     +      VEF +  
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66

Query: 144 QAKAAFNSLAYTKFKEVPLYLEWA 167
            A AA  ++   K     + + WA
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWA 90

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 12/42 (28%), Positives = 20/42 (47%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           +     TLY+ NL+ + TE  I + F + GP  S  +  +  
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT 52

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 13/43 (30%), Positives = 24/43 (55%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
            + +   TL + NL + ++ DS+RR F+K G +  V + R+  
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH 50

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V NL YRT P  L+ +FE +G +G V +P    T        V F  +  A+ A  ++
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75

>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 = 45.7 bits (109), Expect = 7e-07
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                E    L + NL+F  ++  I+  F + G +    V   +  +S G
Sbjct: 22  GGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG 71

>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 = 40.7 bits (96), Expect = 4e-05
 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 5/59 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSL 152
           +LV NL +     D++ LF  FG L +  V     G    T  V F +K  A  A    
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90

>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 = 45.7 bits (109), Expect = 7e-07
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
            P+P+  L +  L+  +TE  +R  F K GPIA V++
Sbjct: 11  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 47

>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 = 40.3 bits (95), Expect = 5e-05
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
           + V  L   T   DL+ +F  +G +  V +     +        V F   + AK A    
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 15/112 (13%)

Query: 85  DAFNQVVEARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLV---PPYGITGLV 137
           D  +        +++L+ N+        L+    AL    GD+  ++V           +
Sbjct: 18  DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77

Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEE 189
            F  +  A+A   +     F+  PL + +        ++       ++ + E
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVITF--------SETPQSQVAEDGSLE 121

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 9/78 (11%)

Query: 197 KENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH----FKKCG 252
           KE  A +  +Q +   +           EP   + I N+N    ++ ++          G
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPH---TEPSQVVLITNINPEVPKEKLQALLYALASSQG 58

Query: 253 PIASVTVARKKDPKSPGQ 270
            I  + V       + G+
Sbjct: 59  DILDIVV--DLSDDNSGK 74

>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 = 46.8 bits (112), Expect = 9e-07
 Identities = 27/179 (15%), Positives = 54/179 (30%), Gaps = 59/179 (32%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAA 148
           SK  ++V  LP      + ++LF   G++    +    ITG       V ++    A+ A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 149 FNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQG 208
            N+L   + +   + + +A           S    ++ N                     
Sbjct: 61  INTLNGLRLQTKTIKVSYA---------RPSSASIRDAN--------------------- 90

Query: 209 VPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                                LY+  L    T+  + + F + G I +  +    D  +
Sbjct: 91  ---------------------LYVSGLPKTMTQKELEQLFSQYGRIITSRILV--DQVT 126

>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 = 45.2 bits (107), Expect = 1e-06
 Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
           RS+  ++V  LP      DLK      GD+    V   G TG+VEF++K     A   L 
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 71

Query: 154 YTKFKEVPLYLEWA 167
            TKF+       + 
Sbjct: 72  NTKFRSHEGETAYI 85

>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 = 46.4 bits (110), Expect = 1e-06
 Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 1/91 (1%)

Query: 172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEP-DTTL 230
             EA + +  ++  K    +   + +    +      V E   +      R+  P D  +
Sbjct: 17  TTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKV 76

Query: 231 YIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           Y+ NL  N  +  + R F   GP+ SV VAR
Sbjct: 77  YVGNLGNNGNKTELERAFGYYGPLRSVWVAR 107

>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 = 38.7 bits (90), Expect = 4e-04
 Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTK 156
           + V NL      T+L+  F  +G L  V V   P G    VEF     A  A   L    
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAADAVRELDGRT 134

Query: 157 FKEVPLYLEWA 167
                + +E +
Sbjct: 135 LCGCRVRVELS 145

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQ 270
           E  P+ T+YI NLN    +D +++     F + G I  + V   +  K  GQ
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQ 53

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 25/102 (24%), Positives = 39/102 (38%), Gaps = 15/102 (14%)

Query: 92  EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 144
           E R    I + NL  +    +LK    A+F  FG +  +LV           V F + + 
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEK 186
           A  A  S+    F + P+ +++        AK  S    K K
Sbjct: 64  ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMK 97

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 153
           +LV NL +     D++ LF  FG L +  V     G    T  V F ++  A  A     
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150

Query: 154 YTKFKEVPLYLEWAPE 169
                  P+ ++    
Sbjct: 151 GVPLDGRPMDIQLVAS 166

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 44.8 bits (106), Expect = 5e-06
 Identities = 11/48 (22%), Positives = 20/48 (41%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
              E    L + NL+F  ++  I+  F + G +    V   +  +S G
Sbjct: 83  EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 130

>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 = 44.6 bits (106), Expect = 2e-06
 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 214 ENVEEDEEREPEPD-TTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
             +E+    +      TL  KNL+FN TED ++  F+    I  V+
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS 47

>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 = 37.2 bits (87), Expect = 6e-04
 Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 11/67 (16%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFG------DLGRVLVPPYGITGLVEFLQKNQA 145
           + R+ R +L KNL +     +LK +FE           G+      GI   +EF  +  A
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK----SKGI-AYIEFKSEADA 66

Query: 146 KAAFNSL 152
           +      
Sbjct: 67  EKNLEEK 73

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 9/40 (22%), Positives = 19/40 (47%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
                     + T++++ L  N T +S+  +FK+ G I +
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKT 42

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 9/106 (8%)

Query: 56  SGAATRLAMGETEIVEKT---RAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTD 112
           S     +     E V  T         +G    +      A +KR++ V  L        
Sbjct: 20  SDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKV 79

Query: 113 LKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
           L A F PFGD+  + +P    T        VEF     A AA +++
Sbjct: 80  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 41.7 bits (98), Expect = 4e-05
 Identities = 6/59 (10%), Positives = 14/59 (23%)

Query: 201 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
              +  +   +                  LY+  L     +  +   F   G I  + +
Sbjct: 37  TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95

>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 = 46.5 bits (111), Expect = 2e-06
 Identities = 28/180 (15%), Positives = 49/180 (27%), Gaps = 55/180 (30%)

Query: 88  NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQ 141
           N    +     + V +L        L   F P G +  + V    IT        V F Q
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 142 KNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTA 201
              A+ A +++ +   K  P+ + W+         ++     K                 
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWS---------QRDPSLRKSG--------------- 102

Query: 202 EEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
                                       ++IKNL+ +    ++   F   G I S  V  
Sbjct: 103 -------------------------VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137

>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 = 41.9 bits (99), Expect = 7e-05
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
              P  +LY+ +L+ + TE  +   F   GPI S+ V R  
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM 51

>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 = 46.1 bits (110), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +  +EPE    L+I  L+F +T++S+R HF++ G +    V   +DP +
Sbjct: 5   ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNT 51

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V NL YRT P  L+ +FE +G +G V +P    T        V F  K  A+ A +++
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 13/41 (31%), Positives = 24/41 (58%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
             + E  T+L + NL + ++ D++RR F+K G +  V + R
Sbjct: 41  PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81

>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 = 45.2 bits (107), Expect = 3e-06
 Identities = 17/103 (16%), Positives = 43/103 (41%), Gaps = 2/103 (1%)

Query: 164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED--NQQGVPEVEENVEEDEE 221
           ++ A E    E  ++   + KEK +  +G     ++   E   + + V   +++  E   
Sbjct: 7   IDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGP 66

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           +       L++ +++  + ED I+  F   G I ++ +   + 
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR 109

>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 = 41.0 bits (96), Expect = 9e-05
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 98  IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
           I+ V ++       +++  F  +G++  + +     TG      LVE+    QA AA  +
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 152 LAYTKFKEVPLYLEWA 167
           L   +     + ++W 
Sbjct: 134 LNGAEIMGQTIQVDWC 149

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 9/48 (18%), Positives = 21/48 (43%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           +    + ++YIK    ++T D I+   +  G + ++ + R       G
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 53

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 6/98 (6%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAK 146
                R + +K  P      D+K   E  G +  + +          +  V F     AK
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 147 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 184
                    K+KE  L + +  +    + +E+ + K +
Sbjct: 67  KFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQNKVE 103

>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 = 44.2 bits (105), Expect = 4e-06
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA-RKKDPKSPGQ-FLSM 274
            EP+  LY+KNL+   TE  +   F +        +  R    +  GQ F++ 
Sbjct: 22  GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITF 74

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSLAY 154
           +KNL  R    DL +LF  F +     +    +TG       + F  K  A  A + +  
Sbjct: 30  LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG 89

Query: 155 TKFKEVPLYLEWA 167
            K     L +E+ 
Sbjct: 90  YKLYGKILVIEFG 102

>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 = 44.3 bits (105), Expect = 4e-06
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                E    L + NL+F  ++  I+  F + G +    V   +  +S G
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGI---TGLVEFLQKNQAKAAFNSLA 153
           +LV NL +     D++ LF  FG L +  V     G    T  V F ++  A  A     
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97

Query: 154 YTKFKEVPLYLEWAPE 169
                  P+ ++    
Sbjct: 98  GVPLDGRPMDIQLVAS 113

>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 = 43.3 bits (103), Expect = 4e-06
 Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 6/66 (9%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAK 146
           A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A 
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 147 AAFNSL 152
           AA +++
Sbjct: 64  AAIDNM 69

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 36.7 bits (86), Expect = 6e-04
 Identities = 6/35 (17%), Positives = 11/35 (31%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
                LY+  L     +  +   F   G I  + +
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 39

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 10/36 (27%), Positives = 22/36 (61%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
           E++   + T++++ L  N T +S+  +FK+ G I +
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKT 36

>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 = 44.1 bits (104), Expect = 5e-06
 Identities = 9/70 (12%), Positives = 24/70 (34%), Gaps = 1/70 (1%)

Query: 201 AEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTV 259
               +   +   ++        +   D  + ++ L F  T++ I + F     +   +T+
Sbjct: 16  PRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75

Query: 260 ARKKDPKSPG 269
               + K  G
Sbjct: 76  PVDPEGKITG 85

>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 = 38.3 bits (89), Expect = 5e-04
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 6/76 (7%)

Query: 79  ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG--- 135
             G Q+   +   ++ +   + ++ LP+     ++   F     +   +  P    G   
Sbjct: 25  TGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKIT 84

Query: 136 ---LVEFLQKNQAKAA 148
               V+F  +  A+ A
Sbjct: 85  GEAFVQFASQELAEKA 100

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 42.9 bits (102), Expect = 6e-06
 Identities = 7/38 (18%), Positives = 17/38 (44%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
                 ++++NL F+ T   ++  F +CG +    +  
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM 42

>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 = 43.0 bits (102), Expect = 7e-06
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                       TL + NL++++TE++++  F+K      + V + ++ KS G
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSKG 54

>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 = 43.4 bits (102), Expect = 7e-06
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 93  ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
           + + + ++V N  L        L  + E  G +  +L+PP        +    ++K A+ 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81

Query: 151 SLAYTKF-----KEVPLYLEWA 167
           +L   +      +++ LYL + 
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFV 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 = 37.2 bits (86), Expect = 9e-04
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 217 EEDEEREPEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVARKK 263
            E  E       +L + N  L    + + +    +KCG + ++ +   K
Sbjct: 15  HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK 63

>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 = 45.3 bits (106), Expect = 7e-06
 Identities = 26/123 (21%), Positives = 46/123 (37%), Gaps = 15/123 (12%)

Query: 92  EARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQ 144
           E R    I + NL  +    +LK    A+F  FG +  +LV           V F + + 
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 145 AKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEED 204
           A  A  S+    F + P+ +++        AK  S    K K    E + ++++   +  
Sbjct: 65  ATNALRSMQGFPFYDKPMRIQY--------AKTDSDIIAKMKGTFVERDRKREKRKPKSQ 116

Query: 205 NQQ 207
              
Sbjct: 117 ETP 119

>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 = 42.9 bits (100), Expect = 5e-05
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRH----FKKCGPIASVTVARKKDPKSPGQ 270
           E  P+ T+YI NLN    +D +++     F + G I  + V   +  K  GQ
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMRGQ 54

>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 = 42.2 bits (98), Expect = 9e-05
 Identities = 26/145 (17%), Positives = 44/145 (30%), Gaps = 2/145 (1%)

Query: 25  HTWNSLFLGTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQL 84
                +              +   +   +   G      +   +I        +    Q+
Sbjct: 136 AVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQM 195

Query: 85  DAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPPYGITGLVEFLQKN 143
                + E     I+ + NLP  T    L  LF  F       LVP       VEF  + 
Sbjct: 196 PPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEV 255

Query: 144 QAKAAFNSLAYTKF-KEVPLYLEWA 167
           QA AA ++L   K  +   + + +A
Sbjct: 256 QAGAARDALQGFKITQNNAMKISFA 280

>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 = 43.0 bits (102), Expect = 7e-06
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
               +  L++  L+F++ E S+ + F K G I+ V V
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV 44

>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 = 43.2 bits (102), Expect = 8e-06
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
              +  E   ++ +Y++ LN + T D +   FK+CG +  
Sbjct: 5   SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKM 44

>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 = 42.2 bits (100), Expect = 9e-06
 Identities = 14/42 (33%), Positives = 23/42 (54%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
                +T+Y+ NL F+ T + + R F K G +  VT+ + KD
Sbjct: 12  LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD 53

>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 = 40.7 bits (96), Expect = 4e-05
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQA 145
            A SK  + V NLP+     DL  +F  +G + +V +     T        + FL K+ A
Sbjct: 12  LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

Query: 146 KAAFNSL 152
           +    ++
Sbjct: 72  QNCTRAI 78

>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 = 42.6 bits (101), Expect = 9e-06
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 6/58 (10%)

Query: 217 EEDEEREPEPDT---TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
                R   P +   T ++ NL ++ TE+SI+  F+    I++V + R  +P +P + 
Sbjct: 6   HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL 60

>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 = 42.1 bits (100), Expect = 9e-06
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 2/45 (4%)

Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQ 270
             T ++I  L  N T+D I   F   G I  + +    +   P  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP--VERMHPHL 45

>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 = 42.6 bits (101), Expect = 9e-06
 Identities = 22/113 (19%), Positives = 33/113 (29%), Gaps = 20/113 (17%)

Query: 86  AFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEF 139
           +   + E      + V  L  +     L  LF   G +    +P   +TG       VEF
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 140 LQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEG 192
           L +  A  A   +   K    P+ +  A                  KN  G  
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKA--------------SAHNKNLSGPS 103

>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 = 39.9 bits (94), Expect = 8e-05
 Identities = 9/43 (20%), Positives = 20/43 (46%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
            E   D T+Y+  L+   +E  +   F + GP+ +  + + + 
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV 52

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQA 145
            A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 146 KAAFNSL 152
            AA +++
Sbjct: 68  AAAIDNM 74

>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 = 38.7 bits (91), Expect = 2e-04
 Identities = 6/35 (17%), Positives = 11/35 (31%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
                LY+  L     +  +   F   G I  + +
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 44

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 9/48 (18%), Positives = 18/48 (37%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                   L+I  L F+ T++ +    K  G +  + +   +  K  G
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 7/64 (10%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP------PYGITGLVEFLQKNQAKAA 148
            K  + +  LP+     +L+ + +  G +  + +       P G+   VE+  ++QA  A
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL-AYVEYENESQASQA 74

Query: 149 FNSL 152
              +
Sbjct: 75  VMKM 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           +Y+ NL   + +  + R F   GP+ +V +AR
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR 34

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           V NL       +L+  F  +G L  V +   P G    VEF     A+ A   L      
Sbjct: 5   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF-AFVEFEDPRDAEDAVRGLDGKVIC 63

Query: 159 EVPLYLEWA 167
              + +E +
Sbjct: 64  GSRVRVELS 72

>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 = 42.3 bits (100), Expect = 1e-05
 Identities = 8/38 (21%), Positives = 17/38 (44%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
                 L+++NL    TE+ + + F + G +  V   +
Sbjct: 8   MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK 45

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-PYGITGLVEFLQKNQAKAAFNSLAYT 155
           +++ V+NL        L+  F  FG L RV     Y     + F +++ A  A   +   
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY---AFIHFDERDGAVKAMEEMNGK 68

Query: 156 KFKEVPLYLEWA 167
             +   + + +A
Sbjct: 69  DLEGENIEIVFA 80

>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 = 43.3 bits (103), Expect = 1e-05
 Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +    ++I  LN+++TED++R +F K G +  + +   KDP +
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI--MKDPAT 41

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 219 DEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
              R P  P  T ++ NL ++ TE+SI+  F+    I++V + R  +P +P + 
Sbjct: 6   SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR--EPSNPERL 56

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 8/41 (19%), Positives = 16/41 (39%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
                      L++ N+ F   +  +R+ F + G I  V +
Sbjct: 7   GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 47

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 12/62 (19%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 150
           + V N+P+R    DL+ +F  FG +  V +    I         G V F     A  A  
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRARE 73

Query: 151 SL 152
            L
Sbjct: 74  KL 75

>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 = 42.9 bits (101), Expect = 2e-05
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIR 245
             + +    +  +  E +  +   E  E +      EP EP+  +Y+KNL  +  E  ++
Sbjct: 4   GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLK 63

Query: 246 RHFKKCGPIASVTVARKKD 264
             F +    +S T     D
Sbjct: 64  YIFGRYVDFSSETQRIMFD 82

>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 = 41.5 bits (98), Expect = 2e-05
 Identities = 8/38 (21%), Positives = 19/38 (50%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
            +  T L++ N++   T   +R  F++ GP+    + +
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK 44

>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 = 38.0 bits (89), Expect = 3e-04
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSL 152
           ++   + V N+       +L+A FE +G +    +V  Y     V   +   A  A   L
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGL 64

Query: 153 AYTKFKEVPLYLEWA 167
             T+F+   ++++ +
Sbjct: 65  DNTEFQGKRMHVQLS 79

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 9/42 (21%), Positives = 18/42 (42%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
            T+++  ++    E  IR  F + G +  V +   +   S G
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG 51

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 8/48 (16%), Positives = 17/48 (35%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
                        L++ N+ F   +  +R+ F + G I  V +   + 
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER 66

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 12/60 (20%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFNSL 152
           V N+P+R    DL+ +F  FG +  V +    I         G V F     A  A   L
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSKGFGFVTFENSADADRAREKL 89

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 210 PEVEENVEEDEEREP-EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKS 267
            +     +    R P E    +Y+K L F +    +   FKK   +  S+ +A   + K+
Sbjct: 7   GKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 66

Query: 268 PG 269
            G
Sbjct: 67  TG 68

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
           ++       LY+ +L+FN TED +R  F+  G I S+ +
Sbjct: 20  QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQL 58

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V +L +      L+ +FEPFG +  + +     TG       + F     AK A   L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

>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 = 40.7 bits (96), Expect = 3e-05
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           E R P    TLY+   +   T   +R  F   G I  +++   +
Sbjct: 8   ERRAPRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR 49

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 21/184 (11%), Positives = 42/184 (22%), Gaps = 65/184 (35%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-----------GLVEFLQKN 143
           S R + V N+P+      +   F     LG +   P                 +EF   +
Sbjct: 3   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 144 QAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEE 203
           +   A  +     F+   L +                                 +     
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRP---------------------------HDYQPLPGA 94

Query: 204 DNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
                                     L+I  L     +D ++      GP+ +  + +  
Sbjct: 95  HK------------------------LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK-- 128

Query: 264 DPKS 267
           D  +
Sbjct: 129 DSAT 132

>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 = 41.1 bits (97), Expect = 4e-05
 Identities = 13/50 (26%), Positives = 21/50 (42%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
            +++ +  T LYI NL  +  E  +    K  G + S  + R     S G
Sbjct: 18  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 67

>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 = 40.7 bits (96), Expect = 4e-05
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
              +I V+N+P+     ++   F  +  +   +   Y   G      +V F  +++A AA
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 149 FNSLAYTKFKEVPLYLEWAPEG 170
              L         + L     G
Sbjct: 74  VIDLNDRPIGSRKVKLSGPSSG 95

>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 = 37.7 bits (88), Expect = 4e-04
 Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTVARKKDPKSPG 269
               T + ++N+ F  + D I   F     I  SV +   +     G
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG 58

>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 = 41.6 bits (98), Expect = 4e-05
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 98  IILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAAFN 150
           I+ V  +       D+   F  +G++  + +          G   LVE+    +A+AA  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY-TLVEYETYKEAQAAME 82

Query: 151 SLAYTKFKEVPLYLEWA 167
            L        P+ ++W 
Sbjct: 83  GLNGQDLMGQPISVDWC 99

>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 = 40.2 bits (95), Expect = 4e-05
 Identities = 9/41 (21%), Positives = 16/41 (39%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
               + LYI+ L   +T+  + +  +  G I S      K 
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT 42

>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 = 38.7 bits (91), Expect = 1e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 101 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL------VEFLQKNQAKAAFNSL 152
           ++ L   T   DL  L +P+G +          T        V+F   + A+ A  +L
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

>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 = 40.3 bits (95), Expect = 4e-05
 Identities = 6/40 (15%), Positives = 16/40 (40%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
                   +++ N++   T   +R  F++ G +    V +
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK 43

>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 = 37.2 bits (87), Expect = 6e-04
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
           I V N+       +L++LFE  G +    +V  Y     V   ++  AKAA   L   + 
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY---AFVHMEKEADAKAAIAQLNGKEV 68

Query: 158 KEVPLYLEWA 167
           K   + +E +
Sbjct: 69  KGKRINVELS 78

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 7/39 (17%), Positives = 18/39 (46%)

Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           P   +Y+ ++ ++ TE+ I       GP+ ++ +     
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ 39

>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 = 41.4 bits (97), Expect = 4e-05
 Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
           + +   +      ++++ L + +TE+ I   F    P+  V +    D +  G
Sbjct: 36  DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGRVTG 87

>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 = 40.2 bits (95), Expect = 5e-05
 Identities = 9/49 (18%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +  +  E    +++  L++++++  ++ +F K G +   T+  K DP +
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI--KMDPNT 49

>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 = 40.4 bits (95), Expect = 5e-05
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
              II V+N+P+     ++   F  +  +   +   Y   G      +V F  +++A AA
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 149 FNSL 152
              L
Sbjct: 74  VIDL 77

>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 = 40.7 bits (95), Expect = 6e-05
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 97  RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
           R+I + NLP+     + +  L EP+G +   ++        +E   +  A A  +     
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVD----- 80

Query: 156 KFKEVPLYLEWAP 168
              +  L+ +   
Sbjct: 81  HCLKKALWFQGRC 93

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 3/65 (4%)

Query: 204 DNQQGVPEVEENV-EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK 262
               G+ +  E V  E ++RE E    L+I  L+F +TE+S+R ++++ G +    V   
Sbjct: 3   SGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV--M 60

Query: 263 KDPKS 267
           +DP S
Sbjct: 61  RDPAS 65

>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 = 42.4 bits (99), Expect = 6e-05
 Identities = 10/80 (12%), Positives = 21/80 (26%), Gaps = 2/80 (2%)

Query: 187 NEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR 246
           +       E ++         G    +                LYI NL + +T++ +  
Sbjct: 28  SANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTE 87

Query: 247 HFKKCGP--IASVTVARKKD 264
                G   I  +     + 
Sbjct: 88  AVHSLGVNDILEIKFFENRA 107

>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 = 40.2 bits (94), Expect = 6e-05
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 96  KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN 150
           +R++ + +    + L   L  L EPFG +   L+        +E      A+AA +
Sbjct: 15  RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 4/57 (7%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVARKKDPKSPG 269
           E  +    E    + ++ L F +T + +   F +  PI      +      D +  G
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG 69

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 98  IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
           I+ V  +       D+   F  +G++  + +     TG      LVE+    +A+AA   
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 152 LAYTKFKEVPLYLEWA 167
           L        P+ ++W 
Sbjct: 85  LNGQDLMGQPISVDWC 100

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 10/45 (22%), Positives = 17/45 (37%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           ++ E      L+I +L    T+  +   F   G + S  V   K 
Sbjct: 33  KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 77

>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 = 40.0 bits (94), Expect = 8e-05
 Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 14/111 (12%)

Query: 63  AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
           A+   E V        E G Q         +    I+ V ++       +++  F  +G+
Sbjct: 1   AIHSYERVRNEDDDELEPGPQ--------RSVEGWILFVTSIHEEAQEDEIQEKFCDYGE 52

Query: 123 LGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
           +  + +     TG      LVE+    QA AA  +L   +     + ++W 
Sbjct: 53  IKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103

>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 = 39.5 bits (93), Expect = 9e-05
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
             L+I NL   +TE  IR  F++ G +    + +
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42

>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 = 38.3 bits (90), Expect = 2e-04
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNS 151
           +     + + NLP      ++++LFE +G +    ++  Y   G V    K  A+ A  +
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY---GFVHIEDKTAAEDAIRN 61

Query: 152 LAYTKFKEVPLYLEWA 167
           L + K   V + +E +
Sbjct: 62  LHHYKLHGVNINVEAS 77

>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 = 39.6 bits (93), Expect = 9e-05
 Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                 T+ ++   FN TE ++        P+ ++ + R       G
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTG 51

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           R  +  + L +  L + +TE  ++ +F   G +  V V  KKD K+
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV--KKDLKT 53

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           EP  T Y+ NL FN+ +  I   FK    I SV + R KD
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD 51

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 11/42 (26%), Positives = 18/42 (42%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           +         LY+KNL+    ++ +R+ F   G I S  V  
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM 49

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 226 PDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
           P + L+I NL   + +++ + R F   G I  + +  
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45

>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 = 39.3 bits (92), Expect = 1e-04
 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
                 +      ++++ L + +TE+ I   F    P+  V +    D +  G
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTG 56

>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 = 39.3 bits (92), Expect = 2e-04
 Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
           E          +I N+ F+ T+  + +  +       +V V    + +  G
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLG 58

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKA 147
            +K    + N+P+     D+    E        +       G      LV+F  ++ A+ 
Sbjct: 13  SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 72

Query: 148 A 148
           +
Sbjct: 73  S 73

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 1/54 (1%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKDPKSPG 269
                 +   D  + ++ L F  +++ I + F     +   +T+      +S G
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG 58

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 8/54 (14%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 214 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
                      +    L++  L++++T++++R +F + G +    +   KD  +
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI--MKDKTT 54

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 9/46 (19%), Positives = 17/46 (36%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
             ++E      L+I +L     +  + + F   G + S  V   K 
Sbjct: 17  GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62

>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 = 40.2 bits (93), Expect = 2e-04
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 8/87 (9%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-----TGLVEFLQKNQAKAAFNS 151
           R + +K  P      D+K   E  G +  + +          +  V F     AK    +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169

Query: 152 LAYTKFKEVPLYLEWAPEGVFAEAKEK 178
               K+KE  L + +  +  +   K +
Sbjct: 170 PG-QKYKETDLLILFKDD--YFAKKNE 193

>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 = 38.8 bits (91), Expect = 2e-04
 Identities = 9/45 (20%), Positives = 19/45 (42%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
              +      L+I  +  N  E  ++  F++ G I  +TV + + 
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF 50

>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 = 39.3 bits (92), Expect = 3e-04
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 6/66 (9%)

Query: 199 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT 258
              ++  QQ +P  + N       EP+    L +  +     E  +R+ F++ GPI SV 
Sbjct: 20  QQLQQQQQQHIPPTQMN------PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73

Query: 259 VARKKD 264
           +   ++
Sbjct: 74  IVCDRE 79

>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 = 38.7 bits (90), Expect = 3e-04
 Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPG 269
           E E +    +  + L ++ T + +   F  C        +     +D K  G
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRG 56

>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 = 38.3 bits (90), Expect = 3e-04
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
              + LY+ +L+FN TED +R  F+  G I ++ + +  D
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD 42

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 6/60 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
           + V +L +      L+ +FEPFG +  +++     TG       + F     A+ A   L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           ++++           +  +F   GP+ASV + + K
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK 44

>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 = 38.0 bits (89), Expect = 3e-04
 Identities = 11/40 (27%), Positives = 15/40 (37%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
                 LYI NL+   T D +R+ F       +  V  K 
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS 44

>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 = 38.0 bits (89), Expect = 4e-04
 Identities = 10/46 (21%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           ++    T +++  L +++T+ S+R++F+  G I    V    D ++
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV--ITDRQT 55

>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 = 38.4 bits (89), Expect = 4e-04
 Identities = 6/52 (11%), Positives = 19/52 (36%), Gaps = 3/52 (5%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKC---GPIASVTVARKKDPKSPG 269
             E      + ++ L ++ + + ++     C     +A V     ++ +  G
Sbjct: 11  GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62

>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 = 38.1 bits (89), Expect = 5e-04
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 207 QGVPEVEENVEEDEEREPEPD-TTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
            G+    +      + +P+   + ++I NLN     +  +   F K G +A  +V +
Sbjct: 6   SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62

>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 = 37.7 bits (88), Expect = 5e-04
 Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 99  ILVKNLPYRTL-PTDLKALFEPFGDLGRV-LVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
           + + NLP + +   DL  +F P+G + ++ +   +   G ++F      + A    +   
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF---GFIQFDNPQSVRDAIEXESQEM 81

Query: 157 FKEVPLYLEWA 167
                L LE +
Sbjct: 82  NFGKKLILEVS 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 = 37.3 bits (87), Expect = 7e-04
 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 222 REPEPDTTLYIKNLNFNS-TEDSIRRHFKKCGPIASVTVAR 261
           R     + L+I NL   + +++ + R F   G I  + +  
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57

>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 = 37.6 bits (88), Expect = 5e-04
 Identities = 7/45 (15%), Positives = 23/45 (51%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
           +        ++++ N+ + +TE+ ++  F + GP+ S  +   ++
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE 45

>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 = 37.5 bits (87), Expect = 6e-04
 Identities = 9/88 (10%), Positives = 24/88 (27%), Gaps = 10/88 (11%)

Query: 90  VVEARSKRIILVKNLPYRTLPTDLKALFEPFGD--LGRVLVPPYGITG------LVEFLQ 141
              +     + +  +P      ++        +  L  ++               VE+  
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 142 KNQAKAAFNSLAYTKFK--EVPLYLEWA 167
              A  A   L   + +     + ++WA
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWA 89

>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 = 37.5 bits (87), Expect = 7e-04
 Identities = 6/48 (12%), Positives = 12/48 (25%), Gaps = 3/48 (6%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKDPKSPGQF 271
             +  L+I  +      + I     K    +  V V          + 
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIV--YASAADKMKN 51

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           P     ++IKNL+ +    ++   F   G I S  V  
Sbjct: 2   PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 39

>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 = 37.4 bits (87), Expect = 8e-04
 Identities = 7/47 (14%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
               D  + +  + F++ E+ +R  F     + +V + +    ++ G
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNG 57

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	274
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.93
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.93
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.92
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.92
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.92
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.92
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.92
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.91
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.91
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.91
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.9
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.9
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.9
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.9
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.89
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.89
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.89
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.87
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.75
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.75
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.74
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.73
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.72
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.72
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.72
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.72
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.71
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.71
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.71
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.7
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.7
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.69
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.68
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.68
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.68
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.68
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.68
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.67
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.67
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.67
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.67
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
2div_A	99	TRNA selenocysteine associated protein; structural	99.67
1x5p_A	97	Negative elongation factor E; structure genomics,	99.66
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.66
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.66
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.66
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.66
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.65
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.65
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.65
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.65
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.65
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.65
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.64
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.64
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.64
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.64
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.63
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.63
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.63
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.63
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.63
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.63
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.63
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.62
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.62
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.62
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.62
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.62
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.61
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.61
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.61
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.61
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.6
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.6
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.6
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.6
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.59
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.59
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.59
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.59
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.58
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.58
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.57
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.57
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.57
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.57
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.56
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.55
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.55
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.32
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.54
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.53
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.52
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.51
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.51
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.51
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.51
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.5
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.5
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.5
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.5
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.49
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.48
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.48
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.48
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.47
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.47
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.47
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.45
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.44
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.42
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.41
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.4
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.36
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.35
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.35
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.33
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.0
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	98.99
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.93
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.86
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.86
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.83
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.79
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.79
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.76
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.76
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.75
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.73
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.73
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.73
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.72
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.71
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.71
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.7
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.69
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.69
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.69
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.69
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.68
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.68
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.68
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.68
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.68
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.67
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.67
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.66
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.66
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.66
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.65
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.65
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.64
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.63
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.63
2div_A	99	TRNA selenocysteine associated protein; structural	98.63
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.63
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.63
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.63
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.62
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.62
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.61
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.61
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.61
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.61
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.6
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.6
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.6
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.6
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.6
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.59
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.59
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.59
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.59
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.58
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.57
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.57
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.56
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.56
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.56
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.56
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.56
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.56
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.56
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.55
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.55
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.55
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.55
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.55
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.53
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.52
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.52
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.52
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.51
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.51
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.49
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.48
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.48
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.48
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.46
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.46
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.46
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.46
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.45
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.45
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.44
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.43
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.43
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.43
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.42
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.41
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.41
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.41
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.41
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.4
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.4
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.38
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.38
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.37
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.36
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.36
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.36
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.36
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.33
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.33
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.33
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.32
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.32
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.29
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.28
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.27
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	97.58
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.24
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.23
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.23
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.2
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.17
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.16
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.16
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.1
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.05
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.05
1x5p_A	97	Negative elongation factor E; structure genomics,	98.01
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	97.99
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	97.93
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	97.84
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	97.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	97.75
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	97.75
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.72
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.59
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.55
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.16
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	97.12
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.12
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	97.09
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	96.69
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.68
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	96.67
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	96.42
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	95.41
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	94.8
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	94.05
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	89.96
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	89.43
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.02
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	87.9
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	85.92

>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=5.4e-25  Score=177.43  Aligned_cols=118  Identities=19%  Similarity=0.355  Sum_probs=106.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC------eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~------~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+++++++|+++|++||.|..|.+.+++      |||||+|.+.++|..|+..|+|..+.|++|.|.|+.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            46899999999999999999999999999999997744      899999999999999999999999999999999985


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ...                                                   .....++|||+|||+.+|+++|+++|
T Consensus        81 ~~~---------------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f  109 (167)
T 1fxl_A           81 PSS---------------------------------------------------ASIRDANLYVSGLPKTMTQKELEQLF  109 (167)
T ss_dssp             CCC---------------------------------------------------GGGTTCEEEEESCCTTCCHHHHHHHH
T ss_pred             CCc---------------------------------------------------ccCCCCcEEECCCCCcCCHHHHHHHH
Confidence            330                                                   01134789999999999999999999


Q ss_pred             hhcCCeeEEEEecCC
Q psy3343         249 KKCGPIASVTVARKK  263 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~  263 (274)
                      ++||.|.++++++++
T Consensus       110 ~~~G~i~~~~i~~~~  124 (167)
T 1fxl_A          110 SQYGRIITSRILVDQ  124 (167)
T ss_dssp             GGGSCEEEEEEEECT
T ss_pred             HhcCCEeEEEEEecC
Confidence            999999999999886

>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=99.93  E-value=6.7e-25  Score=184.78  Aligned_cols=155  Identities=15%  Similarity=0.128  Sum_probs=110.6

Q ss_pred             CCcEEEEeCCC-CCCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Q psy3343          95 SKRIILVKNLP-YRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  172 (274)
Q Consensus        95 ~~~~l~V~nLp-~~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f  172 (274)
                      ++++|||+||| +.+++++|+++|++||.|.+|+++++ +|||||+|.+.++|..|++.|||..+.|++|.|.|+.....
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~   82 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI   82 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCcc
Confidence            46899999999 89999999999999999999999884 69999999999999999999999999999999999864421


Q ss_pred             cccccccccccccccccccchhhhhccchhhcc-cCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhc
Q psy3343         173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDN-QQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC  251 (274)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~f  251 (274)
                      .+....       .....   .+. ...+.... ......    ..........++++|||+|||+++|+++|+++|++|
T Consensus        83 ~p~~~~-------~~~~~---~~~-~~~~~~~~~~r~~~~----~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~  147 (205)
T 3tyt_A           83 MPGQSY-------GLEDG---SCS-YKDFSESRNNRFSTP----EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL  147 (205)
T ss_dssp             CCCSCC-------BCTTS---CBS-EEECTTCTTCSCSSH----HHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHH
T ss_pred             CCCccc-------ccccC---Ccc-ccccCCCccccccCc----ccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhc
Confidence            100000       00000   000 00000000 000000    000001123467899999999999999999999999


Q ss_pred             CCe--eEEEEecCCC
Q psy3343         252 GPI--ASVTVARKKD  264 (274)
Q Consensus       252 G~I--~~v~v~~~~~  264 (274)
                      |.|  .+++|+.++.
T Consensus       148 G~v~~~~v~~~~~~~  162 (205)
T 3tyt_A          148 GVKRPTSVKVFSGKS  162 (205)
T ss_dssp             TCCCCSEEEECSCCS
T ss_pred             CCcceEEEEEEcCCC
Confidence            999  8999998763

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.93  E-value=8.8e-25  Score=176.70  Aligned_cols=121  Identities=26%  Similarity=0.350  Sum_probs=108.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ++++|||+|||+++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            4689999999999999999999999999999998763      3799999999999999999999999999999999985


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ...                                                   ...+.++|||+|||+.+|+++|+++|
T Consensus        82 ~~~---------------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f  110 (168)
T 1b7f_A           82 PGG---------------------------------------------------ESIKDTNLYVTNLPRTITDDQLDTIF  110 (168)
T ss_dssp             CCS---------------------------------------------------STTTTCEEEEESCCTTCCHHHHHHHH
T ss_pred             CCc---------------------------------------------------ccCCCCCEEEeCCCCCCCHHHHHHhh
Confidence            330                                                   11245799999999999999999999


Q ss_pred             hhcCCeeEEEEecCC-CCC
Q psy3343         249 KKCGPIASVTVARKK-DPK  266 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~-~~~  266 (274)
                      ++||.|.++++++++ +++
T Consensus       111 ~~~G~i~~~~i~~~~~~~~  129 (168)
T 1b7f_A          111 GKYGSIVQKNILRDKLTGR  129 (168)
T ss_dssp             TSSSCEEEEEEEECTTTCC
T ss_pred             hcCCcEEEEEEEEcCCCCC
Confidence            999999999999987 443

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.92  E-value=1.2e-24  Score=189.41  Aligned_cols=119  Identities=24%  Similarity=0.395  Sum_probs=110.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCc
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFA  173 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~  173 (274)
                      ...++|||+|||+++|+++|+++|++||.|..|.+.+++|||||+|.+.++|..|+..|+|..+.|++|.|.|+..    
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~----   95 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH----   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC----
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc----
Confidence            3458999999999999999999999999999999999999999999999999999999999999999999999741    


Q ss_pred             ccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCC
Q psy3343         174 EAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP  253 (274)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~  253 (274)
                                                                           +++|||+|||+.+|+++|+++|++||.
T Consensus        96 -----------------------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~  122 (261)
T 3sde_A           96 -----------------------------------------------------GAALTVKNLSPVVSNELLEQAFSQFGP  122 (261)
T ss_dssp             -----------------------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSC
T ss_pred             -----------------------------------------------------CCcccccCCCCCCCHHHHHHHHHhcCC
Confidence                                                                 368999999999999999999999999


Q ss_pred             eeEEEEecCCCCCCCC
Q psy3343         254 IASVTVARKKDPKSPG  269 (274)
Q Consensus       254 I~~v~v~~~~~~~~~g  269 (274)
                      |.+|+|++++++++.|
T Consensus       123 i~~v~i~~~~~g~~~g  138 (261)
T 3sde_A          123 VEKAVVVVDDRGRATG  138 (261)
T ss_dssp             EEEEEEEEETTSCEEE
T ss_pred             eEEEEeeeCCCCCcCc
Confidence            9999999997766544

>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=8.1e-25  Score=177.90  Aligned_cols=125  Identities=26%  Similarity=0.330  Sum_probs=106.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--------CCeEEEEEecCHHHHHHHHHHhCCCeeC---CeEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--------YGITGLVEFLQKNQAKAAFNSLAYTKFK---EVPLY  163 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--------~~~~afV~F~~~~~A~~A~~~l~~~~~~---g~~l~  163 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|.+++        ++|||||+|.+.++|..|++.|++..+.   ++++.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            358999999999999999999999999999999874        3479999999999999999999998876   56777


Q ss_pred             EEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHH
Q psy3343         164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS  243 (274)
Q Consensus       164 v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~  243 (274)
                      +.++...       .                                           ....+.++|||+|||+.+|+++
T Consensus        82 ~~~~~~~-------~-------------------------------------------~~~~~~~~l~v~nl~~~~t~~~  111 (175)
T 3nmr_A           82 MKPADSE-------K-------------------------------------------NNAVEDRKLFIGMISKKCTEND  111 (175)
T ss_dssp             EEECGGG-------C-------------------------------------------CSCGGGSEEEEESCCTTCCHHH
T ss_pred             Ecccccc-------c-------------------------------------------cccCCCCeEEEcCCCCcCCHHH
Confidence            7765321       0                                           0112357999999999999999


Q ss_pred             HHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         244 IRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       244 L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      |+++|++||.|.+|+|++++++++.|
T Consensus       112 l~~~F~~~G~i~~v~~~~~~~g~~~g  137 (175)
T 3nmr_A          112 IRVMFSSFGQIEECRILRGPDGLSRG  137 (175)
T ss_dssp             HHHHHGGGSCEEEEEEEECTTSCEEE
T ss_pred             HHHHHHhCCCEEEEEEEECCCCCEEE
Confidence            99999999999999999998765443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.92  E-value=2.2e-24  Score=173.63  Aligned_cols=119  Identities=21%  Similarity=0.302  Sum_probs=106.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  171 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~  171 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|.+.++     +|||||+|.+.++|..|+..|+|..+.|++|.|.|+....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999763     4899999999999999999999999999999999985330


Q ss_pred             CcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhc
Q psy3343         172 FAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC  251 (274)
Q Consensus       172 f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~f  251 (274)
                            .                                           ....+.++|||+|||+.+|+++|+++|++|
T Consensus        81 ------~-------------------------------------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~  111 (166)
T 3md3_A           81 ------Q-------------------------------------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDF  111 (166)
T ss_dssp             ------C-------------------------------------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTS
T ss_pred             ------C-------------------------------------------CCCCCCceEEECCCCCCCCHHHHHHHHhcc
Confidence                  0                                           022346799999999999999999999999


Q ss_pred             CCeeEEEEecCCC
Q psy3343         252 GPIASVTVARKKD  264 (274)
Q Consensus       252 G~I~~v~v~~~~~  264 (274)
                      |.|.++.+++++.
T Consensus       112 G~i~~~~i~~~~~  124 (166)
T 3md3_A          112 PSYLSGHVMWDMQ  124 (166)
T ss_dssp             TTEEEEEEEECTT
T ss_pred             CCeeEEEEEecCC
Confidence            9999999998854

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.92  E-value=2.1e-24  Score=182.47  Aligned_cols=123  Identities=20%  Similarity=0.249  Sum_probs=106.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .+.++|||+|||+++|+++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|+..+++..+.|+.|.+.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34589999999999999999999999999999999763      379999999999999999999999999999999998


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      ....      ..                                           ......+|||+|||+.+|+++|+++
T Consensus        93 ~~~~------~~-------------------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~  123 (213)
T 4f02_A           93 QRDP------SL-------------------------------------------RKSGVGNIFIKNLDKSIDNKALYDT  123 (213)
T ss_dssp             CCCT------HH-------------------------------------------HHHCTTEEEEESCCTTCCHHHHHHH
T ss_pred             cccc------cc-------------------------------------------cccccccceECCcccccHHHHHHHH
Confidence            5330      00                                           0012368999999999999999999


Q ss_pred             hhhcCCeeEEEEecCCCC
Q psy3343         248 FKKCGPIASVTVARKKDP  265 (274)
Q Consensus       248 F~~fG~I~~v~v~~~~~~  265 (274)
                      |++||.|.+|+|++++++
T Consensus       124 F~~~G~i~~~~i~~d~~~  141 (213)
T 4f02_A          124 FSAFGNILSCKVVCDENG  141 (213)
T ss_dssp             HGGGSCEEEEEEEEETTE
T ss_pred             HhhcCCeEEEEeeccCCC
Confidence            999999999999998654

>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=99.92  E-value=2.5e-24  Score=174.80  Aligned_cols=121  Identities=17%  Similarity=0.265  Sum_probs=107.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccC----C-------CeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPF----G-------DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~----G-------~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      ..++|||+|||+++|+++|+++|++|    |       .|..+.+.+++|||||+|.+.++|..|+ .|+|..+.|++|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            46899999999999999999999999    7       8899999999999999999999999999 8999999999999


Q ss_pred             EEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHH
Q psy3343         164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS  243 (274)
Q Consensus       164 v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~  243 (274)
                      |.++...       .                                            .....++|||+|||+.+|+++
T Consensus        82 v~~~~~~-------~--------------------------------------------~~~~~~~l~v~nlp~~~t~~~  110 (172)
T 2g4b_A           82 IRRPHDY-------Q--------------------------------------------PLPGAHKLFIGGLPNYLNDDQ  110 (172)
T ss_dssp             EECCSSC-------C--------------------------------------------CCTTTTCEEEECCCTTCCHHH
T ss_pred             ecCCccc-------C--------------------------------------------CCCCCCEEEEEcCCCcCCHHH
Confidence            9986422       0                                            112357999999999999999


Q ss_pred             HHHHhhhcCCeeEEEEecCC-CCCC
Q psy3343         244 IRRHFKKCGPIASVTVARKK-DPKS  267 (274)
Q Consensus       244 L~~~F~~fG~I~~v~v~~~~-~~~~  267 (274)
                      |+++|++||.|.+|+|++++ ++++
T Consensus       111 l~~~f~~~G~v~~v~i~~~~~~g~~  135 (172)
T 2g4b_A          111 VKELLTSFGPLKAFNLVKDSATGLS  135 (172)
T ss_dssp             HHHHHHTTSCEEEEEEEECTTTCSE
T ss_pred             HHHHHHhcCCceEEEEEecCCCCCc
Confidence            99999999999999999986 4443

>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=99.91  E-value=5.2e-24  Score=176.49  Aligned_cols=126  Identities=17%  Similarity=0.271  Sum_probs=105.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++|+++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+.. ++..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            445699999999999999999999999999999998763      47999999999999999975 99999999999999


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +....    ...         .                                .....+.++|||+|||+++|+++|++
T Consensus        89 ~~~~~----~~~---------~--------------------------------~~~~~~~~~l~V~nLp~~~t~~~l~~  123 (196)
T 1l3k_A           89 AVSRE----DSQ---------R--------------------------------PGAHLTVKKIFVGGIKEDTEEHHLRD  123 (196)
T ss_dssp             CCC--------------------------------------------------------CCSEEEEECCTTTCCHHHHHH
T ss_pred             ccCcc----ccc---------c--------------------------------cccCCCcceEEEeCCCCCCCHHHHHH
Confidence            85330    000         0                                00123457999999999999999999


Q ss_pred             HhhhcCCeeEEEEecCCC
Q psy3343         247 HFKKCGPIASVTVARKKD  264 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~~  264 (274)
                      +|++||.|.+|+|++++.
T Consensus       124 ~F~~~G~i~~v~i~~~~~  141 (196)
T 1l3k_A          124 YFEQYGKIEVIEIMTDRG  141 (196)
T ss_dssp             HHTTTSCEEEEEEEECTT
T ss_pred             HHhcCCCeEEEEEeecCC
Confidence            999999999999999863

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.91  E-value=1.9e-23  Score=173.44  Aligned_cols=137  Identities=14%  Similarity=0.202  Sum_probs=108.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccC----C-------CeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPF----G-------DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~----G-------~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+.+++|||||+|.+.++|.+|+ .|+|..+.|++|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            46899999999999999999999999    6       7888888889999999999999999999 8999999999999


Q ss_pred             EEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHH
Q psy3343         164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDS  243 (274)
Q Consensus       164 v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~  243 (274)
                      |.|+....-......    .    ...            .           ...........+.++|||+|||+.+|+++
T Consensus        82 v~~~~~~~~~~~~~~----~----~~~------------~-----------~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  130 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSE----N----PSV------------Y-----------VPGVVSTVVPDSAHKLFIGGLPNYLNDDQ  130 (198)
T ss_dssp             EECCCCCCCCCCSSS----C----SSC------------C-----------CTTSSCCCSSCCCCEEEEECCCTTCCHHH
T ss_pred             EeCCCCCCCCCCCcC----C----CcC------------C-----------CCCCccCCCCCCCCEEEEeCCCCCCCHHH
Confidence            999854310000000    0    000            0           00000111234678999999999999999


Q ss_pred             HHHHhhhcCCeeEEEEecCC
Q psy3343         244 IRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       244 L~~~F~~fG~I~~v~v~~~~  263 (274)
                      |+++|++||.|.+|+|++++
T Consensus       131 l~~~f~~~G~v~~~~~~~~~  150 (198)
T 2yh0_A          131 VKELLTSFGPLKAFNLVKDS  150 (198)
T ss_dssp             HHHHHHTBSCEEEEEEEECT
T ss_pred             HHHHHHHcCCccEEEEeecC
Confidence            99999999999999999986

>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=2.3e-24  Score=190.08  Aligned_cols=193  Identities=12%  Similarity=0.157  Sum_probs=140.4

Q ss_pred             ccccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHhh------hhhh----hHHHHHHHHHHHCCCCccccch
Q psy3343          25 HTWNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRLA------MGET----EIVEKTRAFLEENGVQLDAFNQ   89 (274)
Q Consensus        25 ~~wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~a------l~e~----~~~~~~~~~l~~~g~~~~~~~~   89 (274)
                      ..-.+|||+..+        +.++..+|.+     |....|++.      .+++    .-.+++..++..+|..+..-.-
T Consensus        39 ~~~~~l~V~nLp--------~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i  110 (292)
T 2ghp_A           39 RELTTVLVKNLP--------KSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEI  110 (292)
T ss_dssp             ---CEEEEEEEC--------TTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCEEEEeCCC--------CCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcEeCCcEE
Confidence            456788888774        6677666654     433334331      2333    3356666666666655432211


Q ss_pred             hhhcCCCcEEEEeCCCCCCCHHHHHHccccCC-CeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          90 VVEARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        90 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .......++|||+|||+.+++++|+++|++|| .|..|.++.     .+|||||+|.+.++|..|+..|+|..+.|++|.
T Consensus       111 ~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  190 (292)
T 2ghp_A          111 IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV  190 (292)
T ss_dssp             EEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             EEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            12234679999999999999999999999999 999999976     458999999999999999999999999999999


Q ss_pred             EEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCC-CCHH
Q psy3343         164 LEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFN-STED  242 (274)
Q Consensus       164 v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~-~tee  242 (274)
                      |.|+....    ...    +.                                    .....+.++|||+|||+. +|++
T Consensus       191 v~~a~~~~----~~~----~~------------------------------------~~~~~~~~~l~v~nlp~~~~t~~  226 (292)
T 2ghp_A          191 TKVSNPLE----KSK----RT------------------------------------DSATLEGREIMIRNLSTELLDEN  226 (292)
T ss_dssp             EEECCCC-----------------------------------------------------CCTTTEEEEEEECTTTCCHH
T ss_pred             EEECCCCc----ccc----cc------------------------------------cccCCCCceEEEECCCcccCCHH
Confidence            99985330    000    00                                    012335689999999999 9999


Q ss_pred             HHHHHhhhcCCeeEEEEecCCC--CCCCC
Q psy3343         243 SIRRHFKKCGPIASVTVARKKD--PKSPG  269 (274)
Q Consensus       243 ~L~~~F~~fG~I~~v~v~~~~~--~~~~g  269 (274)
                      +|+++|++||.|.+|+|+++++  +++.|
T Consensus       227 ~l~~~F~~~G~v~~v~i~~~~~~tg~~~g  255 (292)
T 2ghp_A          227 LLRESFEGFGSIEKINIPAGQKEHSFNNC  255 (292)
T ss_dssp             HHHHHHGGGSCEEEEECCSCCC---CCCE
T ss_pred             HHHHHHhccCCeeEEEEEecCCcCCCCce
Confidence            9999999999999999999887  55544

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.90  E-value=8.8e-24  Score=185.61  Aligned_cols=187  Identities=19%  Similarity=0.212  Sum_probs=138.8

Q ss_pred             cccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh--hhhhh----hHHHHHHHHHH-HCCCCccccc-hhhh
Q psy3343          26 TWNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL--AMGET----EIVEKTRAFLE-ENGVQLDAFN-QVVE   92 (274)
Q Consensus        26 ~wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~--al~e~----~~~~~~~~~l~-~~g~~~~~~~-~~~~   92 (274)
                      .=.+|||+...        ..+++.+|.+     | ...+++  ..|++    .-.+.+...+. .+|..+.... ....
T Consensus        21 ~~~~l~V~nLp--------~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           21 NRRKILIRGLP--------GDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             CCCEEEEECCC--------TTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCC--------CCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            33578888774        6677777655     3 222222  22333    23445555553 3665433111 0112


Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            445689999999999999999999999999999988752      47999999999999999999999999999999999


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCC-CHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNS-TEDSIR  245 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~-tee~L~  245 (274)
                      +...      ..                                          .....+.++|||+|||+++ |+++|+
T Consensus       172 a~~~------~~------------------------------------------~~~~~~~~~l~v~nlp~~~~~~~~l~  203 (284)
T 3smz_A          172 TDAG------QL------------------------------------------TPALLHSRCLCVDRLPPGFNDVDALC  203 (284)
T ss_dssp             CCGG------GC------------------------------------------CTTTTSCSEEEEECCCTTCCCHHHHH
T ss_pred             CCCC------CC------------------------------------------CcccCCccEEEEecCCcccCCHHHHH
Confidence            8532      00                                          0022356899999999995 999999


Q ss_pred             HHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         246 RHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       246 ~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ++|++||.|.+|+|+++++|++.|
T Consensus       204 ~~f~~~G~i~~v~i~~~~~g~~~g  227 (284)
T 3smz_A          204 RALSAVHSPTFCQLACGQDGQLKG  227 (284)
T ss_dssp             HHTCSSSCCSEEEEEECSSCCEEE
T ss_pred             HHhhCCCCeEEEEEEECCCCCccc
Confidence            999999999999999998776544

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.90  E-value=4.5e-23  Score=181.08  Aligned_cols=114  Identities=24%  Similarity=0.383  Sum_probs=106.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  172 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f  172 (274)
                      .++.++|||+|||+++|+++|+++|+.|| |..|.+.+++|||||+|.+.++|..|+..|+|..+.|++|.|.|++.   
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~---   94 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT---   94 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC---
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC---
Confidence            34579999999999999999999999999 99999988899999999999999999999999999999999998642   


Q ss_pred             cccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcC
Q psy3343         173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCG  252 (274)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG  252 (274)
                                                                            .++|||+|||+++|+++|+++|++||
T Consensus        95 ------------------------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G  120 (284)
T 3smz_A           95 ------------------------------------------------------DALLCVANLPPSLTQQQFEELVRPFG  120 (284)
T ss_dssp             ------------------------------------------------------SCEEEEESCCTTCCHHHHHHHHGGGS
T ss_pred             ------------------------------------------------------CCEEEEcCCCCcCCHHHHHHHHHhcC
Confidence                                                                  36899999999999999999999999


Q ss_pred             CeeEEEEecCCC
Q psy3343         253 PIASVTVARKKD  264 (274)
Q Consensus       253 ~I~~v~v~~~~~  264 (274)
                      .|.+|+|++++.
T Consensus       121 ~i~~~~i~~~~~  132 (284)
T 3smz_A          121 SLERCFLVYSER  132 (284)
T ss_dssp             CEEEEEEEECTT
T ss_pred             CeeEEEEEeeCC
Confidence            999999998863

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.90  E-value=3.1e-23  Score=174.41  Aligned_cols=130  Identities=17%  Similarity=0.230  Sum_probs=106.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++|+++|+++|++||.|..|.+++      .+|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            358999999999999999999999999999999976      35899999999999999999999999999999999875


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ........          ..          . .                   .......++|||+|||+++|+++|+++|
T Consensus       107 ~~~~~~~~----------~~----------~-~-------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f  146 (216)
T 2qfj_A          107 NIGQAQPI----------ID----------Q-L-------------------AEEARAFNRIYVASVHQDLSDDDIKSVF  146 (216)
T ss_dssp             CCGGGHHH----------HH----------H-H-------------------HHHHTTSCEEEEECCCTTCCHHHHHHHH
T ss_pred             Cccccchh----------hh----------h-h-------------------hcccCCCcEEEEeCCCCcCCHHHHHHHH
Confidence            43100000          00          0 0                   0011245799999999999999999999


Q ss_pred             hhcCCeeEEEEecCCC
Q psy3343         249 KKCGPIASVTVARKKD  264 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~~  264 (274)
                      ++||.|.+|+|++++.
T Consensus       147 ~~~G~v~~v~i~~~~~  162 (216)
T 2qfj_A          147 EAFGKIKSATLARDPT  162 (216)
T ss_dssp             TTSSCEEEEEEEECTT
T ss_pred             hccCCeeEEEEEecCC
Confidence            9999999999999864

>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=99.90  E-value=6.8e-24  Score=171.42  Aligned_cols=122  Identities=12%  Similarity=0.236  Sum_probs=104.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|.++++      +|||||+|.+.++|..|+.  ++..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            4689999999999999999999999999999999763      4899999999999999998  4678999999998874


Q ss_pred             CCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHh
Q psy3343         169 EGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHF  248 (274)
Q Consensus       169 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F  248 (274)
                      ..      ..                                             ..+.++|||+|||+++|+++|+++|
T Consensus        80 ~~------~~---------------------------------------------~~~~~~l~V~nlp~~~t~~~l~~~F  108 (167)
T 2cjk_A           80 PR------DE---------------------------------------------QDKTGKIFVGGIGPDVRPKEFEEFF  108 (167)
T ss_dssp             CH------HH---------------------------------------------HHHCEEEEEEEECTTCCHHHHHHHH
T ss_pred             ch------hh---------------------------------------------ccCCCeEEECCCCCCCCHHHHHHHH
Confidence            22      00                                             0124689999999999999999999


Q ss_pred             hhcCCeeEEEEecCCC-CCCCC
Q psy3343         249 KKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       249 ~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ++||.|.+|+|++++. +++.|
T Consensus       109 ~~~G~i~~~~i~~~~~~g~~~g  130 (167)
T 2cjk_A          109 SQWGTIIDAQLMLDKDTGQSRG  130 (167)
T ss_dssp             HTTSCCSEEECCCSSSSSTTSE
T ss_pred             HhCccEEEEEEEEcCCCCccce
Confidence            9999999999999864 44443

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.89  E-value=1.6e-22  Score=168.29  Aligned_cols=153  Identities=21%  Similarity=0.274  Sum_probs=110.1

Q ss_pred             CCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Q psy3343          95 SKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  172 (274)
Q Consensus        95 ~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f  172 (274)
                      ++++|||+|||+ ++++++|+++|++||.|..|.+.++ +|||||+|.+.++|..|+..|+|..+.|++|.|.|+.....
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~   81 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV   81 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCc
Confidence            468999999999 9999999999999999999999886 58999999999999999999999999999999999864411


Q ss_pred             cccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcC
Q psy3343         173 AEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCG  252 (274)
Q Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG  252 (274)
                      .......   ......          ..+.....  . ...............++++|||+|||+.+|+++|+++|++||
T Consensus        82 ~~~~~~~---~~~~~~----------~~~~~~~~--~-r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G  145 (198)
T 1qm9_A           82 QLPREGQ---EDQGLT----------KDYGNSPL--H-RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG  145 (198)
T ss_dssp             CCSSSSS---SSSSCE----------EESSCCCT--T-SSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTT
T ss_pred             CCCCcCC---cccccc----------ccccCCch--h-hccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcC
Confidence            1000000   000000          00000000  0 000000000112234678999999999999999999999999


Q ss_pred             -CeeEEEEecCC
Q psy3343         253 -PIASVTVARKK  263 (274)
Q Consensus       253 -~I~~v~v~~~~  263 (274)
                       .|.+|+|+.+.
T Consensus       146 ~~v~~v~i~~~~  157 (198)
T 1qm9_A          146 GVVKGFKFFQKD  157 (198)
T ss_dssp             SCCCEEEESSTT
T ss_pred             CCceEEEEEeCC
Confidence             99999997643

>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=99.89  E-value=2.9e-22  Score=171.04  Aligned_cols=155  Identities=21%  Similarity=0.276  Sum_probs=111.6

Q ss_pred             hcCCCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          92 EARSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .....++|||+|||+ ++++++|+++|++||.|..|.+.++ +|||||+|.+.++|.+|++.|+|..+.|++|.|.|+..
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            345679999999999 9999999999999999999999886 49999999999999999999999999999999999864


Q ss_pred             CCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q psy3343         170 GVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFK  249 (274)
Q Consensus       170 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~  249 (274)
                      ..........   ......          ..+......   ...............++++|||+|||+.+|+++|+++|+
T Consensus       110 ~~~~~~~~~~---~~~~~~----------~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~  173 (229)
T 2adc_A          110 QNVQLPREGQ---EDQGLT----------KDYGNSPLH---RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFS  173 (229)
T ss_dssp             CCCCCCCSSS---STTTTE----------EECTTCSSC---CCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHH
T ss_pred             ccccCccccc---cccccc----------cccccCccc---ccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHH
Confidence            4111100000   000000          000000000   000000000112234678999999999999999999999


Q ss_pred             hcC-CeeEEEEecC
Q psy3343         250 KCG-PIASVTVARK  262 (274)
Q Consensus       250 ~fG-~I~~v~v~~~  262 (274)
                      +|| .|.+|+|+.+
T Consensus       174 ~~G~~i~~v~i~~~  187 (229)
T 2adc_A          174 SNGGVVKGFKFFQK  187 (229)
T ss_dssp             TTSCCEEEEEECSS
T ss_pred             HcCCCeeEEEEEEC
Confidence            999 9999999653

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.89  E-value=2.7e-22  Score=175.89  Aligned_cols=78  Identities=26%  Similarity=0.411  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHH----HccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .+..++|||+|||+++++++|+    ++|++||.|.+|.+.+   .+|||||+|.+.++|..|++.|+|..+.|+.|.|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            4567999999999999999976    8999999999999886   46899999999999999999999999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        86 ~a~~~   90 (282)
T 3pgw_A           86 YAKTD   90 (282)
T ss_pred             EeccC
Confidence            99644

>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=1.4e-22  Score=178.71  Aligned_cols=119  Identities=20%  Similarity=0.193  Sum_probs=100.7

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..+..++|||+|||+++|+++|+++|+.||.|..|.|.+    ++|||||+|.+.++|..|+. ++|..+.|++|.|.++
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            456779999999999999999999999999999999987    46899999999999999995 9999999999999986


Q ss_pred             cCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHH
Q psy3343         168 PEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRH  247 (274)
Q Consensus       168 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~  247 (274)
                      .                                                          .++|||+|||+.+|+++|+++
T Consensus       116 ~----------------------------------------------------------~~~l~v~nlp~~~t~~~l~~~  137 (292)
T 2ghp_A          116 T----------------------------------------------------------ECTLWMTNFPPSYTQRNIRDL  137 (292)
T ss_dssp             C----------------------------------------------------------SCEEEEECCCTTCCHHHHHHH
T ss_pred             C----------------------------------------------------------CCEEEEECCCCCCCHHHHHHH
Confidence            2                                                          368999999999999999999


Q ss_pred             hhhcC-CeeEEEEecCCCCCCCC
Q psy3343         248 FKKCG-PIASVTVARKKDPKSPG  269 (274)
Q Consensus       248 F~~fG-~I~~v~v~~~~~~~~~g  269 (274)
                      |++|| .|.+|+|+++++++..|
T Consensus       138 f~~~G~~i~~v~i~~~~~~~~~g  160 (292)
T 2ghp_A          138 LQDINVVALSIRLPSLRFNTSRR  160 (292)
T ss_dssp             HHHTTCCCCEEECC-------CC
T ss_pred             HHHhCCCeEEEEEEeCCCCCcce
Confidence            99999 99999999988766554

>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=99.88  E-value=1e-22  Score=155.82  Aligned_cols=76  Identities=18%  Similarity=0.193  Sum_probs=70.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+++    +|||||+|.+.++|.+|++.|+|..+.|++|.|.|+..+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            4689999999999999999999999999999999763    589999999999999999999999999999999998543

>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=99.87  E-value=1e-21  Score=160.01  Aligned_cols=124  Identities=25%  Similarity=0.249  Sum_probs=100.9

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE-----EEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR-----VLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-----v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      .....++|||+|||+++++++|+++|+.||.+..     .....++|||||+|.+.++|.+|++ |+|..+.|++|.|.|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            3566799999999999999999999999986544     3333367999999999999999995 999999999999999


Q ss_pred             ecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHH
Q psy3343         167 APEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRR  246 (274)
Q Consensus       167 a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~  246 (274)
                      +....      .                                           ....+.++|||+|||+.+|+++|++
T Consensus        88 ~~~~~------~-------------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~  118 (175)
T 1fje_B           88 PKGRD------S-------------------------------------------KKVRAARTLLAKNLSFNITEDELKE  118 (175)
T ss_dssp             CCCSS------C-------------------------------------------STTGGGGEEEEESCCSSCCHHHHHH
T ss_pred             CCCcc------c-------------------------------------------cccccCCEEEEeCCCCCCCHHHHHH
Confidence            85430      0                                           0112357999999999999999999


Q ss_pred             HhhhcCCeeEEEEecCCCCCCCC
Q psy3343         247 HFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       247 ~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +|++||.|..+    ..++++.|
T Consensus       119 ~F~~~g~v~~~----~~~~~~~g  137 (175)
T 1fje_B          119 VFEDALEIRLV----SQDGKSKG  137 (175)
T ss_dssp             HCTTCSEEEEE----CSSSSCCS
T ss_pred             HHHhcCeEEEe----cCCCCCce
Confidence            99999998877    44444444

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=3.8e-19  Score=132.07  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=73.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCe--eCCeEEEEEEecC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK--FKEVPLYLEWAPE  169 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~--~~g~~l~v~~a~~  169 (274)
                      ...++++|||+|||+++|+++|+++|++||.|.+|.+++++|||||+|.+.++|..|++.|++..  +.|++|+|+|+..
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            45567999999999999999999999999999999999999999999999999999999999875  7899999999864


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      +
T Consensus        97 k   97 (100)
T 3r27_A           97 Q   97 (100)
T ss_dssp             S
T ss_pred             c
Confidence            4

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=5.7e-19  Score=131.43  Aligned_cols=76  Identities=18%  Similarity=0.297  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...+++|||+|||+++|+++|+++|++||.|.+|.++++      +|||||+|.+.++|.+|++.|+|..+.|++|.|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999763      37999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      |.
T Consensus        96 Ak   97 (99)
T 4fxv_A           96 AR   97 (99)
T ss_dssp             CC
T ss_pred             ee
Confidence            84

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.9e-19  Score=135.77  Aligned_cols=83  Identities=58%  Similarity=0.984  Sum_probs=78.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF  172 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f  172 (274)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+++++||||+|.+.++|..|+..|+|..|.|++|+|+|++...|
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   86 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             ccc
Q psy3343         173 AEA  175 (274)
Q Consensus       173 ~~~  175 (274)
                      ...
T Consensus        87 ~~~   89 (111)
T 1whx_A           87 GAA   89 (111)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=3.1e-19  Score=133.81  Aligned_cols=78  Identities=18%  Similarity=0.352  Sum_probs=72.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~a~~~  170 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|++++|||||+|.+.++|..|++.|++  ..|.|++|+|.|+..+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            55679999999999999999999999999999999999999999999999999999998864  7899999999999654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=6.6e-19  Score=126.85  Aligned_cols=75  Identities=17%  Similarity=0.156  Sum_probs=72.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .....|||+||++.+|+++|+++|.+||+|.++.+..++|||||+|.++++|.+|++.||+..+.|++|.|.+|.
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 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            456899999999999999999999999999999999999999999999999999999999999999999999983

>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=3.9e-18  Score=127.30  Aligned_cols=78  Identities=19%  Similarity=0.377  Sum_probs=72.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh--CCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL--AYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l--~~~~~~g~~l~v~~a~~~  170 (274)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.+++++|||||+|.+.++|..|++.|  ++..+.|++|+|.|+..+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            345689999999999999999999999999999999999999999999999999999977  467899999999999655

>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=99.77  E-value=8.2e-19  Score=131.14  Aligned_cols=77  Identities=18%  Similarity=0.304  Sum_probs=71.6

Q ss_pred             cCCCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~a~~  169 (274)
                      ..+.++|||+|||+ .+|+++|+++|++||.|.+|.|+++++||||+|.+.++|..|++.|++  ..|.|++|+|.|+..
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~   91 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   91 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCC
Confidence            34569999999999 999999999999999999999999999999999999999999999986  459999999999964

>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=99.76  E-value=6.2e-19  Score=134.37  Aligned_cols=75  Identities=21%  Similarity=0.329  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.   ++|||||+|.+.++|..|+..|+|..+.|+.|.|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4568999999999999999999999999999999976   35899999999999999999999999999999999984

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=1.4e-18  Score=131.85  Aligned_cols=89  Identities=18%  Similarity=0.259  Sum_probs=76.3

Q ss_pred             CCCCccccchhhhcCCCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--Ce
Q psy3343          80 NGVQLDAFNQVVEARSKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TK  156 (274)
Q Consensus        80 ~g~~~~~~~~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~  156 (274)
                      +|.....+..  ...+.++|||+|||++ +++++|+++|++||.|.+|.|.+++|||||+|.+.++|..|++.|++  ..
T Consensus        11 ~~~~~k~~~~--~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~   88 (112)
T 1x4f_A           11 EGKPDQKFDQ--KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALW   88 (112)
T ss_dssp             CCCCCCCCCC--SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCC
T ss_pred             cCChhhhccc--cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCce
Confidence            3444444432  3556799999999998 99999999999999999999999999999999999999999998864  56


Q ss_pred             eCCeEEEEEEecCC
Q psy3343         157 FKEVPLYLEWAPEG  170 (274)
Q Consensus       157 ~~g~~l~v~~a~~~  170 (274)
                      |.|++|+|.|+...
T Consensus        89 l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           89 FQGRCVKVDLSEKY  102 (112)
T ss_dssp             SSSSCCEEEEECSC
T ss_pred             ECCEEEEEEECccc
Confidence            99999999999644

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=9.9e-19  Score=130.13  Aligned_cols=74  Identities=20%  Similarity=0.163  Sum_probs=70.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ++|||+|||+++++++|+++|++||.|..|.++.+ +|||||+|.+.++|..|+..|+|..+.|++|.|.|+...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999986 899999999999999999999999999999999999644

>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=99.75  E-value=3.2e-18  Score=128.48  Aligned_cols=78  Identities=21%  Similarity=0.313  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCC--eeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT--KFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~--~~~g~~l~v~~a~~~  170 (274)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++++|||||+|.+.++|..|++.|++.  .+.|++|+|+|+..+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            445689999999999999999999999999999999999999999999999999999988764  599999999999654

>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=99.75  E-value=3.4e-18  Score=131.12  Aligned_cols=78  Identities=18%  Similarity=0.352  Sum_probs=72.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~~a~~~  170 (274)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++++|||||+|.+.++|..|++.|++  ..|.|++|+|.|+..+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            44568999999999999999999999999999999999999999999999999999998874  6899999999999655

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.74  E-value=7.9e-18  Score=127.63  Aligned_cols=78  Identities=17%  Similarity=0.092  Sum_probs=71.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|.+|++.|||..+.|++|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999998753      48999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            9644

>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=6.7e-18  Score=121.47  Aligned_cols=76  Identities=20%  Similarity=0.306  Sum_probs=72.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l-~~~~~~g~~l~v~~a  167 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.+++++|||||+|.+.++|..|+..| ++..+.|++|.|.|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            3456799999999999999999999999999999999999999999999999999999999 999999999999997

>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=99.73  E-value=1.3e-17  Score=123.70  Aligned_cols=78  Identities=21%  Similarity=0.319  Sum_probs=73.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++++++||||+|.+.++|.+|++.|+|..+.|++|.|.|+...
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            445689999999999999999999999999999999999999999999999999999999999999999999998644

>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=99.73  E-value=2.4e-17  Score=117.90  Aligned_cols=74  Identities=22%  Similarity=0.256  Sum_probs=69.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .+|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+..+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999764      589999999999999999999999999999999998643

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=9.4e-18  Score=123.86  Aligned_cols=75  Identities=12%  Similarity=0.206  Sum_probs=67.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCC--eeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCC----eeCCeE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGD--LGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYT----KFKEVP  161 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~--i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~----~~~g~~  161 (274)
                      ..-.+|||+|||+++|+++|+++|++||.  +.+|++++      ++|||||+|.+.++|.+|++.|+|.    .++|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34489999999999999999999999995  57888876      3589999999999999999999996    589999


Q ss_pred             EEEEEec
Q psy3343         162 LYLEWAP  168 (274)
Q Consensus       162 l~v~~a~  168 (274)
                      |.|+||.
T Consensus        87 i~V~~Ak   93 (95)
T 2lkz_A           87 IGVDFAK   93 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEcc
Confidence            9999985

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.72  E-value=4.1e-18  Score=124.74  Aligned_cols=75  Identities=13%  Similarity=0.193  Sum_probs=67.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCC-CeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhC-CCeeCCeEEEEEEe
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLA-YTKFKEVPLYLEWA  167 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~-~~~~~g~~l~v~~a  167 (274)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++      ++|||||+|.+.++|.+|++.++ +..+.|++|.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 799999876      35899999999999999999874 56799999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      .++
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            544

>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=99.72  E-value=2.5e-17  Score=118.42  Aligned_cols=75  Identities=27%  Similarity=0.356  Sum_probs=70.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|++.|+|..+.|++|.|.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346799999999999999999999999999999998652      58999999999999999999999999999999999


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      +
T Consensus        84 a   84 (85)
T 3mdf_A           84 A   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=1.4e-17  Score=123.92  Aligned_cols=76  Identities=22%  Similarity=0.266  Sum_probs=72.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...++|||+|||+++++++|+++|++||.|.+|.+.+++|||||+|.+.++|..|+..|+|..+.|+.|.|.|+..
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            3468999999999999999999999999999999999999999999999999999999999999999999999853

>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=99.72  E-value=2.2e-17  Score=121.98  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=73.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeC--CeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK--EVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~--g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.+.++++||||+|.+.++|.+|+..|++..+.  |++|.|.|+..+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            345689999999999999999999999999999999998999999999999999999999999999  999999999644

>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=99.72  E-value=3e-17  Score=118.45  Aligned_cols=75  Identities=23%  Similarity=0.320  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|..|+..|+|..+.|+.|.|.|+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            4689999999999999999999999999999999764      4799999999999999999999999999999999985


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      .
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.72  E-value=7.1e-17  Score=120.45  Aligned_cols=79  Identities=23%  Similarity=0.268  Sum_probs=73.4

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.+    ++||||+|.+.++|.+|+..|++..|.|++|.|.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3456799999999999999999999999999999999874    689999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        91 ~~~   93 (103)
T 2cq3_A           91 TAR   93 (103)
T ss_dssp             CSS
T ss_pred             ccC
Confidence            654

>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=99.72  E-value=4.1e-17  Score=120.22  Aligned_cols=76  Identities=13%  Similarity=0.185  Sum_probs=71.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|..|+..|+|..+.|+.|.|.|+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            3589999999999999999999999999999999764      5899999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      .+
T Consensus        81 ~~   82 (96)
T 2x1f_A           81 NS   82 (96)
T ss_dssp             CS
T ss_pred             CC
Confidence            55

>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=99.72  E-value=2.7e-17  Score=124.14  Aligned_cols=78  Identities=18%  Similarity=0.229  Sum_probs=74.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++++++||||+|.+.++|..|+..|+|..+.|++|.|.|+...
T Consensus        22 ~~~~~~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           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            455699999999999999999999999999999999999999999999999999999999999999999999999654

>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=99.71  E-value=2.6e-17  Score=121.44  Aligned_cols=77  Identities=22%  Similarity=0.291  Sum_probs=71.8

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH----HccccCCCeeEEEeeCC---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPY---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~l~~~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...++|||+|||+++++++|+    ++|++||.|.+|.|+.+   ++||||+|.+.++|.+|++.|+|..+.|++|.|.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            346899999999999999999    99999999999999875   78999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        87 a~~~   90 (96)
T 2dgx_A           87 ATGA   90 (96)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9644

>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=99.71  E-value=1.7e-17  Score=126.11  Aligned_cols=77  Identities=18%  Similarity=0.332  Sum_probs=71.4

Q ss_pred             CCCcEEEE--eCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCee-----CCeEEEEEE
Q psy3343          94 RSKRIILV--KNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF-----KEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V--~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~-----~g~~l~v~~  166 (274)
                      .+.++|||  +|||+++++++|+++|++||.|.+|.|++++|||||+|.+.++|.+|++.|||..+     .|++|+|.|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            45688999  66999999999999999999999999998999999999999999999999999998     789999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..-
T Consensus       103 a~~~  106 (114)
T 2cq2_A          103 VEKV  106 (114)
T ss_dssp             ESCC
T ss_pred             cccC
Confidence            8644

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.71  E-value=2.6e-17  Score=119.45  Aligned_cols=78  Identities=26%  Similarity=0.347  Sum_probs=73.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  171 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~  171 (274)
                      .++.++|||+|||+++++++|+++|++| .|..|.++..+|||||+|.+.++|..|++.|+|..+.|++|.|+|++.+.
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            3567899999999999999999999999 99999998888999999999999999999999999999999999998663

>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=99.71  E-value=5.9e-17  Score=117.10  Aligned_cols=75  Identities=12%  Similarity=0.170  Sum_probs=69.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..++|||+|||+++++++|+++|++||.|..|.++.       .+|||||+|.+.++|.+|+..|+|..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            468999999999999999999999999999999865       3579999999999999999999999999999999998


Q ss_pred             cC
Q psy3343         168 PE  169 (274)
Q Consensus       168 ~~  169 (274)
                      ..
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.71  E-value=5.2e-17  Score=122.46  Aligned_cols=77  Identities=29%  Similarity=0.291  Sum_probs=72.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC-----eEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE-----VPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g-----~~l~v~~a  167 (274)
                      .+..++|||+|||+++++++|+++|++||.|..|.|+.+ +||||+|.+.++|..|++.|++..|.|     +.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a   90 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   90 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeC
Confidence            456799999999999999999999999999999999988 899999999999999999999999999     99999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        91 ~~~   93 (108)
T 1x4c_A           91 GPR   93 (108)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.71  E-value=5.5e-17  Score=121.04  Aligned_cols=79  Identities=20%  Similarity=0.251  Sum_probs=72.9

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.    .++||||+|.+.++|.+|+..|++..+.|++|.|.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            345679999999999999999999999999999999987    3589999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        91 ~~~   93 (103)
T 2cqi_A           91 TTP   93 (103)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            644

>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=99.71  E-value=3.8e-17  Score=119.97  Aligned_cols=76  Identities=22%  Similarity=0.224  Sum_probs=70.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+     +|||||+|.+.++|.+|+..|++..+.|++|.|.|+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            445699999999999999999999999999999999874     479999999999999999999999999999999998


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        93 ~   93 (95)
T 2ywk_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.71  E-value=6e-17  Score=119.88  Aligned_cols=78  Identities=22%  Similarity=0.292  Sum_probs=72.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345699999999999999999999999999999999764      48999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        85 a~~~   88 (99)
T 1whw_A           85 STIK   88 (99)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=5.1e-17  Score=121.94  Aligned_cols=79  Identities=35%  Similarity=0.623  Sum_probs=73.2

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-------CeEEEEEecCHHHHHHHHHHh-CCCeeCCeEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-------GITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLY  163 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-------~~~afV~F~~~~~A~~A~~~l-~~~~~~g~~l~  163 (274)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.+       +|||||+|.+.++|.+|+..| ++..|.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3556799999999999999999999999999999999775       589999999999999999999 99999999999


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |.|+...
T Consensus        91 v~~a~~~   97 (107)
T 2cph_A           91 LEWADSE   97 (107)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            9999644

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.1e-17  Score=120.03  Aligned_cols=77  Identities=16%  Similarity=0.146  Sum_probs=71.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEE-EeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      .+.++|||+|||+++++++|+++|++||.|..| .++.+      +|||||+|.+.++|.+|+..|+|..+.|++|.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456999999999999999999999999999998 88764      58999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        83 a~~~   86 (96)
T 1x5t_A           83 AFKK   86 (96)
T ss_dssp             SCCC
T ss_pred             eccc
Confidence            8644

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=7.8e-17  Score=118.29  Aligned_cols=77  Identities=19%  Similarity=0.341  Sum_probs=71.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            35689999999999999999999999999999999874      479999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        83 ~~~   85 (95)
T 2dnz_A           83 TER   85 (95)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5.8e-17  Score=117.99  Aligned_cols=76  Identities=21%  Similarity=0.321  Sum_probs=71.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++  ++||||+|.+.++|..|+..|++..+.|++|.|.|+...
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            3456999999999999999999999999999999998  689999999999999999999999999999999998644

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=5.1e-17  Score=120.04  Aligned_cols=77  Identities=21%  Similarity=0.281  Sum_probs=70.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ...++|||+|||+++++++|+++|++||.|..|.++.         .+|||||+|.+.++|..|+..|+|..+.|++|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4568999999999999999999999999999999874         2479999999999999999999999999999999


Q ss_pred             EEecCC
Q psy3343         165 EWAPEG  170 (274)
Q Consensus       165 ~~a~~~  170 (274)
                      .|+...
T Consensus        83 ~~a~~~   88 (98)
T 2cpf_A           83 RISERA   88 (98)
T ss_dssp             ECSSCS
T ss_pred             EEccCC
Confidence            998644

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=7.8e-17  Score=118.06  Aligned_cols=75  Identities=23%  Similarity=0.327  Sum_probs=70.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+      ++||||+|.+.++|.+|++.|++..+.|++|.|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            456699999999999999999999999999999999763      47999999999999999999999999999999999


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      |
T Consensus        93 a   93 (94)
T 2e5h_A           93 A   93 (94)
T ss_dssp             C
T ss_pred             c
Confidence            7

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.1e-17  Score=119.83  Aligned_cols=78  Identities=28%  Similarity=0.457  Sum_probs=72.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            445699999999999999999999999999999999764      37999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        92 a~~~   95 (103)
T 2cq0_A           92 AKPS   95 (103)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=9.7e-17  Score=119.03  Aligned_cols=78  Identities=17%  Similarity=0.257  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC-----eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG-----ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~-----~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.++     |||||+|.+.++|.+|+..|+|..+.|++|.|.|+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            4556999999999999999999999999999999998743     89999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        94 ~~~   96 (100)
T 2do4_A           94 NSG   96 (100)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.70  E-value=1.1e-16  Score=120.71  Aligned_cols=79  Identities=20%  Similarity=0.270  Sum_probs=72.5

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.+   ++||||+|.+.++|.+|++.|++..|.|++|.|.|+.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            3456699999999999999999999999999999999774   5799999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        98 ~~   99 (109)
T 1x4a_A           98 SG   99 (109)
T ss_dssp             CC
T ss_pred             cC
Confidence            44

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.2e-17  Score=120.39  Aligned_cols=78  Identities=24%  Similarity=0.245  Sum_probs=72.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+    ++||||+|.+.++|..|+..|++..+.|++|.|.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            345699999999999999999999999999999999854    6899999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        92 ~~   93 (103)
T 2d9p_A           92 RK   93 (103)
T ss_dssp             SC
T ss_pred             cc
Confidence            44

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.7e-17  Score=122.13  Aligned_cols=79  Identities=23%  Similarity=0.265  Sum_probs=72.9

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.+..+    +|||||+|.+.++|.+|+..|+|..+.|++|.|.|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3456699999999999999999999999999999999864    689999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6e-17  Score=120.55  Aligned_cols=78  Identities=26%  Similarity=0.323  Sum_probs=72.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|++.|++..|.|++|.|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            446799999999999999999999999999999999763      58999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        89 a~~~   92 (102)
T 2cqb_A           89 AKPM   92 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9644

>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=99.69  E-value=6e-17  Score=122.78  Aligned_cols=77  Identities=16%  Similarity=0.267  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHH---HccccCCCeeEEEeeCCC---------eEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLK---ALFEPFGDLGRVLVPPYG---------ITGLVEFLQKNQAKAAFNSLAYTKFKEVP  161 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~---~~F~~~G~i~~v~l~~~~---------~~afV~F~~~~~A~~A~~~l~~~~~~g~~  161 (274)
                      ...++|||+|||+++++++|+   ++|++||.|..|.++++.         |||||+|.+.++|.+|++.|+|..|.|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346899999999999999999   999999999999998632         79999999999999999999999999999


Q ss_pred             EEEEEecCC
Q psy3343         162 LYLEWAPEG  170 (274)
Q Consensus       162 l~v~~a~~~  170 (274)
                      |.|.|+..+
T Consensus        93 l~V~~a~~k  101 (111)
T 2cpi_A           93 LKASLGTTK  101 (111)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEecccc
Confidence            999999755

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.69  E-value=1.5e-16  Score=117.75  Aligned_cols=77  Identities=19%  Similarity=0.330  Sum_probs=71.0

Q ss_pred             hcCCCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          92 EARSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..+..++|||+|||+ ++++++|+++|++||.|..|.+.  +|||||+|.+.++|..|+..|+|..+.|+.|.|+|+...
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            355679999999998 99999999999999999999995  789999999999999999999999999999999998543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.69  E-value=5.5e-17  Score=123.08  Aligned_cols=77  Identities=23%  Similarity=0.226  Sum_probs=71.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCC-CeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ....++|||+|||+++++++|+++|++|| .|..+.+..  .+|||||+|.+.++|.+|++.|+|..|.|++|.|+++..
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            45568999999999999999999999999 899999863  679999999999999999999999999999999999853

>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=99.69  E-value=1e-16  Score=119.98  Aligned_cols=77  Identities=23%  Similarity=0.301  Sum_probs=71.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCC---eEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKE---VPLYLE  165 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g---~~l~v~  165 (274)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+     +|||||+|.+.++|..|+..|+|..+.|   ++|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            45699999999999999999999999999999999875     5899999999999999999999999998   999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        93 ~a~~~   97 (105)
T 2dnh_A           93 FADTD   97 (105)
T ss_dssp             ESCSS
T ss_pred             ECccC
Confidence            99644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.4e-16  Score=116.45  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=70.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.+.++  ||||+|.+.++|..|+..|++..+.|+.|.|.|+...
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   82 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR   82 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCC
Confidence            455699999999999999999999999999999999854  9999999999999999999999999999999999644

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.69  E-value=1.3e-16  Score=121.45  Aligned_cols=78  Identities=23%  Similarity=0.333  Sum_probs=72.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            456799999999999999999999999999999999864      47999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        92 a~~~   95 (115)
T 2dgo_A           92 ATRK   95 (115)
T ss_dssp             SSCC
T ss_pred             ccCC
Confidence            9654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=1.2e-16  Score=120.69  Aligned_cols=77  Identities=22%  Similarity=0.371  Sum_probs=71.8

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.+.  +|||||+|.+.++|..|+..|+|..+.|++|.|.|+...
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            45667999999999999999999999999999999998  789999999999999999999999999999999998644

>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=99.69  E-value=1.6e-16  Score=119.33  Aligned_cols=77  Identities=23%  Similarity=0.289  Sum_probs=71.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.+     +|||||+|.+.++|.+|+..|+|..+.|++|.|.|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456799999999999999999999999999999999853     57999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            84

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.68  E-value=6.2e-17  Score=118.10  Aligned_cols=78  Identities=19%  Similarity=0.173  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.+++    .++||||+|.+.++|..|+..|++..+.|++|.|.|+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            44569999999999999999999999999999999986    35899999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        85 ~~   86 (92)
T 2dgv_A           85 NA   86 (92)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.68  E-value=9e-17  Score=118.41  Aligned_cols=78  Identities=26%  Similarity=0.408  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHH----HccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ..+.++|||+|||+++++++|+    ++|++||.|..|.++.   .+|||||+|.+.++|..|+..|+|..+.|++|.|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4567999999999999999999    9999999999999974   56899999999999999999999999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        85 ~a~~~   89 (97)
T 1nu4_A           85 YAKTD   89 (97)
T ss_dssp             ECSSC
T ss_pred             EccCC
Confidence            99644

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=5.6e-17  Score=121.48  Aligned_cols=74  Identities=20%  Similarity=0.254  Sum_probs=69.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.     ++|||||+|.+.++|..|+. +++..+.|++|.|.|+.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            3458999999999999999999999999999999987     46899999999999999998 89999999999999975

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.6e-16  Score=116.60  Aligned_cols=76  Identities=17%  Similarity=0.139  Sum_probs=70.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..|+|..+.|++|.|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345689999999999999999999999999999999753      47999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus        92 a~   93 (95)
T 2cqc_A           92 PS   93 (95)
T ss_dssp             CS
T ss_pred             cC
Confidence            85

>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=99.68  E-value=1.3e-16  Score=120.43  Aligned_cols=78  Identities=17%  Similarity=0.247  Sum_probs=71.8

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3455689999999999999999999999999999999764      4899999999999999999999999999999999


Q ss_pred             EecC
Q psy3343         166 WAPE  169 (274)
Q Consensus       166 ~a~~  169 (274)
                      |+..
T Consensus       102 ~a~~  105 (110)
T 1oo0_B          102 WCFV  105 (110)
T ss_dssp             ESEE
T ss_pred             Eccc
Confidence            9853

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.9e-16  Score=117.24  Aligned_cols=77  Identities=18%  Similarity=0.273  Sum_probs=70.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+. |++..+.|++|.|.|
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            345699999999999999999999999999999999763      5899999999999999998 999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus        86 a~~~   89 (99)
T 2dgs_A           86 AEPR   89 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=8.9e-17  Score=119.61  Aligned_cols=78  Identities=21%  Similarity=0.300  Sum_probs=72.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+      ++||||+|.+.++|..|++.|++..|.|++|.|.|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            445699999999999999999999999999999999773      57999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        89 a~~~   92 (102)
T 1x5s_A           89 AGKS   92 (102)
T ss_dssp             EECC
T ss_pred             CCCC
Confidence            9644

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=9.5e-17  Score=119.74  Aligned_cols=78  Identities=27%  Similarity=0.414  Sum_probs=72.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..+.|++|.|.|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            445699999999999999999999999999999999763      58999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        90 a~~~   93 (103)
T 2dnm_A           90 ARYG   93 (103)
T ss_dssp             CSSC
T ss_pred             CCcC
Confidence            9644

>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=99.68  E-value=9.1e-17  Score=121.27  Aligned_cols=80  Identities=20%  Similarity=0.291  Sum_probs=72.8

Q ss_pred             hhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          91 VEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        91 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ......++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|++.|+|..+.|++|.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34556799999999999999999999999999999999753      479999999999999999999999999999999


Q ss_pred             EEecCC
Q psy3343         165 EWAPEG  170 (274)
Q Consensus       165 ~~a~~~  170 (274)
                      .|+..+
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            998643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=118.29  Aligned_cols=76  Identities=18%  Similarity=0.212  Sum_probs=70.1

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--------EEeeCC------CeEEEEEecCHHHHHHHHHHhCCCee
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--------VLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKF  157 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~  157 (274)
                      .....++|||+|||+++++++|+++|++||.|..        |.++.+      +|||||+|.+.++|..|++.|+|..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456699999999999999999999999999998        888753      47999999999999999999999999


Q ss_pred             CCeEEEEEEe
Q psy3343         158 KEVPLYLEWA  167 (274)
Q Consensus       158 ~g~~l~v~~a  167 (274)
                      .|+.|.|.||
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999999997

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=8.8e-17  Score=120.48  Aligned_cols=77  Identities=18%  Similarity=0.301  Sum_probs=71.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            445689999999999999999999999999999999753      48999999999999999999999999999999999


Q ss_pred             ecC
Q psy3343         167 APE  169 (274)
Q Consensus       167 a~~  169 (274)
                      +..
T Consensus       100 a~~  102 (106)
T 1p27_B          100 CFV  102 (106)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            853

>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=99.68  E-value=1.8e-16  Score=114.89  Aligned_cols=73  Identities=22%  Similarity=0.285  Sum_probs=68.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+ .|+|..+.|++|.|.|+..
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            489999999999999999999999999999999763      689999999999999999 8999999999999999854

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.68  E-value=3.7e-17  Score=121.64  Aligned_cols=73  Identities=23%  Similarity=0.215  Sum_probs=68.9

Q ss_pred             CcEEEEeCCCC------CCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCC-eEE
Q psy3343          96 KRIILVKNLPY------RTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKE-VPL  162 (274)
Q Consensus        96 ~~~l~V~nLp~------~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g-~~l  162 (274)
                      +++|||+|||+      ++++++|+++|++||.|.+|.|+.      ++|||||+|.+.++|.+|++.|+|..+.| ++|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            58999999999      999999999999999999999975      35899999999999999999999999999 999


Q ss_pred             EEEEec
Q psy3343         163 YLEWAP  168 (274)
Q Consensus       163 ~v~~a~  168 (274)
                      .|.|+.
T Consensus        86 ~V~~a~   91 (100)
T 3ns6_A           86 FLYTMK   91 (100)
T ss_dssp             EEEESH
T ss_pred             EEEECc
Confidence            999984

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.5e-16  Score=115.72  Aligned_cols=76  Identities=24%  Similarity=0.267  Sum_probs=70.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++++  ||||+|.+.++|..|+..|+|..+.|++|.|.|+...
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--CEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            445699999999999999999999999999999999854  9999999999999999999999999999999998644

>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=99.67  E-value=1.4e-16  Score=119.17  Aligned_cols=79  Identities=23%  Similarity=0.243  Sum_probs=72.4

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..|++..|.|++|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456699999999999999999999999999999999773      4799999999999999999999999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        91 ~a~~~   95 (105)
T 1x5u_A           91 KASAH   95 (105)
T ss_dssp             ETTTT
T ss_pred             ECCCC
Confidence            98644

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.1e-16  Score=118.01  Aligned_cols=76  Identities=20%  Similarity=0.329  Sum_probs=70.1

Q ss_pred             cCCCcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+ .+++++|+++|++||.|..|.++  +|||||+|.+.++|..|+..|+|..+.|++|.|.|+...
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   83 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN   83 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcC
Confidence            44579999999999 99999999999999999999996  689999999999999999999999999999999999644

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=9.8e-17  Score=124.63  Aligned_cols=78  Identities=18%  Similarity=0.286  Sum_probs=70.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHH----HccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+..   .+|||||+|.+.++|..|+..|+|..|.|++|.|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            4456899999999999999876    6999999999999875   46899999999999999999999999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus       106 ~a~~~  110 (127)
T 2a3j_A          106 FSETP  110 (127)
T ss_dssp             ECCCC
T ss_pred             EccCc
Confidence            99654

>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=99.67  E-value=1.6e-16  Score=120.88  Aligned_cols=78  Identities=21%  Similarity=0.210  Sum_probs=71.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|.+|++.|++..|.|++|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999998764      37999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus       102 a~~~  105 (115)
T 2cpz_A          102 KRSK  105 (115)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8644

>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=99.67  E-value=1.9e-16  Score=119.51  Aligned_cols=78  Identities=18%  Similarity=0.293  Sum_probs=72.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhC------CCeeCCe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLA------YTKFKEV  160 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~------~~~~~g~  160 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|+      +..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            455789999999999999999999999999999999853      5899999999999999999999      9999999


Q ss_pred             EEEEEEecCC
Q psy3343         161 PLYLEWAPEG  170 (274)
Q Consensus       161 ~l~v~~a~~~  170 (274)
                      +|.|.|+..+
T Consensus        92 ~l~v~~a~~~  101 (111)
T 1x4h_A           92 QLKVDLAVTR  101 (111)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999998644

>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=99.67  E-value=1.9e-16  Score=121.06  Aligned_cols=78  Identities=21%  Similarity=0.199  Sum_probs=72.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+     +|||||+|.+.++|.+|+..|+|..+.|++|.|.|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            345689999999999999999999999999999999874     389999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        84 ~~~   86 (116)
T 2fy1_A           84 KKP   86 (116)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3e-16  Score=119.07  Aligned_cols=77  Identities=22%  Similarity=0.204  Sum_probs=71.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+     ++||||+|.+.++|..|+..|++..|.|+.|.|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            455799999999999999999999999999999999874     579999999999999999999999999999999998


Q ss_pred             cC
Q psy3343         168 PE  169 (274)
Q Consensus       168 ~~  169 (274)
                      ..
T Consensus        92 ~~   93 (114)
T 2do0_A           92 ER   93 (114)
T ss_dssp             SC
T ss_pred             cc
Confidence            53

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.8e-16  Score=121.11  Aligned_cols=75  Identities=21%  Similarity=0.247  Sum_probs=70.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|+|..+.|+.|.|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            445699999999999999999999999999999999763      58999999999999999999999999999999998


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=99.67  E-value=3.1e-16  Score=113.24  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=68.2

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++ +++..+.|++|.|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999999763      4799999999999999996 68889999999999


Q ss_pred             Ee
Q psy3343         166 WA  167 (274)
Q Consensus       166 ~a  167 (274)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.67  E-value=1.7e-16  Score=118.41  Aligned_cols=75  Identities=19%  Similarity=0.275  Sum_probs=70.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ...++|||+|||+++++++|+++|++||.|..|.++  ++||||+|.+.++|.+|+..|++..|.|++|.|.|+...
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            456899999999999999999999999999999997  459999999999999999999999999999999999644

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=5e-17  Score=116.91  Aligned_cols=75  Identities=17%  Similarity=0.159  Sum_probs=69.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..|+|..+.|+.|.+.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45689999999999999999999999999999999764      589999999999999999999999999999988775


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.4e-16  Score=117.90  Aligned_cols=78  Identities=13%  Similarity=0.100  Sum_probs=71.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCee-EEEeeCCC------eEEEEEecCHHHHHHHHHHhCCCeeCCeE----
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLG-RVLVPPYG------ITGLVEFLQKNQAKAAFNSLAYTKFKEVP----  161 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~-~v~l~~~~------~~afV~F~~~~~A~~A~~~l~~~~~~g~~----  161 (274)
                      ....++|||+|||+++++++|+++|++||.|. .|.+++++      |||||+|.+.++|.+|+..|+|..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34569999999999999999999999999999 99997643      89999999999999999999999999999    


Q ss_pred             EEEEEecCC
Q psy3343         162 LYLEWAPEG  170 (274)
Q Consensus       162 l~v~~a~~~  170 (274)
                      |.|.|+...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998644

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=5.1e-16  Score=114.57  Aligned_cols=76  Identities=24%  Similarity=0.317  Sum_probs=71.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+||  ++++++|+++|++||.|..|.|...+|||||+|.+.++|.+|+..|+|..+.|++|.|.|+...
T Consensus        12 ~~~~~~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           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            446699999996  8999999999999999999999988999999999999999999999999999999999999644

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.8e-16  Score=115.11  Aligned_cols=76  Identities=22%  Similarity=0.251  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccC--CCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPF--GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+.+++++|+++|++|  |.|..|.++  ++||||+|.+.++|..|+..|+|..|.|++|.|.|+...
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            4456999999999999999999999999  999999886  569999999999999999999999999999999999644

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.66  E-value=1.5e-16  Score=119.30  Aligned_cols=76  Identities=17%  Similarity=0.250  Sum_probs=70.0

Q ss_pred             CCCcEEEEeCCCCCC------CHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCe-EE
Q psy3343          94 RSKRIILVKNLPYRT------LPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEV-PL  162 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~------te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~-~l  162 (274)
                      ...++|||+|||+.+      ++++|+++|++||.|..|.|++    ++|||||+|.+.++|..|+..|+|..+.|+ +|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            346899999999999      7899999999999999999984    468999999999999999999999999998 99


Q ss_pred             EEEEecC
Q psy3343         163 YLEWAPE  169 (274)
Q Consensus       163 ~v~~a~~  169 (274)
                      .|.|+..
T Consensus        93 ~V~~a~~   99 (105)
T 2nlw_A           93 RVNLFTD   99 (105)
T ss_dssp             EEECSCC
T ss_pred             EEEEcch
Confidence            9999853

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3e-16  Score=119.01  Aligned_cols=78  Identities=19%  Similarity=0.163  Sum_probs=71.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCee--------EEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLG--------RVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--------~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      ....++|||+|||+++++++|+++|++||.|.        .|.|+.+      +|||||+|.+.++|.+|+..|+|..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            45679999999999999999999999999998        5888764      579999999999999999999999999


Q ss_pred             CeEEEEEEecCC
Q psy3343         159 EVPLYLEWAPEG  170 (274)
Q Consensus       159 g~~l~v~~a~~~  170 (274)
                      |+.|.|.|+...
T Consensus        92 g~~l~V~~a~~~  103 (113)
T 2cpe_A           92 GSKLKVSLARKK  103 (113)
T ss_dssp             TEECEEECSSCC
T ss_pred             CCEEEEEECCCC
Confidence            999999998644

>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=99.66  E-value=4.1e-16  Score=116.51  Aligned_cols=76  Identities=20%  Similarity=0.288  Sum_probs=69.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ....++|||+|||+++++++|+++|++|| |..|.|+.+       +|||||+|.+.++|.+|+ .|++..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34569999999999999999999999999 999999763       579999999999999999 899999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        90 ~a~~~   94 (104)
T 1wi8_A           90 VADQA   94 (104)
T ss_dssp             ECCCC
T ss_pred             EccCC
Confidence            98644

>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=99.66  E-value=1.7e-16  Score=126.48  Aligned_cols=78  Identities=22%  Similarity=0.178  Sum_probs=73.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|.+|.++++ +|||||+|.+.++|..|+..|+|..+.|++|.|.|+..+
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            445699999999999999999999999999999999986 899999999999999999999999999999999998643

>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=99.66  E-value=2.3e-16  Score=121.91  Aligned_cols=79  Identities=18%  Similarity=0.291  Sum_probs=72.4

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|+|..|.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3445689999999999999999999999999999999764      6899999999999999999999999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        98 ~a~~~  102 (126)
T 3ex7_B           98 WCFVR  102 (126)
T ss_dssp             ESEES
T ss_pred             EecCC
Confidence            99543

>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=99.66  E-value=1.1e-16  Score=117.24  Aligned_cols=77  Identities=16%  Similarity=0.181  Sum_probs=69.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCC-eeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC-CeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGD-LGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY-TKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~-~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||. |..+.+. .++||||+|.+.++|..|+..|+| ..+.|++|.|.|+..+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            345689999999999999999999999999 6666553 578999999999999999999999 9999999999999644

>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=99.66  E-value=1.4e-16  Score=118.82  Aligned_cols=76  Identities=24%  Similarity=0.325  Sum_probs=70.6

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|++.|+|..+.|++|.|.|+.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            4589999999999999999999999999999998763      5899999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        87 ~~   88 (104)
T 1p1t_A           87 SE   88 (104)
T ss_dssp             CT
T ss_pred             Cc
Confidence            44

>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=99.65  E-value=2.5e-16  Score=117.99  Aligned_cols=78  Identities=21%  Similarity=0.258  Sum_probs=71.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCee---CCeEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKF---KEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~---~g~~l~  163 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|++..+   .|++|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            455699999999999999999999999999999999873      58999999999999999999999988   899999


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |.|+...
T Consensus        90 v~~a~~~   96 (106)
T 2dgp_A           90 VKPADSE   96 (106)
T ss_dssp             EEECCCC
T ss_pred             EEECCcc
Confidence            9999644

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=1.1e-16  Score=114.21  Aligned_cols=69  Identities=19%  Similarity=0.285  Sum_probs=63.9

Q ss_pred             CcEEEEeCCCCCC------CHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCe-EEEE
Q psy3343          96 KRIILVKNLPYRT------LPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEV-PLYL  164 (274)
Q Consensus        96 ~~~l~V~nLp~~~------te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~-~l~v  164 (274)
                      +++|||+|||+.+      ++++|+++|++||.|.+|.+++    .+|||||+|.+.++|..|+..|+|..+.|+ +|.|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3789999999999      7899999999999999999985    468999999999999999999999999999 8765

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.65  E-value=6e-16  Score=120.18  Aligned_cols=74  Identities=20%  Similarity=0.252  Sum_probs=68.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeE-EEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGIT-GLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~-afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~  170 (274)
                      ..|||+||++.+|+++|+++|++||.|.+|.+.. .+|| |||+|.+.++|..|++.|+|..|.|  ++|+|+|+...
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            6778999999999999999999999999998866 5677 9999999999999999999999988  99999999654

>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=99.65  E-value=2.3e-16  Score=118.76  Aligned_cols=77  Identities=13%  Similarity=0.154  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCC-eeEEEee-------CCCeEEEEEecCHHHHHHHHHHhC--CCeeCCeEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGD-LGRVLVP-------PYGITGLVEFLQKNQAKAAFNSLA--YTKFKEVPLY  163 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~l~-------~~~~~afV~F~~~~~A~~A~~~l~--~~~~~g~~l~  163 (274)
                      ...++|||+|||+++++++|+++|++||. |..|.++       ..+|||||+|.+.++|..|+..|+  +..+.|++|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35689999999999999999999999998 9999998       356899999999999999999996  5899999999


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |.|+...
T Consensus        86 V~~a~~~   92 (109)
T 2dis_A           86 VDWAEPE   92 (109)
T ss_dssp             EEESCSS
T ss_pred             EEEcCCC
Confidence            9999644

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.9e-16  Score=115.19  Aligned_cols=77  Identities=18%  Similarity=0.200  Sum_probs=68.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEee--CCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~--~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+++++++|+++|++||.|. +.+.  ..+|||||+|.+.++|..|+..|+|..+.|++|.|.|+..+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            34568999999999999999999999999995 4443  46799999999999999999999999999999999998643

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.65  E-value=2.6e-16  Score=113.48  Aligned_cols=72  Identities=18%  Similarity=0.260  Sum_probs=68.4

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccC----C-------CeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPF----G-------DLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPL  162 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G-------~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l  162 (274)
                      +..++|||+|||+++++++|+++|++|    |       .|.++.+.+++|||||+|.+.++|.+|+ .|+|..+.|++|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l   82 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL   82 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEE
Confidence            346899999999999999999999999    8       9999999999999999999999999999 999999999999


Q ss_pred             EEEE
Q psy3343         163 YLEW  166 (274)
Q Consensus       163 ~v~~  166 (274)
                      .|++
T Consensus        83 ~V~r   86 (87)
T 2hzc_A           83 KIRR   86 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9975

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.65  E-value=7.3e-16  Score=118.89  Aligned_cols=78  Identities=22%  Similarity=0.285  Sum_probs=72.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.     .+|||||+|.+.++|..|+..|+|..+.|++|.|.|+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            34568999999999999999999999999999999987     3589999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus       112 ~~~  114 (124)
T 2kt5_A          112 ASQ  114 (124)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            755

>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=99.65  E-value=8.4e-17  Score=117.24  Aligned_cols=74  Identities=15%  Similarity=0.101  Sum_probs=64.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCC--CeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .+|||+|||+++++++|+++|++||  .|.+|.++.+      +|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  9999988763      4799999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>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=99.65  E-value=1.5e-16  Score=116.68  Aligned_cols=76  Identities=16%  Similarity=0.186  Sum_probs=67.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..+.++.      .+|||||+|.+.++|.+|++.|++..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            44569999999999999999999999999997666654      248999999999999999999999999999999998


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.5e-16  Score=118.14  Aligned_cols=78  Identities=24%  Similarity=0.299  Sum_probs=71.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|.+|+..|++ .|.|++|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            3556799999999999999999999999999999999874      47999999999999999999998 8999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        92 ~a~~~   96 (116)
T 2cqd_A           92 LAYLG   96 (116)
T ss_dssp             ESTTT
T ss_pred             EcccC
Confidence            99543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.65  E-value=7e-16  Score=115.05  Aligned_cols=76  Identities=21%  Similarity=0.254  Sum_probs=69.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++|| |..|.|+.+      +|||||+|.+.++|..|+ .|++..|.|++|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            44569999999999999999999999997 999999764      479999999999999999 8999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        90 a~~~   93 (103)
T 2dng_A           90 AEGR   93 (103)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8644

>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=99.65  E-value=2e-16  Score=116.83  Aligned_cols=77  Identities=17%  Similarity=0.190  Sum_probs=68.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..+.++.      .+|||||+|.+.++|.+|++.|+|..|.|++|.|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            44568999999999999999999999999997655543      248999999999999999999999999999999999


Q ss_pred             ecC
Q psy3343         167 APE  169 (274)
Q Consensus       167 a~~  169 (274)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            853

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.65  E-value=1.5e-16  Score=111.60  Aligned_cols=69  Identities=20%  Similarity=0.271  Sum_probs=64.7

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++ |++..+.|++|.|.||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999999763      4899999999999999998 9999999999999986

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.64  E-value=5.9e-16  Score=121.50  Aligned_cols=75  Identities=27%  Similarity=0.356  Sum_probs=69.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.|+|..|.|++|.|.|
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            445699999999999999999999999999999999763      58999999999999999999999999999999998


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.64  E-value=4.6e-16  Score=117.51  Aligned_cols=73  Identities=18%  Similarity=0.225  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ..++|||+|||+. +++++|+++|++||.|..|.+  .++||||+|.+.++|..|+..|++..+.|++|.|.|+..
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4489999999999 999999999999999999999  578999999999999999999999999999999999853

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-16  Score=117.72  Aligned_cols=78  Identities=17%  Similarity=0.083  Sum_probs=71.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHcccc-CCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCe-eCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEP-FGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTK-FKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~-~~g~~l~v~  165 (274)
                      ....++|||+|||+++++++|+++|++ ||.|..|.|+.+     +|||||+|.+.++|..|+..|++.. +.|++|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            345699999999999999999999999 999999999764     5899999999999999999999999 999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      |+...
T Consensus        86 ~a~~~   90 (104)
T 2dhg_A           86 VAIPK   90 (104)
T ss_dssp             BCCCC
T ss_pred             EccCC
Confidence            98544

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=3.6e-16  Score=113.68  Aligned_cols=72  Identities=17%  Similarity=0.336  Sum_probs=65.2

Q ss_pred             CCcEEEEeCCCCCCCHHH----HHHccccC-CCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYRTLPTD----LKALFEPF-GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~----l~~~F~~~-G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      +.+.|||+|||+.+++++    |+++|++| |.|..|    .+|+|||.|.+.++|.+|++.|+|..+.||+|.|.||+.
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~   83 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPK   83 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----ecCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCC
Confidence            445699999999999988    55899999 599888    459999999999999999999999999999999999975


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      +
T Consensus        84 ~   84 (96)
T 2diu_A           84 N   84 (96)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=1.8e-16  Score=111.71  Aligned_cols=70  Identities=17%  Similarity=0.289  Sum_probs=65.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|+..++ ..+.|++|.|.||
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            57999999999999999999999999999999763      4799999999999999999999 9999999999987

>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=99.64  E-value=3.6e-16  Score=121.77  Aligned_cols=78  Identities=17%  Similarity=0.168  Sum_probs=71.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.      .+|||||+|.+.++|.+|+..|+|..|.|++|.|.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999975      358999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8543

>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=99.64  E-value=7.4e-16  Score=117.03  Aligned_cols=73  Identities=22%  Similarity=0.333  Sum_probs=68.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.      .+|||||+|.+.++|.+|+ .|+|..|.|+.|.|.|+.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            348999999999999999999999999999999975      3579999999999999999 899999999999999984

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=111.04  Aligned_cols=76  Identities=9%  Similarity=0.136  Sum_probs=69.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++| .|..|.|+.+     +|||||+|.+.++|.+|+. |+|..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            4456999999999999999999999999 8999998763     5799999999999999999 9999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            644

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.63  E-value=8.5e-16  Score=123.56  Aligned_cols=74  Identities=12%  Similarity=0.098  Sum_probs=68.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCC--CeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..++|||+|||+++++++|+++|++||  .|..|.++.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            458999999999999999999999999  9999999753      47999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus       134 a~  135 (156)
T 3n9u_C          134 AT  135 (156)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>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=99.63  E-value=8.5e-16  Score=124.50  Aligned_cols=78  Identities=17%  Similarity=0.241  Sum_probs=71.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.+      +|||||+|.+.++|..|+..|+|..|.|++|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999864      48999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       149 a~~~  152 (165)
T 1rk8_A          149 CFVK  152 (165)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            8543

>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=99.63  E-value=1.3e-15  Score=115.62  Aligned_cols=77  Identities=14%  Similarity=0.259  Sum_probs=70.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCee--------CC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKF--------KE  159 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~--------~g  159 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+     +|||||+|.+.++|..|+..|+|..+        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            345699999999999999999999999999999999764     48999999999999999999999999        57


Q ss_pred             eEEEEEEecC
Q psy3343         160 VPLYLEWAPE  169 (274)
Q Consensus       160 ~~l~v~~a~~  169 (274)
                      ++|.|.|+..
T Consensus       102 ~~l~v~~a~p  111 (114)
T 1x5o_A          102 EPLLCKFSGP  111 (114)
T ss_dssp             SCBEEEECCC
T ss_pred             CceeEEccCC
Confidence            8899999853

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=112.11  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=67.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ...++|||+|||+++++++|+++|++||.|.+|.+.+. +.||||+|.+.++|.+|+. |+|..|.|+.|.|.++...
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            34589999999999999999999999999999855442 2399999999999999999 9999999999999988644

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.5e-15  Score=112.76  Aligned_cols=75  Identities=23%  Similarity=0.295  Sum_probs=67.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|   .++.     .+|||||+|.+.++|.+|+..|++..|.|++|.|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            4557999999999999999999999999987   3333     3689999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        89 ~~~   91 (101)
T 2fc9_A           89 GPR   91 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            644

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.63  E-value=6.7e-16  Score=121.34  Aligned_cols=78  Identities=23%  Similarity=0.293  Sum_probs=71.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|+.||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999999753      57999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       119 a~~~  122 (139)
T 1u6f_A          119 AASG  122 (139)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9644

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=1.2e-15  Score=117.69  Aligned_cols=74  Identities=20%  Similarity=0.228  Sum_probs=66.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeE-EEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT-GLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~-afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~  170 (274)
                      ..|||+|||+.+++++|+++|++||.|.+|.|....|| |||+|.+.++|..|++.|+|..|.|  ++|.|.||...
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            34679999999999999999999999999988664575 9999999999999999999999987  69999999654

>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=99.63  E-value=1.6e-16  Score=115.52  Aligned_cols=73  Identities=27%  Similarity=0.300  Sum_probs=66.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ++|||+|||+++++++|+++|++||.|.+|.++.+      +|||||+|.+.+ |..|+..|+|..+.|++|.|.||...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999763      589999999999 99999999999999999999998644

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.62  E-value=7.5e-16  Score=118.68  Aligned_cols=75  Identities=24%  Similarity=0.334  Sum_probs=69.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+ .|+|..|.|+.|.|.|+.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999999999998753      589999999999999999 799999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.62  E-value=3.7e-16  Score=116.08  Aligned_cols=75  Identities=20%  Similarity=0.288  Sum_probs=67.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ....++|||+|||+++++++|+++|++|| |.+|.|+.+       +|||||+|.+.++|.+|+ .|+|..|.|+.|.|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            44569999999999999999999999999 999999763       479999999999999999 899999999999999


Q ss_pred             EecC
Q psy3343         166 WAPE  169 (274)
Q Consensus       166 ~a~~  169 (274)
                      |+..
T Consensus        94 ~a~~   97 (100)
T 2j76_E           94 VADQ   97 (100)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            9854

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=8.6e-16  Score=112.96  Aligned_cols=78  Identities=19%  Similarity=0.275  Sum_probs=70.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEE-EeeCC--CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPPY--GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~l~~~--~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ....++|||+|||+++++++|+++|++||.|..| .++.+  .+.|||+|.+.++|..|+..|+|..+.|++|.|.|+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            3456899999999999999999999999999999 47664  35699999999999999999999999999999999964


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus        92 ~   92 (96)
T 2e44_A           92 E   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.62  E-value=2.3e-15  Score=120.68  Aligned_cols=78  Identities=18%  Similarity=0.299  Sum_probs=71.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.+      ++||||+|.+.++|.+|+..|++..|.|++|.|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345699999999999999999999999999999999763      37999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       116 a~~~  119 (156)
T 1h2v_Z          116 DAGF  119 (156)
T ss_dssp             ESCC
T ss_pred             CCCC
Confidence            9643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.62  E-value=1.5e-15  Score=114.64  Aligned_cols=77  Identities=17%  Similarity=0.241  Sum_probs=67.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..+ +..+.|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            455699999999999999999999999999999999763      479999999999999999975 5999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus       101 a~~~  104 (109)
T 2rs2_A          101 AFPR  104 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8644

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.62  E-value=5.5e-16  Score=124.21  Aligned_cols=76  Identities=21%  Similarity=0.269  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..+.+..+      +|||||+|.+.++|.+|+..|+|..+.|++|.|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            445689999999999999999999999999999999753      47999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      |.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            84

>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=99.62  E-value=2.3e-15  Score=109.54  Aligned_cols=75  Identities=16%  Similarity=0.293  Sum_probs=62.4

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCe--eCCeEEEEEEec
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTK--FKEVPLYLEWAP  168 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~--~~g~~l~v~~a~  168 (274)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+. ++|||||+|.+.++|.+    +++..  +.|+.|.|.++.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            355679999999999999999999999999999999987 58999999999999983    56655  469999999985


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      .+
T Consensus        83 ~k   84 (89)
T 3d2w_A           83 PK   84 (89)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.62  E-value=6.4e-16  Score=117.86  Aligned_cols=75  Identities=29%  Similarity=0.308  Sum_probs=66.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeE-----EEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP-----LYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~-----l~v~~a  167 (274)
                      .+..++|||+|||+++++++|+++|++||.|..|.|+.+ |||||+|.+.++|..|++.|+|..|.|+.     |.|..+
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~   91 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   91 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccC
Confidence            356799999999999999999999999999999999887 89999999999999999999999999988     555554


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        92 ~   92 (115)
T 3beg_B           92 G   92 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.62  E-value=1.3e-15  Score=122.22  Aligned_cols=77  Identities=29%  Similarity=0.453  Sum_probs=71.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            44699999999999999999999999999999999763      479999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus       148 ~~~  150 (158)
T 2kn4_A          148 RYG  150 (158)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            644

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.6e-15  Score=115.54  Aligned_cols=75  Identities=19%  Similarity=0.229  Sum_probs=69.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+.. ++..|.|+.|.|.|+.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            3489999999999999999999999999999999874      47999999999999999987 9999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      .+
T Consensus       105 ~~  106 (116)
T 1x4b_A          105 AR  106 (116)
T ss_dssp             SC
T ss_pred             CC
Confidence            44

>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=99.61  E-value=9.4e-16  Score=116.52  Aligned_cols=78  Identities=21%  Similarity=0.251  Sum_probs=69.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCe----eEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDL----GRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i----~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|    ..+.+..  .+|||||+|.+.++|..|+..|+|..+.|++|.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456999999999999999999999999998    5665554  468999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       102 a~~~  105 (115)
T 2cpx_A          102 GKNK  105 (115)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9644

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=9.5e-16  Score=112.71  Aligned_cols=77  Identities=21%  Similarity=0.274  Sum_probs=68.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+.+++++|+++|++||.|..+ ...  .+|||||+|.+.++|..|+..|+|..+.|++|.|.|+..+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            4456999999999999999999999999998777 222  4589999999999999999999999999999999998544

>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=99.61  E-value=1.2e-15  Score=122.84  Aligned_cols=74  Identities=20%  Similarity=0.269  Sum_probs=68.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~  170 (274)
                      .+|||+|||+.+|+++|+++|++||.|.+|.|..  .++||||+|.+.++|..|++.|+|..|.|  ++|.|+|+...
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            6789999999999999999999999999999864  46899999999999999999999999966  99999999654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=9.3e-16  Score=114.72  Aligned_cols=77  Identities=16%  Similarity=0.187  Sum_probs=70.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+.. ++..|.|+.|.|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            455699999999999999999999999999999999774      37999999999999999998 99999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus        92 a~~~   95 (105)
T 2dh8_A           92 CTPR   95 (105)
T ss_dssp             SCCS
T ss_pred             ccCC
Confidence            8644

>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=99.61  E-value=1.2e-15  Score=115.98  Aligned_cols=75  Identities=16%  Similarity=0.140  Sum_probs=68.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCe-eEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDL-GRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i-~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++|+++|+++|+.||.| ..|.|+.     .+|||||+|.+.++|.+|+.. ++..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            4456899999999999999999999999999 7888875     468999999999999999986 99999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus        91 a~   92 (114)
T 2cpy_A           91 VT   92 (114)
T ss_dssp             EC
T ss_pred             CC
Confidence            85

>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=99.60  E-value=3.8e-15  Score=110.96  Aligned_cols=76  Identities=20%  Similarity=0.225  Sum_probs=68.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|..|+.  ++..+.|+.|.|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            445689999999999999999999999999999999764      3799999999999999998  57899999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus        90 a~~~   93 (103)
T 2cqg_A           90 PNSK   93 (103)
T ss_dssp             CCTT
T ss_pred             cCCC
Confidence            8644

>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=99.60  E-value=2.7e-15  Score=112.27  Aligned_cols=77  Identities=10%  Similarity=0.194  Sum_probs=68.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE-EEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|.. |.|+.     .+|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            345699999999999999999999999999987 77765     358999999999999999996 99999999999998


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.60  E-value=2.7e-15  Score=114.91  Aligned_cols=75  Identities=11%  Similarity=0.088  Sum_probs=68.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCC---eeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGD---LGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.+     +|||||+|.+.++|.+|+. +++..|.|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            445689999999999999999999999999   888888753     4799999999999999999 9999999999999


Q ss_pred             EEec
Q psy3343         165 EWAP  168 (274)
Q Consensus       165 ~~a~  168 (274)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9984

>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=99.59  E-value=2.1e-15  Score=119.12  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=69.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--------EEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--------VLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVP  161 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~  161 (274)
                      ....++|||+|||+.+|+++|+.+|++||.|..        +.+..   .+|||||+|.+.++|..|+..|+|..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            446699999999999999999999999999865        43333   5689999999999999999999999999999


Q ss_pred             EEEEEecCC
Q psy3343         162 LYLEWAPEG  170 (274)
Q Consensus       162 l~v~~a~~~  170 (274)
                      |.|.|+...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999999543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.6e-15  Score=110.21  Aligned_cols=78  Identities=23%  Similarity=0.255  Sum_probs=66.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ....++|||+|||+++++++|+++|+.|+.|.-+.-..   .++||||+|.+.++|.+|+..|++..|.|+.|.|.|+..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   91 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP   91 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            45569999999999999999999999986443332222   248999999999999999999999999999999999964


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      +
T Consensus        92 ~   92 (102)
T 2fc8_A           92 K   92 (102)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.59  E-value=6.4e-16  Score=121.26  Aligned_cols=78  Identities=28%  Similarity=0.448  Sum_probs=71.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|++|.|.|
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999763      57999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       124 a~~~  127 (135)
T 2lea_A          124 ARYG  127 (135)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9644

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.59  E-value=4.9e-16  Score=121.14  Aligned_cols=78  Identities=14%  Similarity=0.183  Sum_probs=70.2

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--EEeeCC------CeEEEEEecCHHHHHHHHHHhCCC----eeCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--VLVPPY------GITGLVEFLQKNQAKAAFNSLAYT----KFKE  159 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~----~~~g  159 (274)
                      .....++|||+|||+++|+++|+++|++||.|..  |+|+.+      +|||||+|.+. +|.+|+..|+|.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456689999999999999999999999999966  888763      48999999999 999999999999    9999


Q ss_pred             eEEEEEEecCC
Q psy3343         160 VPLYLEWAPEG  170 (274)
Q Consensus       160 ~~l~v~~a~~~  170 (274)
                      ++|.|.|+...
T Consensus        98 r~l~V~~a~~~  108 (131)
T 2m2b_A           98 KTINVEFAKGS  108 (131)
T ss_dssp             CCCCCEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999998543

>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=99.58  E-value=5e-15  Score=110.54  Aligned_cols=76  Identities=21%  Similarity=0.290  Sum_probs=67.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++|+++|+++|++||.+ .|.|+.+     +|||||+|.+.++|.+|+. +++..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3456899999999999999999999999954 8888753     4799999999999999995 8999999999999988


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.58  E-value=7.2e-16  Score=108.08  Aligned_cols=69  Identities=17%  Similarity=0.233  Sum_probs=64.0

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+. +++..+.|++|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            5899999999999999999999999999999763      5899999999999999998 5899999999999875

>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=99.57  E-value=3.3e-15  Score=117.28  Aligned_cols=75  Identities=11%  Similarity=0.067  Sum_probs=68.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCC---eeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGD---LGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ....++|||+|||+++|+++|+++|++||.   |..|.|+.+     +|||||+|.+.++|.+|++ |++..|.|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            445689999999999999999999999999   888888753     4899999999999999999 9999999999999


Q ss_pred             EEec
Q psy3343         165 EWAP  168 (274)
Q Consensus       165 ~~a~  168 (274)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9974

>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=99.57  E-value=1.1e-15  Score=117.92  Aligned_cols=75  Identities=16%  Similarity=0.203  Sum_probs=65.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEE-Eee--C---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRV-LVP--P---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v-~l~--~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++|+++|+++|+.||.|..+ .+.  .   .+|||||+|.+.++|.+|+. |++..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            345899999999999999999999999999763 332  1   25899999999999999999 9999999999999998


Q ss_pred             cC
Q psy3343         168 PE  169 (274)
Q Consensus       168 ~~  169 (274)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=8.6e-16  Score=114.08  Aligned_cols=76  Identities=17%  Similarity=0.104  Sum_probs=67.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+++++++|+++|++||.|.. .++.      .+|||||+|.+.++|.+|++ |+|..+.|+.|.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            445689999999999999999999999998766 2322      57899999999999999998 999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +..+
T Consensus        92 a~~~   95 (101)
T 1fj7_A           92 PKGR   95 (101)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            8644

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=9.3e-15  Score=110.41  Aligned_cols=71  Identities=17%  Similarity=0.254  Sum_probs=65.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..+|||+|||+++|+++|+++|+.| .|..|.|+.     .+|||||+|.+.++|.+|+ .+++..|.|+.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4799999999999999999999999 899999976     3589999999999999999 599999999999998874

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.57  E-value=1.6e-15  Score=112.79  Aligned_cols=76  Identities=17%  Similarity=0.229  Sum_probs=69.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+     +|||||+|.+.++|..|+.  ++..+.|+.|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            344589999999999999999999999999999999873     4899999999999999998  999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            644

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.56  E-value=3.2e-15  Score=127.83  Aligned_cols=79  Identities=18%  Similarity=0.340  Sum_probs=72.5

Q ss_pred             hcCCCcEEEEeCCCCCC---------CHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCee-----
Q psy3343          92 EARSKRIILVKNLPYRT---------LPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF-----  157 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~---------te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~-----  157 (274)
                      .....++|||+|||..+         ++++|+.+|++||.|.+|.++.++|||||+|.+.++|..|++.|+|..|     
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            35567999999999998         7999999999999999999999999999999999999999999999999     


Q ss_pred             -------CCeEEEEEEecCC
Q psy3343         158 -------KEVPLYLEWAPEG  170 (274)
Q Consensus       158 -------~g~~l~v~~a~~~  170 (274)
                             .|+.|.|.||...
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                   8999999999644

>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=99.56  E-value=2.2e-15  Score=113.27  Aligned_cols=75  Identities=11%  Similarity=0.036  Sum_probs=68.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCC---eeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGD---LGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~---i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      ....++|||+|||+++|+++|+++|+.||.   |..|.|+.     .+|||||+|.+.++|.+|+. +++..+.|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            345689999999999999999999999988   88998876     35899999999999999999 9999999999999


Q ss_pred             EEec
Q psy3343         165 EWAP  168 (274)
Q Consensus       165 ~~a~  168 (274)
                      .++.
T Consensus        87 ~~a~   90 (107)
T 2lmi_A           87 YEIN   90 (107)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9984

>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=99.56  E-value=4.4e-15  Score=107.43  Aligned_cols=74  Identities=16%  Similarity=0.272  Sum_probs=63.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..++|||+|||+++++++|+++|++||.|..|.++. .+|||||+|.+.++|++|..  ....+.|++|.|.|+..+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCCC
Confidence            469999999999999999999999999999999987 48999999999999975432  134458999999998644

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.56  E-value=1.1e-14  Score=122.56  Aligned_cols=136  Identities=18%  Similarity=0.207  Sum_probs=98.0

Q ss_pred             cccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHhh--------hhhh----hHHHHHHHHHH-HCCCCccc-
Q psy3343          26 TWNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRLA--------MGET----EIVEKTRAFLE-ENGVQLDA-   86 (274)
Q Consensus        26 ~wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~a--------l~e~----~~~~~~~~~l~-~~g~~~~~-   86 (274)
                      .-.+|||+...        +.+++++|.+     |....|++.        .|++    .-...+...+. .+|..+.. 
T Consensus        14 p~~tlfVgnLp--------~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~   85 (213)
T 4f02_A           14 PMASLYVGDLH--------PDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK   85 (213)
T ss_dssp             -CCEEEEESCC--------TTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCcEEEEeCCC--------CCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCc
Confidence            34579998874        7777777755     444444432        1222    22344444443 34433211 


Q ss_pred             -----cc---hhhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCC
Q psy3343          87 -----FN---QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAY  154 (274)
Q Consensus        87 -----~~---~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~  154 (274)
                           +.   ........++|||+|||+.+|+++|+++|++||.|..|.|++    .+|||||+|.+.++|.+|++.|||
T Consensus        86 ~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng  165 (213)
T 4f02_A           86 PVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG  165 (213)
T ss_dssp             ECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             ccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCC
Confidence                 00   111233457999999999999999999999999999999976    358999999999999999999999


Q ss_pred             CeeCCeEEEEEEecC
Q psy3343         155 TKFKEVPLYLEWAPE  169 (274)
Q Consensus       155 ~~~~g~~l~v~~a~~  169 (274)
                      ..|.|++|.|.|+..
T Consensus       166 ~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          166 MLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CEETTEECEEEECCC
T ss_pred             CEECCEEEEEEEcCC
Confidence            999999999999853

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.55  E-value=8.1e-15  Score=120.22  Aligned_cols=77  Identities=22%  Similarity=0.284  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+     +|||||+|.+.++|..|+..|+|..|.|++|.|.|+.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34689999999999999999999999999999999763     5899999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            44

>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=99.55  E-value=6.4e-15  Score=125.72  Aligned_cols=74  Identities=15%  Similarity=0.124  Sum_probs=68.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCC--CeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFG--DLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..++|||+|||+++|+++|+++|++||  .|.+|.|+.+      +|||||+|.+.++|.+|+..|++..|.|+.|.|.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            458999999999999999999999999  9999999763      47999999999999999999999999999999999


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            85

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.32  E-value=3.5e-16  Score=119.26  Aligned_cols=78  Identities=18%  Similarity=0.206  Sum_probs=70.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--------EEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--------VLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      ....++|||+|||+.+++++|+++|++||.|..        |.++.+      +|||||+|.+.++|.+|+..|+|..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            345689999999999999999999999999988        777653      579999999999999999999999999


Q ss_pred             CeEEEEEEecCC
Q psy3343         159 EVPLYLEWAPEG  170 (274)
Q Consensus       159 g~~l~v~~a~~~  170 (274)
                      |++|.|.|+..+
T Consensus        84 g~~l~V~~a~~~   95 (116)
T 2lcw_A           84 GNPIKVSFATRR   95 (116)
Confidence            999999998644

>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=99.54  E-value=1.5e-14  Score=116.76  Aligned_cols=73  Identities=18%  Similarity=0.236  Sum_probs=69.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|+..|+|..+.|++|.|.||
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            4589999999999999999999999999999999764      489999999999999999999999999999999997

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.53  E-value=2.9e-14  Score=119.30  Aligned_cols=78  Identities=21%  Similarity=0.247  Sum_probs=72.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+++++|+++|++||.|..|.+.++      +|||||+|.+.++|.+|+..|+|..|.|++|.|.|
T Consensus       122 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~  201 (216)
T 2qfj_A          122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK  201 (216)
T ss_dssp             HTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEE
T ss_pred             cCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEE
Confidence            345689999999999999999999999999999999864      58999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus       202 a~~~  205 (216)
T 2qfj_A          202 AVTP  205 (216)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            8644

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=7e-14  Score=104.86  Aligned_cols=77  Identities=17%  Similarity=0.215  Sum_probs=67.8

Q ss_pred             cCCCcEEEEeCCCC-----CCCHHHHHHccccCCCeeEEEeeC-------CCeEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3343          93 ARSKRIILVKNLPY-----RTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNSLAYTKFKEV  160 (274)
Q Consensus        93 ~~~~~~l~V~nLp~-----~~te~~l~~~F~~~G~i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~  160 (274)
                      ..+.++|+|+||..     +-++++|+++|++||.|.+|.++.       ++|||||+|.+.++|.+|+..|||..|.|+
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            34578999999963     247899999999999999999874       258999999999999999999999999999


Q ss_pred             EEEEEEecC
Q psy3343         161 PLYLEWAPE  169 (274)
Q Consensus       161 ~l~v~~a~~  169 (274)
                      +|.|.|++.
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999863

>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=99.52  E-value=3.3e-14  Score=132.21  Aligned_cols=77  Identities=14%  Similarity=0.251  Sum_probs=71.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+|+++|..+|++||.|..|.|+.+      +|||||+|.+.++|..||..|+|..|.|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34589999999999999999999999999999999763      589999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.51  E-value=3.9e-14  Score=116.88  Aligned_cols=77  Identities=19%  Similarity=0.253  Sum_probs=71.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+++++|+++|++||.|..|.++++      +|||||+|.+.++|..|+..|+|..+.|++|.|.|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45699999999999999999999999999999999864      589999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus       192 ~~~  194 (198)
T 2yh0_A          192 SVG  194 (198)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.51  E-value=6e-14  Score=112.65  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=69.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v  164 (274)
                      ....++|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|+..|+|..+.|  ++|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            345689999999999999999999999999999998764      3799999999999999999999999988  99999


Q ss_pred             EEe
Q psy3343         165 EWA  167 (274)
Q Consensus       165 ~~a  167 (274)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1e-14  Score=112.59  Aligned_cols=75  Identities=15%  Similarity=0.185  Sum_probs=66.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCe----eEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDL----GRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i----~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .....+|||+|||+++|+++|+++|++||.|    ..|.|+.     .+|||||+|.+.++|.+|+.. ++..|.|+.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            3456899999999999999999999999975    5787765     248999999999999999985 99999999999


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98874

>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=99.51  E-value=6.7e-15  Score=115.96  Aligned_cols=76  Identities=21%  Similarity=0.274  Sum_probs=67.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++|+++|+++|++|| |..|.|+.     .+|||||+|.+.++|.+|+ .+++..|.|+.|.|.++
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999 77999876     3589999999999999999 78999999999999987


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=99.50  E-value=3.6e-14  Score=114.58  Aligned_cols=73  Identities=15%  Similarity=0.340  Sum_probs=67.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeC---CeEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFK---EVPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~---g~~l~v~~  166 (274)
                      ..++|||+|||+.+|+++|+++|++||.|.+|.++++     +|||||+|.+.++|.+|+..|+|..+.   +++|.|.|
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            4589999999999999999999999999999999874     579999999999999999999998776   49999999


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      |
T Consensus       174 a  174 (175)
T 3nmr_A          174 A  174 (175)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=99.50  E-value=5.9e-14  Score=122.62  Aligned_cols=75  Identities=28%  Similarity=0.321  Sum_probs=70.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC-eEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~-~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a~  168 (274)
                      ...++|||+|||+.+++++|+++|++||.|.+|.+.+++ |||||+|.+.++|.+|+..|+|..|. |++|.|.|+.
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 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            356899999999999999999999999999999999865 89999999999999999999999999 9999999984

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=4.5e-14  Score=107.28  Aligned_cols=73  Identities=19%  Similarity=0.202  Sum_probs=62.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      ....++|||+|||+++++++|+++|++||.|. +.++.         .+|||||+|.+.++|.+|++.|+  .++|+.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34568999999999999999999999999999 77754         25899999999999999999884  47888888


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      +..++
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            77654

>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=99.50  E-value=3.4e-14  Score=109.99  Aligned_cols=73  Identities=11%  Similarity=0.223  Sum_probs=65.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCee--EEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLG--RVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~--~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...++|||+|||+++|+++|+++|++| .|.  .|.|+.     .+|||||+|.+.++|.+|+. +++..|.|+.|.|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            456899999999999999999999999 566  898876     35899999999999999998 578999999999988


Q ss_pred             ec
Q psy3343         167 AP  168 (274)
Q Consensus       167 a~  168 (274)
                      +.
T Consensus       118 a~  119 (126)
T 2hgm_A          118 SS  119 (126)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>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=99.49  E-value=4e-14  Score=113.67  Aligned_cols=76  Identities=13%  Similarity=0.206  Sum_probs=69.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++ ++|..+.|++|.|.|+
T Consensus        85 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a  163 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRA  163 (167)
T ss_dssp             HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEEC
T ss_pred             cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeec
Confidence            34679999999999999999999999999999999763      4899999999999999998 8999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      .++
T Consensus       164 ~pk  166 (167)
T 2cjk_A          164 EPR  166 (167)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.48  E-value=1e-13  Score=117.92  Aligned_cols=75  Identities=17%  Similarity=0.185  Sum_probs=70.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCC-CeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEecC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAPE  169 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a~~  169 (274)
                      +.++|||+|||+.+++++|+++|++|| .|..|.+.+ ++|||||+|.+.++|.+|+..|+|..+. |++|.|.|+..
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            358999999999999999999999999 999999944 7899999999999999999999999999 99999999864

>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=99.48  E-value=1.8e-13  Score=103.66  Aligned_cols=79  Identities=18%  Similarity=0.197  Sum_probs=68.3

Q ss_pred             hcCCCcEEEEeCCCCCCC-----------HHHHHHccccCCCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          92 EARSKRIILVKNLPYRTL-----------PTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~t-----------e~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      .....++|+|+||.....           +++|+++|++||.|..|.|+.  .+|||||+|.+.++|..|+..|+|..|.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            345679999999954432           689999999999999998753  5799999999999999999999999999


Q ss_pred             CeEEEEEEecCC
Q psy3343         159 EVPLYLEWAPEG  170 (274)
Q Consensus       159 g~~l~v~~a~~~  170 (274)
                      |++|.|.|+...
T Consensus        91 gr~l~v~~a~~~  102 (112)
T 2dit_A           91 GRQITAQAWDGT  102 (112)
T ss_dssp             TEECEEEECCSC
T ss_pred             CcEEEEEEeCCC
Confidence            999999998543

>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=99.48  E-value=9.3e-14  Score=112.59  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=68.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEee--CCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP--PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~--~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ...++|||+|||+.+++++|+++|++||.|..+ ..  ..+|||||+|.+.++|.+|+..|+|..+.|++|.|.|+.++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            345899999999999999999999999998877 22  15689999999999999999999999999999999998643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.47  E-value=6.9e-14  Score=115.82  Aligned_cols=76  Identities=17%  Similarity=0.178  Sum_probs=70.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCC-CeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFG-DLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G-~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a~~~  170 (274)
                      +.++|||+|||+.+++++|+++|++|| .|..|.+.+ ++|||||+|.+.++|.+|+..|+|..+. |++|.|.|+...
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 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            368999999999999999999999999 999999955 7899999999999999999999999999 999999998643

>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=99.47  E-value=1.4e-13  Score=113.31  Aligned_cols=137  Identities=15%  Similarity=0.170  Sum_probs=96.4

Q ss_pred             ccccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHhh--------hhhh----hHHHHHHHHHHHCCCCcccc
Q psy3343          25 HTWNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRLA--------MGET----EIVEKTRAFLEENGVQLDAF   87 (274)
Q Consensus        25 ~~wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~a--------l~e~----~~~~~~~~~l~~~g~~~~~~   87 (274)
                      ..-.+|||+...        +.+++.+|.+     |....|++.        .|++    .-.+++..++..++..+...
T Consensus        11 ~~~~~l~V~nLp--------~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~   82 (196)
T 1l3k_A           11 EQLRKLFIGGLS--------FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGR   82 (196)
T ss_dssp             GGGGEEEEESCC--------TTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTE
T ss_pred             CCCCEEEEeCCC--------CCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCE
Confidence            455678888763        6666666654     333333331        2232    23456666666665432210


Q ss_pred             ------ch-------hhhcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHH
Q psy3343          88 ------NQ-------VVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAA  148 (274)
Q Consensus        88 ------~~-------~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A  148 (274)
                            ..       +......++|||+|||+++++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|
T Consensus        83 ~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A  162 (196)
T 1l3k_A           83 VVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  162 (196)
T ss_dssp             ECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             EeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHH
Confidence                  00       111234589999999999999999999999999999999763      47999999999999999


Q ss_pred             HHHhCCCeeCCeEEEEEEecCC
Q psy3343         149 FNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus       149 ~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +.. ++..|.|+.|.|.|+..+
T Consensus       163 ~~~-~~~~~~G~~i~v~~a~~k  183 (196)
T 1l3k_A          163 VIQ-KYHTVNGHNCEVRKALSK  183 (196)
T ss_dssp             HHC-SCCEETTEECEEEECC--
T ss_pred             HHh-CCcEECCEEEEEEecCCh
Confidence            985 899999999999999644

>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=99.47  E-value=1e-13  Score=115.25  Aligned_cols=73  Identities=21%  Similarity=0.280  Sum_probs=66.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .++|||+|||+++++++|+++|++||.|..|+|++     .+|||||+|.+.++|..|+..+ +..+.|++|.|.|+..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            48999999999999999999999999999999986     3589999999999999999855 5699999999999753

>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=99.47  E-value=1.3e-13  Score=110.41  Aligned_cols=75  Identities=20%  Similarity=0.302  Sum_probs=68.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCe--EEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEV--PLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~--~l~v  164 (274)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|+..|+|..+.|+  +|.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            345689999999999999999999999999999998763      48999999999999999999999999996  4888


Q ss_pred             EEe
Q psy3343         165 EWA  167 (274)
Q Consensus       165 ~~a  167 (274)
                      .||
T Consensus       165 ~~A  167 (167)
T 1fxl_A          165 KFA  167 (167)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            886

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.45  E-value=1.7e-13  Score=105.17  Aligned_cols=75  Identities=12%  Similarity=0.055  Sum_probs=65.4

Q ss_pred             CcEEEEeCC----CCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecC----HHH----HHHHHH--HhCCC
Q psy3343          96 KRIILVKNL----PYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQ----KNQ----AKAAFN--SLAYT  155 (274)
Q Consensus        96 ~~~l~V~nL----p~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~----~~~----A~~A~~--~l~~~  155 (274)
                      ++.|||+||    |+.+++.+|+.+|++||+|.+|.+..+      +|||||+|.+    +++    |.+|+.  .|+|.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            378999999    999999999999999999999988763      4899999996    433    889988  78999


Q ss_pred             eeCCeEEEEEEecCC
Q psy3343         156 KFKEVPLYLEWAPEG  170 (274)
Q Consensus       156 ~~~g~~l~v~~a~~~  170 (274)
                      .|.|++|.|.+-..+
T Consensus        82 ~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           82 FIMGFKFEVILNKHS   96 (136)
T ss_dssp             EETTEEEEEEECCTT
T ss_pred             eecCcEEEEEECccc
Confidence            999999999987655

>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=99.44  E-value=2.2e-13  Score=122.36  Aligned_cols=76  Identities=20%  Similarity=0.325  Sum_probs=68.4

Q ss_pred             cCCCcEEEEeC--CCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeC---Ce--EEEEE
Q psy3343          93 ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK---EV--PLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~---g~--~l~v~  165 (274)
                      ..+..+|||+|  |++.+|+++|+++|++||.|.+|.+++++|||||+|.+.++|++|++.|||..+.   |+  +|+|.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            34568999999  5889999999999999999999999999999999999999999999999999883   44  78998


Q ss_pred             Eec
Q psy3343         166 WAP  168 (274)
Q Consensus       166 ~a~  168 (274)
                      |+.
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            874

>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=99.42  E-value=6.6e-13  Score=99.50  Aligned_cols=76  Identities=16%  Similarity=0.245  Sum_probs=66.3

Q ss_pred             CCcEEEEeCC--CCCC--------CHHHHHHccccCCCeeEEEeeCC--------CeEEEEEecCHHHHHHHHHHhCCCe
Q psy3343          95 SKRIILVKNL--PYRT--------LPTDLKALFEPFGDLGRVLVPPY--------GITGLVEFLQKNQAKAAFNSLAYTK  156 (274)
Q Consensus        95 ~~~~l~V~nL--p~~~--------te~~l~~~F~~~G~i~~v~l~~~--------~~~afV~F~~~~~A~~A~~~l~~~~  156 (274)
                      +.++|.++|+  |...        .+++|++.|++||.|.+|.|+++        +|+|||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5688999998  3333        24799999999999999999762        5899999999999999999999999


Q ss_pred             eCCeEEEEEEecCC
Q psy3343         157 FKEVPLYLEWAPEG  170 (274)
Q Consensus       157 ~~g~~l~v~~a~~~  170 (274)
                      |.||+|.|.|++..
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999998643

>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=99.41  E-value=3.4e-13  Score=113.00  Aligned_cols=73  Identities=19%  Similarity=0.240  Sum_probs=65.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCe--eEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCe----EEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDL--GRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEV----PLYL  164 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i--~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~----~l~v  164 (274)
                      +.++|||+|||+.+|+++|+++|++||.|  .++++.++    +|||||+|.+.++|.+|+..|||..|.|.    |+.|
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~v  201 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTL  201 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEEC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEE
Confidence            34689999999999999999999999999  89998764    38999999999999999999999999886    6777


Q ss_pred             EEe
Q psy3343         165 EWA  167 (274)
Q Consensus       165 ~~a  167 (274)
                      .||
T Consensus       202 k~~  204 (205)
T 3tyt_A          202 KLC  204 (205)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            765

>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=99.41  E-value=1.6e-13  Score=119.00  Aligned_cols=137  Identities=20%  Similarity=0.189  Sum_probs=97.5

Q ss_pred             ccccccccChhHHHHHHHHHhCCCcccccC-----CchhHHHh--hhhhh----hHHHHHHHHHH-HCCCCccccc-hhh
Q psy3343          25 HTWNSLFLGTNAIAEAMAETYNATKAEVLT-----GSGAATRL--AMGET----EIVEKTRAFLE-ENGVQLDAFN-QVV   91 (274)
Q Consensus        25 ~~wn~lf~~~~~v~~~~~~~~~~~~~~l~~-----~~~~avr~--al~e~----~~~~~~~~~l~-~~g~~~~~~~-~~~   91 (274)
                      ..=++|||+...        +.++..+|.+     |....|++  ..|++    .-...+..++. .+|..+.... ...
T Consensus        20 ~~~~~l~V~nLp--------~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~   91 (261)
T 3sde_A           20 TQRCRLFVGNLP--------TDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR   91 (261)
T ss_dssp             CGGGEEEEESCC--------TTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEECCC--------CCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEee
Confidence            344578988874        6777777755     44434433  12333    22445555554 5665433211 011


Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhC-CCeeC---CeEE
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLA-YTKFK---EVPL  162 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~-~~~~~---g~~l  162 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|..|.++.+     +|||||+|.+.++|..|+..|+ +..+.   +++|
T Consensus        92 ~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i  171 (261)
T 3sde_A           92 FATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV  171 (261)
T ss_dssp             ECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBC
T ss_pred             ecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceE
Confidence            2345689999999999999999999999999999998763     5899999999999999999995 45554   8999


Q ss_pred             EEEEecC
Q psy3343         163 YLEWAPE  169 (274)
Q Consensus       163 ~v~~a~~  169 (274)
                      .|.++..
T Consensus       172 ~v~~~~~  178 (261)
T 3sde_A          172 IVEPMEQ  178 (261)
T ss_dssp             EEEECCC
T ss_pred             EEeeccc
Confidence            9999853

>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=99.40  E-value=9.3e-14  Score=103.99  Aligned_cols=68  Identities=19%  Similarity=0.266  Sum_probs=60.3

Q ss_pred             EeCCCCCCCHHHHHHcc------------ccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343         101 VKNLPYRTLPTDLKALF------------EPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus       101 V~nLp~~~te~~l~~~F------------~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      +.|||+.+++++|++.|            ++||.|.+|.++++     +|||||+|.+.++|.+|+..|||..+.|++|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777777888777766            99999999999873     68999999999999999999999999999999


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      |.|+|
T Consensus       100 v~~sp  104 (104)
T 1jmt_A          100 AELSP  104 (104)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99975

>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=99.36  E-value=1.7e-12  Score=103.91  Aligned_cols=101  Identities=20%  Similarity=0.260  Sum_probs=67.0

Q ss_pred             CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCC
Q psy3343         131 YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVP  210 (274)
Q Consensus       131 ~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (274)
                      .+|||||+|.+.++|++|+..+++....+..+.+......      ... ... ....                      
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~------~~~-~~~-~~~~----------------------   61 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKT------FTV-TEG-SHHH----------------------   61 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTE------EEE-ECC-CCCS----------------------
T ss_pred             ccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccc------ccc-ccc-cccc----------------------
Confidence            4699999999999999999988864433333232211100      000 000 0000                      


Q ss_pred             cccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         211 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                              .........++|||+|||+++|+++|+++|++||.|.+|+|++++ .+++.|
T Consensus        62 --------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g  113 (158)
T 2kn4_A           62 --------HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRG  113 (158)
T ss_dssp             --------SCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCC
T ss_pred             --------ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccce
Confidence                    001123456899999999999999999999999999999999986 444444

>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=99.35  E-value=7.4e-13  Score=105.27  Aligned_cols=95  Identities=19%  Similarity=0.203  Sum_probs=71.9

Q ss_pred             CeEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCC
Q psy3343         132 GITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVP  210 (274)
Q Consensus       132 ~~~afV~F~~~~~A~~A~~~l-~~~~~~g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (274)
                      +|+++|+|.+.++|++|++.+ +|..+.| ++.+.++....    ...... .   ..                      
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~----~~~~~~-~---~~----------------------   61 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTF----TVTEGS-H---HH----------------------   61 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEE----EEECSS-S---SC----------------------
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcc----cccccc-c---cc----------------------
Confidence            589999999999999999999 9999999 99999874320    000000 0   00                      


Q ss_pred             cccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         211 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                           ..........+.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus        62 -----~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~  108 (150)
T 2i2y_A           62 -----HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN  108 (150)
T ss_dssp             -----CCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS
T ss_pred             -----cccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC
Confidence                 00000123346789999999999999999999999999999999987

>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=99.35  E-value=3.3e-12  Score=97.63  Aligned_cols=76  Identities=17%  Similarity=0.227  Sum_probs=66.3

Q ss_pred             CCcEEEEeCCCC--C---CCHHHHHHccccCCCeeEEEeeCC----------CeEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3343          95 SKRIILVKNLPY--R---TLPTDLKALFEPFGDLGRVLVPPY----------GITGLVEFLQKNQAKAAFNSLAYTKFKE  159 (274)
Q Consensus        95 ~~~~l~V~nLp~--~---~te~~l~~~F~~~G~i~~v~l~~~----------~~~afV~F~~~~~A~~A~~~l~~~~~~g  159 (274)
                      ++++|+++|+-.  +   -.++||++.|++||.|.+|.|+++          +|++||+|.+.++|.+|+..|||..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            578999999942  1   247899999999999999998762          2799999999999999999999999999


Q ss_pred             eEEEEEEecCC
Q psy3343         160 VPLYLEWAPEG  170 (274)
Q Consensus       160 ~~l~v~~a~~~  170 (274)
                      |+|.|.|++..
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998643

>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=99.33  E-value=3.9e-12  Score=96.67  Aligned_cols=83  Identities=14%  Similarity=0.084  Sum_probs=69.4

Q ss_pred             CCcEEEEeCCCCCC----------CHHHHHHccccCCCeeEEEeeCC--CeEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy3343          95 SKRIILVKNLPYRT----------LPTDLKALFEPFGDLGRVLVPPY--GITGLVEFLQKNQAKAAFNSLAYTKFKEVPL  162 (274)
Q Consensus        95 ~~~~l~V~nLp~~~----------te~~l~~~F~~~G~i~~v~l~~~--~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l  162 (274)
                      ..++|.++|+=...          .+++|++.|++||.|.+|.++++  +|+|||+|.+.++|.+|+..|||..|.|+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i   85 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI   85 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45788899984322          24588999999999999999874  6999999999999999999999999999999


Q ss_pred             EEEEecCCCCccccc
Q psy3343         163 YLEWAPEGVFAEAKE  177 (274)
Q Consensus       163 ~v~~a~~~~f~~~~~  177 (274)
                      .|.|++...|....+
T Consensus        86 ~v~~~~~~~y~~~fp  100 (114)
T 3s6e_A           86 TAAYVPLPTYHNLFP  100 (114)
T ss_dssp             EEEEECHHHHHHHCG
T ss_pred             EEEEEcHHHHHHhCc
Confidence            999997665544433

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=7.8e-12  Score=92.72  Aligned_cols=73  Identities=18%  Similarity=0.199  Sum_probs=61.3

Q ss_pred             CcEEEEeCCC-------CCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          96 KRIILVKNLP-------YRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        96 ~~~l~V~nLp-------~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..+|.|.-.+       ..+++++|+++|++||.|..|.|+. .+|||||+|.+.++|..|++.++  .+.|++|.|.|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a   87 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWL   87 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEc
Confidence            3566665443       4589999999999999999999974 67999999999999999999754  468999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        88 ~~~   90 (100)
T 2d9o_A           88 EGQ   90 (100)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            644

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.17  E-value=1.4e-10  Score=88.57  Aligned_cols=75  Identities=13%  Similarity=0.130  Sum_probs=68.1

Q ss_pred             cCCCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCCeEEEEEecC-HHHHHHHHHHhC--CCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQ-KNQAKAAFNSLA--YTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~-~~~A~~A~~~l~--~~~~~g~~l~v~~a  167 (274)
                      -..++.|||+||++. +++++|+++|++||.|..|.+.++...|||+|.+ +.+|..|+..|+  +..|.|..+.++..
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            456799999999999 9999999999999999999999988899999999 799999999995  67889988887754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.00  E-value=1.4e-09  Score=78.22  Aligned_cols=74  Identities=16%  Similarity=0.168  Sum_probs=63.0

Q ss_pred             CCCcEEEEeCCCC----CCCH----HHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          94 RSKRIILVKNLPY----RTLP----TDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        94 ~~~~~l~V~nLp~----~~te----~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ++..+|+|.-.|.    +.-.    .+|.+.|++||.|..+++..++  +||+|.+.++|.+|+. |+|..+.|+.|+|.
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            4567888887762    3333    6799999999999999998876  8999999999999998 99999999999999


Q ss_pred             EecCC
Q psy3343         166 WAPEG  170 (274)
Q Consensus       166 ~a~~~  170 (274)
                      ++.+.
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            98644

>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=98.99  E-value=4.4e-10  Score=82.97  Aligned_cols=41  Identities=29%  Similarity=0.353  Sum_probs=38.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~   56 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV   56 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCC
Confidence            45678999999999999999999999999999999999875

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.93  E-value=1.4e-09  Score=80.94  Aligned_cols=45  Identities=20%  Similarity=0.380  Sum_probs=40.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++++++.|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG   53 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG   53 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCcc
Confidence            345799999999999999999999999999999999998866665

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.86  E-value=4.3e-09  Score=77.72  Aligned_cols=41  Identities=24%  Similarity=0.340  Sum_probs=37.1

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ...++++|||+|||+++|+++|+++|++||.|.+|++++.+
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~k   57 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK   57 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTT
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCC
Confidence            44578899999999999999999999999999999998643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=3.5e-09  Score=78.92  Aligned_cols=40  Identities=15%  Similarity=0.230  Sum_probs=36.9

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .+.+.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~   51 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG   51 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC
Confidence            3456789999999999999999999999999999999976

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.85  E-value=7.6e-10  Score=86.37  Aligned_cols=39  Identities=31%  Similarity=0.583  Sum_probs=36.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+.+|+++|+++|++||.|..|+|++++.
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~   84 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY   84 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            457999999999999999999999999999999998864

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=98.83  E-value=3.6e-09  Score=79.55  Aligned_cols=40  Identities=20%  Similarity=0.243  Sum_probs=37.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~   43 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR   43 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCC
Confidence            4678999999999999999999999999999999999986

>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=98.80  E-value=5.7e-09  Score=74.58  Aligned_cols=41  Identities=15%  Similarity=0.450  Sum_probs=37.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+++++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   48 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN   48 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCC
Confidence            34678999999999999999999999999999999999875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.79  E-value=1.9e-09  Score=78.24  Aligned_cols=43  Identities=28%  Similarity=0.432  Sum_probs=37.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcC-CeeEEEEecCCC-CCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARKKD-PKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG-~I~~v~v~~~~~-~~~~g  269 (274)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++. +++.|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg   45 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRG   45 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCc
Confidence            36899999999999999999999999 899999999875 34443

>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=98.79  E-value=5.4e-09  Score=79.06  Aligned_cols=40  Identities=23%  Similarity=0.355  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~   43 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG   43 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCC
Confidence            3568999999999999999999999999999999998753

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.78  E-value=6.5e-09  Score=75.12  Aligned_cols=73  Identities=16%  Similarity=0.189  Sum_probs=62.3

Q ss_pred             cCCCcEEEEeCCCCC-----CCH----HHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          93 ARSKRIILVKNLPYR-----TLP----TDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~-----~te----~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .++..+|+|.-++..     .-.    .+|.+.|++||.|..+++..++  +||+|.+.++|.+|++ |+|..+.||.|.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            456689999888743     222    5688999999999999998876  9999999999999998 999999999999


Q ss_pred             EEEec
Q psy3343         164 LEWAP  168 (274)
Q Consensus       164 v~~a~  168 (274)
                      |.+..
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98753

>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=98.76  E-value=9.4e-09  Score=76.12  Aligned_cols=44  Identities=32%  Similarity=0.437  Sum_probs=39.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      .+.++|||+|||+.+|+++|+++|++||.|.+|+|+++++++..
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~   56 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSK   56 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcC
Confidence            45789999999999999999999999999999999999865443

>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=98.76  E-value=8.1e-09  Score=74.95  Aligned_cols=44  Identities=27%  Similarity=0.557  Sum_probs=39.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      .+.++|||+|||+.+++++|+++|++||.|.+|+|+++++++..
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~   57 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK   57 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCc
Confidence            45689999999999999999999999999999999999875443

>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=98.75  E-value=8.9e-09  Score=74.31  Aligned_cols=39  Identities=10%  Similarity=0.324  Sum_probs=34.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~   46 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP   46 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC
Confidence            346789999999999999999999999999999999985

>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=98.75  E-value=7.8e-09  Score=76.71  Aligned_cols=40  Identities=13%  Similarity=0.122  Sum_probs=36.7

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~-~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..++++|||+|||+ ++|+++|+++|++||.|.+|+|++++
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k   52 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI   52 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC
Confidence            34678999999999 99999999999999999999998764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.73  E-value=5.2e-09  Score=76.63  Aligned_cols=42  Identities=17%  Similarity=0.369  Sum_probs=36.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCC--eeEEEEecCCC-CCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGP--IASVTVARKKD-PKSPG  269 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~--I~~v~v~~~~~-~~~~g  269 (274)
                      .+|||+|||+.+|+++|+++|++||.  |.+|+|++|+. +++.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG   54 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG   54 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCce
Confidence            59999999999999999999999995  67999999875 34443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.73  E-value=1.4e-08  Score=76.00  Aligned_cols=46  Identities=22%  Similarity=0.445  Sum_probs=37.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ..++++|||+|||+++|+++|+++|++||.|.+|+|+++++ ++..|
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg   68 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG   68 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCc
Confidence            34568999999999999999999999999999999999875 44443

>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=98.73  E-value=1.6e-08  Score=85.10  Aligned_cols=63  Identities=19%  Similarity=0.211  Sum_probs=56.8

Q ss_pred             CCHHHHHHccccCCCeeEEEeeC----------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343         108 TLPTDLKALFEPFGDLGRVLVPP----------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus       108 ~te~~l~~~F~~~G~i~~v~l~~----------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      -.+++|++.|++||.|.++.+++          .+|++||+|.+.++|.+|+..|+|..+.||+|.+.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~  213 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQE  213 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHH
Confidence            45789999999999999999973          3489999999999999999999999999999999998643

>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=1.5e-08  Score=77.20  Aligned_cols=40  Identities=15%  Similarity=0.228  Sum_probs=36.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...++++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~   66 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG   66 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC
Confidence            3456789999999999999999999999999999999976

>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=98.72  E-value=1.8e-08  Score=73.76  Aligned_cols=45  Identities=22%  Similarity=0.548  Sum_probs=39.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~g  269 (274)
                      .+.++|||+|||+.+|+++|+++|++||.|.+|+|++++ .++..|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g   51 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG   51 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCe
Confidence            457899999999999999999999999999999999987 444443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.72  E-value=1.4e-08  Score=74.57  Aligned_cols=45  Identities=18%  Similarity=0.361  Sum_probs=40.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+.+++++..
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~   58 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPK   58 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEE
Confidence            345689999999999999999999999999999999998865543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.71  E-value=2.7e-08  Score=72.10  Aligned_cols=40  Identities=33%  Similarity=0.598  Sum_probs=37.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++++|||+|||+.+|+++|+++|++||.|..|+|+++++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~   42 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD   42 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCC
Confidence            3568999999999999999999999999999999999875

>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=98.71  E-value=2e-08  Score=74.30  Aligned_cols=39  Identities=18%  Similarity=0.203  Sum_probs=36.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|.+|.|+++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~   50 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG   50 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC
Confidence            346789999999999999999999999999999999875

>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=98.70  E-value=1.4e-08  Score=81.64  Aligned_cols=97  Identities=12%  Similarity=0.152  Sum_probs=37.6

Q ss_pred             EEecCHHHHHHHHHHhCCCeeC--CeEEEEEEecCCCCcccccccccccccccccccchhhhhccchhhcccCCCCcccc
Q psy3343         137 VEFLQKNQAKAAFNSLAYTKFK--EVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEE  214 (274)
Q Consensus       137 V~F~~~~~A~~A~~~l~~~~~~--g~~l~v~~a~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  214 (274)
                      .+|.+.++|..|+..|++....  |+.+...+....      ............              ..          
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~------~~~~~~~~~~s~--------------~~----------   60 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTRE------AIHSYERVRNED--------------DD----------   60 (165)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccc------cccCccccccCC--------------CC----------
Confidence            7899999999999999886655  555555543211      000000000000              00          


Q ss_pred             cccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       215 ~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                       ...-......++++|||+|||+.+|+++|+++|++||.|.+|.|++++.
T Consensus        61 -~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~  109 (165)
T 1rk8_A           61 -ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR  109 (165)
T ss_dssp             ------CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             -CCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCC
Confidence             0000012334568999999999999999999999999999999998864

>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=98.70  E-value=1.7e-08  Score=74.91  Aligned_cols=45  Identities=18%  Similarity=0.325  Sum_probs=40.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS-VTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~-v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+.+|+++|+++|++||.|.. |+|+.+..++..|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G   58 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG   58 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcce
Confidence            45689999999999999999999999999997 9999887776665

>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=98.70  E-value=1.8e-08  Score=74.85  Aligned_cols=46  Identities=22%  Similarity=0.397  Sum_probs=40.7

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ...++++|||+|||+.+|+++|+++|++||.|.+|+|++++.++..
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~   70 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL   70 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcc
Confidence            3456789999999999999999999999999999999999865543

>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=98.70  E-value=3.3e-08  Score=73.56  Aligned_cols=40  Identities=15%  Similarity=0.177  Sum_probs=36.4

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+++
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~   50 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF   50 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC
Confidence            3456789999999999999999999999999999999875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.70  E-value=2.9e-08  Score=71.83  Aligned_cols=42  Identities=33%  Similarity=0.600  Sum_probs=38.4

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+++++|+++|++||.|.+|+|++++.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~   53 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD   53 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC
Confidence            345678999999999999999999999999999999999876

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.70  E-value=1.2e-08  Score=71.01  Aligned_cols=37  Identities=22%  Similarity=0.470  Sum_probs=35.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|++++++.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~   37 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL   37 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCC
Confidence            4799999999999999999999999999999999875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=2.4e-08  Score=70.96  Aligned_cols=40  Identities=23%  Similarity=0.353  Sum_probs=37.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++++|||+|||+.+++++|+++|++||.|.+|+|++++.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~   42 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT   42 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            3578999999999999999999999999999999999864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.70  E-value=1.7e-08  Score=74.57  Aligned_cols=44  Identities=16%  Similarity=0.243  Sum_probs=39.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhh-cCCeeEEEEecCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKK-CGPIASVTVARKKDPKS  267 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~-fG~I~~v~v~~~~~~~~  267 (274)
                      ..+.++|||+|||+++|+++|+++|++ ||.|.+|+|++++.++.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~   50 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS   50 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCc
Confidence            346789999999999999999999999 99999999999875543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.69  E-value=3.1e-08  Score=72.50  Aligned_cols=41  Identities=20%  Similarity=0.408  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|+|++++.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   47 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE   47 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC
Confidence            34568999999999999999999999999999999999865

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.69  E-value=1.9e-08  Score=77.83  Aligned_cols=46  Identities=30%  Similarity=0.388  Sum_probs=39.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE--EEEecCC-CCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS--VTVARKK-DPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~--v~v~~~~-~~~~~g  269 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|..  |+|++++ .+++.|
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG   68 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRG   68 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcce
Confidence            345689999999999999999999999999977  9999998 455444

>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=98.69  E-value=2.8e-08  Score=75.30  Aligned_cols=45  Identities=31%  Similarity=0.543  Sum_probs=40.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      .+.++|||+|||+++|+++|+++|++||.|.+|.|+.++.++..|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g   49 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG   49 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCccc
Confidence            356899999999999999999999999999999999998666554

>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=98.69  E-value=1.9e-08  Score=74.56  Aligned_cols=41  Identities=22%  Similarity=0.352  Sum_probs=37.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   50 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF   50 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC
Confidence            34578999999999999999999999999999999999875

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=98.69  E-value=2.8e-09  Score=98.92  Aligned_cols=40  Identities=30%  Similarity=0.635  Sum_probs=37.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++|||+|||+.||+++|+++|++||.|..|.|+.++.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~  139 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR  139 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCC
Confidence            4568999999999999999999999999999999998863

>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=98.69  E-value=1.8e-08  Score=76.03  Aligned_cols=46  Identities=15%  Similarity=0.159  Sum_probs=41.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCe-eEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI-ASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I-~~v~v~~~~~~~~~g  269 (274)
                      ..+.++|||+|||+++|+++|+++|++||.| .+|+|+++++++..|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G   58 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLG   58 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSS
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcce
Confidence            3456899999999999999999999999999 899999998776665

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.69  E-value=1.9e-08  Score=75.59  Aligned_cols=45  Identities=20%  Similarity=0.386  Sum_probs=40.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+++++++..
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~   56 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR   56 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCee
Confidence            345789999999999999999999999999999999999875443

>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=98.69  E-value=4.4e-08  Score=72.19  Aligned_cols=42  Identities=19%  Similarity=0.339  Sum_probs=38.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~   53 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG   53 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC
Confidence            446789999999999999999999999999999999998764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.68  E-value=1e-08  Score=75.51  Aligned_cols=43  Identities=19%  Similarity=0.398  Sum_probs=38.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++.++..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~   50 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSK   50 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCcc
Confidence            4579999999999999999999999999999999998855443

>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=98.68  E-value=2.5e-08  Score=74.47  Aligned_cols=42  Identities=26%  Similarity=0.509  Sum_probs=38.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   52 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD   52 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            345678999999999999999999999999999999999875

>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=98.68  E-value=2.3e-08  Score=73.79  Aligned_cols=41  Identities=20%  Similarity=0.381  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   52 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK   52 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            34568999999999999999999999999999999999875

>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=98.68  E-value=2.9e-08  Score=73.42  Aligned_cols=46  Identities=20%  Similarity=0.432  Sum_probs=39.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC-CCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK-DPKSP  268 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~-~~~~~  268 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|++++ .++..
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   57 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ   57 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCC
Confidence            34467899999999999999999999999999999999987 34433

>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=98.68  E-value=2.4e-08  Score=72.70  Aligned_cols=39  Identities=18%  Similarity=0.479  Sum_probs=36.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++++|||+|||+.+++++|+++|++||.|.+|+|++++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   39 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ   39 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC
Confidence            467999999999999999999999999999999999865

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.68  E-value=3e-08  Score=73.14  Aligned_cols=42  Identities=31%  Similarity=0.564  Sum_probs=38.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|..|.|++++.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~   50 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH   50 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSS
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC
Confidence            344678999999999999999999999999999999999876

>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=98.68  E-value=1.2e-08  Score=75.55  Aligned_cols=45  Identities=20%  Similarity=0.382  Sum_probs=38.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ....++|||+|||+++|+++|+++|++||. .+|+|++++++++.|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G   56 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTG   56 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEee
Confidence            345689999999999999999999999994 599999998766544

>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=98.67  E-value=2.1e-08  Score=71.13  Aligned_cols=40  Identities=15%  Similarity=0.321  Sum_probs=36.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|++++.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~   44 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE   44 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCC
Confidence            4568999999999999999999999999999999998843

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.67  E-value=3e-08  Score=73.56  Aligned_cols=40  Identities=20%  Similarity=0.512  Sum_probs=36.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~   51 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM   51 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCC
Confidence            4467899999999999999999999999999999999883

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.66  E-value=7.1e-09  Score=76.42  Aligned_cols=44  Identities=14%  Similarity=0.291  Sum_probs=39.1

Q ss_pred             CCceEEEeCCCC------CCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         226 PDTTLYIKNLNF------NSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~------~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      .+++|||+|||+      ++++++|+++|++||.|.+|+|++++. +++.|
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG   55 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG   55 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccce
Confidence            357999999999      999999999999999999999999987 44444

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.66  E-value=4.2e-08  Score=73.97  Aligned_cols=42  Identities=21%  Similarity=0.460  Sum_probs=38.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   54 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ   54 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCC
Confidence            344678999999999999999999999999999999999865

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.66  E-value=1.1e-07  Score=70.20  Aligned_cols=73  Identities=12%  Similarity=0.099  Sum_probs=68.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccC-----CCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPF-----GDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~-----G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +.++|-+-|||..++...|+.+..+|     |.|..|.+.++.+-|+|+|.+...|-+|.-.|+|..|.|+.|.|.-.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            46899999999999999999999999     99999999999888999999999999999899999999999999854

>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=98.66  E-value=5e-08  Score=71.89  Aligned_cols=42  Identities=29%  Similarity=0.384  Sum_probs=38.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~   53 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS   53 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC
Confidence            345789999999999999999999999999999999998664

>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=98.65  E-value=3.8e-08  Score=73.95  Aligned_cols=44  Identities=27%  Similarity=0.432  Sum_probs=39.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.++.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~   65 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS   65 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCc
Confidence            34568999999999999999999999999999999999875544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.65  E-value=2.6e-08  Score=73.48  Aligned_cols=43  Identities=26%  Similarity=0.414  Sum_probs=38.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|+++ .++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~   53 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGR   53 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCC
Confidence            3446789999999999999999999999999999999988 443

>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=98.65  E-value=4.3e-08  Score=70.10  Aligned_cols=38  Identities=26%  Similarity=0.653  Sum_probs=35.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   43 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF   43 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC
Confidence            47999999999999999999999999999999999863

>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=98.64  E-value=2.6e-08  Score=70.29  Aligned_cols=38  Identities=24%  Similarity=0.376  Sum_probs=35.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~   38 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ   38 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTT
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC
Confidence            36899999999999999999999999999999998864

>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=98.64  E-value=2.9e-08  Score=70.69  Aligned_cols=39  Identities=18%  Similarity=0.311  Sum_probs=36.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||.++|+++|+++|++||.|.+|+|++++.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   43 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA   43 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCC
Confidence            467999999999999999999999999999999999863

>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=98.63  E-value=1.7e-08  Score=78.79  Aligned_cols=46  Identities=11%  Similarity=0.311  Sum_probs=41.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGP---IASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~---I~~v~v~~~~~~~~~g  269 (274)
                      ....++|||+|||+++|+++|+++|++||.   |.+|+|++++++++.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG   89 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG   89 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCe
Confidence            345689999999999999999999999999   8999999998876654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.63  E-value=2.8e-08  Score=72.17  Aligned_cols=39  Identities=21%  Similarity=0.333  Sum_probs=36.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEE-EEecCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV-TVARKK  263 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v-~v~~~~  263 (274)
                      .++++|||+|||+.+|+++|+++|++||.|..| +|++++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~   42 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP   42 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcC
Confidence            357899999999999999999999999999999 999884

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.63  E-value=3.2e-08  Score=72.37  Aligned_cols=40  Identities=25%  Similarity=0.359  Sum_probs=37.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCee-EEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA-SVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~-~v~v~~~~~  264 (274)
                      .+.++|||+|||+++|+++|+++|++||.|. +|+|++++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~   47 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL   47 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCC
Confidence            4578999999999999999999999999999 999999874

>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=98.63  E-value=2.9e-08  Score=74.80  Aligned_cols=41  Identities=20%  Similarity=0.262  Sum_probs=37.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   62 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ   62 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC
Confidence            34568999999999999999999999999999999999874

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.63  E-value=4.8e-08  Score=74.59  Aligned_cols=47  Identities=23%  Similarity=0.451  Sum_probs=41.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...++++|||+|||+.+++++|+++|++||.|.+|+|++++.++..|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g   77 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG   77 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEee
Confidence            34567899999999999999999999999999999999998666554

>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=98.63  E-value=4.3e-08  Score=73.68  Aligned_cols=44  Identities=16%  Similarity=0.342  Sum_probs=38.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++. ++..|
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g   68 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG   68 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCc
Confidence            357999999999999999999999999999999999876 34433

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=3.5e-08  Score=70.63  Aligned_cols=37  Identities=19%  Similarity=0.411  Sum_probs=35.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      +.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~   40 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP   40 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC
Confidence            4689999999999999999999999999999999876

>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=98.62  E-value=1.7e-08  Score=75.29  Aligned_cols=46  Identities=15%  Similarity=0.263  Sum_probs=41.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGP---IASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~---I~~v~v~~~~~~~~~g  269 (274)
                      ....++|||+|||+++|+++|+++|++||.   |.+|+|++++++++.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G   56 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRG   56 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEee
Confidence            345689999999999999999999999988   9999999998877766

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.62  E-value=2.2e-08  Score=69.41  Aligned_cols=40  Identities=15%  Similarity=0.407  Sum_probs=35.8

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSP  268 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~  268 (274)
                      +|||+|||+++|+++|+++|++||.|.+|++++++. +++.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~   41 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHR   41 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcC
Confidence            589999999999999999999999999999999874 4433

>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=98.61  E-value=4.7e-08  Score=72.26  Aligned_cols=39  Identities=31%  Similarity=0.593  Sum_probs=36.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++|||+|||+.+|+++|+++|++|| |.+|+|+++++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~   51 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS   51 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCC
Confidence            4568999999999999999999999999 99999999876

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.61  E-value=4e-08  Score=72.75  Aligned_cols=41  Identities=17%  Similarity=0.366  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|.+|.|++++.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~   60 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR   60 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCC
Confidence            34568999999999999999999999999999999999876

>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=98.61  E-value=4.9e-08  Score=75.18  Aligned_cols=44  Identities=23%  Similarity=0.382  Sum_probs=39.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCee--EEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA--SVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~--~v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+++|+++|+++|++| .|.  +|+|+++++|++.|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrG   85 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITG   85 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCce
Confidence            356799999999999999999999999 687  99999999887766

>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=98.61  E-value=6.4e-08  Score=70.57  Aligned_cols=41  Identities=15%  Similarity=0.387  Sum_probs=38.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHH----HHhhhcCCeeEEEEecCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIR----RHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~----~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+++|||+|||+.+++++|+    ++|++||.|.+|+|++++++
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~   51 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY   51 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC
Confidence            356799999999999999999    99999999999999998876

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.61  E-value=1.9e-08  Score=76.45  Aligned_cols=45  Identities=11%  Similarity=0.355  Sum_probs=40.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCC---eeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP---IASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~---I~~v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+++|+++|+++|++||.   |.+|+|+++++++..|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G   62 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG   62 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCe
Confidence            35689999999999999999999999999   8999999998876544

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.60  E-value=3.5e-08  Score=69.54  Aligned_cols=42  Identities=24%  Similarity=0.386  Sum_probs=35.2

Q ss_pred             CceEEEeCCCCCC------CHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         227 DTTLYIKNLNFNS------TEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~------tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +++|||+|||+.+      |+++|+++|++||.|.+|+|++ ..+++.|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~-~~g~~~g   48 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-EDGKTKG   48 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC-BTTBCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC-CCCcEeE
Confidence            3689999999999      7799999999999999999883 3444444

>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=98.60  E-value=2.3e-08  Score=69.23  Aligned_cols=36  Identities=19%  Similarity=0.457  Sum_probs=34.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +|||+|||+++|+++|+++|++||.|.+|.+++++.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   36 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK   36 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            599999999999999999999999999999998865

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.60  E-value=6.3e-08  Score=73.18  Aligned_cols=42  Identities=24%  Similarity=0.291  Sum_probs=38.2

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~   77 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ   77 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC
Confidence            344678999999999999999999999999999999998864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.60  E-value=5.2e-08  Score=73.28  Aligned_cols=42  Identities=17%  Similarity=0.347  Sum_probs=38.1

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   52 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA   52 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC
Confidence            344678999999999999999999999999999999999863

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.60  E-value=4.8e-08  Score=70.37  Aligned_cols=38  Identities=18%  Similarity=0.494  Sum_probs=35.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~   43 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME   43 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc
Confidence            45689999999999999999999999999999999984

>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=98.60  E-value=2.5e-08  Score=78.11  Aligned_cols=44  Identities=18%  Similarity=0.320  Sum_probs=39.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+++|+++|+++|++|| |.+|+|++++++++.|
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srG   87 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTG   87 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCce
Confidence            3467999999999999999999999999 7799999998877766

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.59  E-value=5.2e-08  Score=71.07  Aligned_cols=40  Identities=43%  Similarity=0.755  Sum_probs=37.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++|||+|||+++|+++|+++|++||.|.+|+|+++++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   42 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN   42 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            3568999999999999999999999999999999998876

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.59  E-value=2.4e-08  Score=76.62  Aligned_cols=44  Identities=18%  Similarity=0.385  Sum_probs=38.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCe----eEEEEecCCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVARKKDPKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I----~~v~v~~~~~~~~~g  269 (274)
                      ..++|||+|||+++|+++|+++|++||.|    ..|+|++++++++.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G   69 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG   69 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEee
Confidence            46799999999999999999999999986    699999988776554

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.59  E-value=7.1e-08  Score=69.82  Aligned_cols=43  Identities=33%  Similarity=0.620  Sum_probs=38.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|.|++++..
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~   53 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQS   53 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCC
Confidence            3456789999999999999999999999999999999998763

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.59  E-value=4.7e-08  Score=73.33  Aligned_cols=42  Identities=17%  Similarity=0.396  Sum_probs=39.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      .++|||+|||+++|+++|+++|++| .|.+|+|++++++++.|
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G   57 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNG   57 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCe
Confidence            4699999999999999999999999 89999999998887766

>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=98.59  E-value=6.8e-08  Score=72.80  Aligned_cols=39  Identities=15%  Similarity=0.248  Sum_probs=35.8

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~-~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..++++|||+|||++ +|+++|+++|++||.|.+|+|++.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~   61 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM   61 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC
Confidence            456789999999998 999999999999999999999864

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=3.9e-08  Score=72.52  Aligned_cols=41  Identities=22%  Similarity=0.481  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~   52 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT   52 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCC
Confidence            44678999999999999999999999999999999999864

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=6.4e-08  Score=72.34  Aligned_cols=42  Identities=19%  Similarity=0.336  Sum_probs=38.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ....++|||+|||.++|+++|+++|++||.|.+|+|++++++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~   67 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG   67 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTB
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCC
Confidence            446789999999999999999999999999999999988653

>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=98.57  E-value=1e-07  Score=71.70  Aligned_cols=42  Identities=33%  Similarity=0.633  Sum_probs=37.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      +.++++|||+|||+.+|+++|+++|++||.|.+|.|+++..+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~   46 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET   46 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCC
Confidence            345789999999999999999999999999999999976543

>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=98.57  E-value=2.5e-08  Score=71.80  Aligned_cols=37  Identities=22%  Similarity=0.433  Sum_probs=33.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcC--CeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG--~I~~v~v~~~~~  264 (274)
                      .+|||+|||+++|+++|+++|++||  .|.+|+|++++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~   40 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA   40 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTT
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCC
Confidence            4799999999999999999999999  999999999864

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.56  E-value=8.1e-08  Score=71.02  Aligned_cols=41  Identities=17%  Similarity=0.502  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~   53 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT   53 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC
Confidence            44678999999999999999999999999999999999864

>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=98.56  E-value=8.2e-08  Score=73.39  Aligned_cols=42  Identities=17%  Similarity=0.361  Sum_probs=38.0

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...++++|||+|||+.+|+++|+++|++||.|.+|.|+.++.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   59 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR   59 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            344578999999999999999999999999999999998863

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=6.2e-08  Score=71.19  Aligned_cols=41  Identities=15%  Similarity=0.315  Sum_probs=37.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~   49 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE   49 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCC
Confidence            34678999999999999999999999999999999998854

>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=98.56  E-value=1.2e-07  Score=70.71  Aligned_cols=38  Identities=13%  Similarity=0.340  Sum_probs=35.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~   50 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   50 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC
Confidence            35689999999999999999999999999999999876

>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=98.56  E-value=8.6e-08  Score=71.49  Aligned_cols=41  Identities=17%  Similarity=0.360  Sum_probs=37.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   63 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR   63 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            34568999999999999999999999999999999998864

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=1e-07  Score=70.04  Aligned_cols=41  Identities=27%  Similarity=0.614  Sum_probs=37.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~   49 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE   49 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC
Confidence            34568999999999999999999999999999999998864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=8.1e-08  Score=72.38  Aligned_cols=39  Identities=28%  Similarity=0.532  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+.+|+++|+++|++||.|..|+|++++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~   64 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA   64 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCC
Confidence            357999999999999999999999999999999999865

>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=98.55  E-value=7.2e-08  Score=68.67  Aligned_cols=39  Identities=26%  Similarity=0.307  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+++++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~   41 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERM   41 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCC
Confidence            467999999999999999999999999999999998875

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.55  E-value=7.7e-08  Score=70.41  Aligned_cols=42  Identities=21%  Similarity=0.424  Sum_probs=38.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE--------EEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS--------VTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~--------v~v~~~~~  264 (274)
                      ...+.++|||+|||+++|+++|+++|++||.|.+        |+|++++.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~   58 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE   58 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCC
Confidence            3456789999999999999999999999999999        99999865

>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=98.55  E-value=1e-07  Score=67.48  Aligned_cols=39  Identities=36%  Similarity=0.555  Sum_probs=35.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+++++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~   47 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR   47 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC
Confidence            345689999999999999999999999999999999975

>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=98.55  E-value=9.3e-08  Score=73.81  Aligned_cols=42  Identities=33%  Similarity=0.631  Sum_probs=38.6

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~   83 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ   83 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            445678999999999999999999999999999999999865

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.55  E-value=9.2e-08  Score=69.00  Aligned_cols=39  Identities=21%  Similarity=0.472  Sum_probs=35.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|+++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~   45 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD   45 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC
Confidence            446789999999999999999999999999999999753

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.55  E-value=9.3e-08  Score=68.69  Aligned_cols=39  Identities=15%  Similarity=0.360  Sum_probs=35.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~   44 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD   44 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC
Confidence            346789999999999999999999999999999999853

>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=98.53  E-value=3.9e-08  Score=72.29  Aligned_cols=45  Identities=29%  Similarity=0.546  Sum_probs=36.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC--CCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK--DPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~--~~~~~g  269 (274)
                      ....++|||+|||+++|+++|+++|++|| |.+|+|++++  .++..|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g   62 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG   62 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCe
Confidence            34568999999999999999999999999 9999999987  454444

>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=98.53  E-value=1.7e-07  Score=69.76  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=36.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|..+..
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~   59 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG   59 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC
Confidence            44678999999999999999999999999999999976543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.52  E-value=1e-07  Score=70.65  Aligned_cols=44  Identities=23%  Similarity=0.349  Sum_probs=36.9

Q ss_pred             CCCceEEEeCCCCCC------CHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNS------TEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~------tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ..+++|||+|||+.+      |+++|+++|++||.|.+|+|+ +..|++.|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G   62 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKG   62 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeee
Confidence            346899999999999      789999999999999999998 34444444

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.52  E-value=9.3e-08  Score=68.77  Aligned_cols=44  Identities=16%  Similarity=0.279  Sum_probs=39.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...++|||+|||+++|+++|+++|++| .|.+|+|+++.+++..|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g   51 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTG   51 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCce
Confidence            456899999999999999999999999 99999999997665443

>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=98.52  E-value=3.2e-08  Score=71.02  Aligned_cols=37  Identities=19%  Similarity=0.538  Sum_probs=35.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++|||+|||+++++++|+++|++||.|.+|+|++++.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   38 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE   38 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCC
Confidence            5899999999999999999999999999999998875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.51  E-value=1.1e-07  Score=70.19  Aligned_cols=40  Identities=43%  Similarity=0.630  Sum_probs=36.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++|| |.+|+|+++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~   51 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD   51 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCC
Confidence            34568999999999999999999999997 99999999875

>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=98.51  E-value=1.6e-07  Score=70.10  Aligned_cols=41  Identities=32%  Similarity=0.524  Sum_probs=37.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~   63 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE   63 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC
Confidence            44568999999999999999999999999999999998865

>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=98.49  E-value=2e-07  Score=67.92  Aligned_cols=39  Identities=23%  Similarity=0.500  Sum_probs=35.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|.++++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~   52 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG   52 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC
Confidence            446789999999999999999999999999999999865

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.49  E-value=1.3e-07  Score=70.90  Aligned_cols=41  Identities=24%  Similarity=0.536  Sum_probs=36.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCee--------EEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA--------SVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~--------~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.        .|+|++++.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~   60 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE   60 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCC
Confidence            34678999999999999999999999999999        599998854

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.48  E-value=1.3e-07  Score=71.23  Aligned_cols=39  Identities=23%  Similarity=0.476  Sum_probs=35.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..++|||+|||+++|+++|+++|++||.|. +.++.++..
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~   45 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAES   45 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCC
Confidence            468999999999999999999999999999 888887764

>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=98.48  E-value=2e-07  Score=68.16  Aligned_cols=39  Identities=26%  Similarity=0.445  Sum_probs=36.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|+++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~   50 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD   50 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC
Confidence            446789999999999999999999999999999999865

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=98.48  E-value=2.3e-07  Score=72.00  Aligned_cols=41  Identities=15%  Similarity=0.315  Sum_probs=37.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+++|++++.
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~  100 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE  100 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTT
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCC
Confidence            34678999999999999999999999999999999998854

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.48  E-value=1.4e-07  Score=68.56  Aligned_cols=40  Identities=15%  Similarity=0.187  Sum_probs=36.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEE-EecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVT-VARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~-v~~~~~  264 (274)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+ |++++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~   53 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE   53 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC
Confidence            3468999999999999999999999999999994 887765

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.46  E-value=2.5e-07  Score=66.34  Aligned_cols=37  Identities=27%  Similarity=0.426  Sum_probs=34.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~   41 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII   41 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE
Confidence            3456899999999999999999999999999999997

>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=98.46  E-value=2.1e-07  Score=68.62  Aligned_cols=38  Identities=21%  Similarity=0.394  Sum_probs=34.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|..|+|++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~   45 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK   45 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC
Confidence            34568999999999999999999999999999999874

>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=98.46  E-value=3.8e-08  Score=72.59  Aligned_cols=39  Identities=18%  Similarity=0.558  Sum_probs=36.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~   45 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE   45 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCC
Confidence            357999999999999999999999999999999998864

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.46  E-value=2.1e-07  Score=75.85  Aligned_cols=47  Identities=23%  Similarity=0.451  Sum_probs=41.4

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...++++|||+|||+.+|+++|+++|++||.|.+|.|+.++.++..|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG  130 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG  130 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEee
Confidence            34567899999999999999999999999999999999988665554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.45  E-value=1.5e-07  Score=75.13  Aligned_cols=39  Identities=10%  Similarity=0.370  Sum_probs=35.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcC--CeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG--~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++|+++|+++|++||  .|.+|+|++++.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~   94 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA   94 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCC
Confidence            457999999999999999999999999  999999999864

>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=98.45  E-value=5.1e-07  Score=74.50  Aligned_cols=43  Identities=21%  Similarity=0.417  Sum_probs=38.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      .++|||+|||+++|+++|+++|++||.|.+|+|+++.+++..|
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG  151 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG  151 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCccc
Confidence            4799999999999999999999999999999999987755443

>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=98.44  E-value=3.9e-07  Score=72.30  Aligned_cols=41  Identities=34%  Similarity=0.515  Sum_probs=38.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|+|+++++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   76 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM   76 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC
Confidence            34678999999999999999999999999999999999876

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.43  E-value=2.9e-07  Score=71.52  Aligned_cols=42  Identities=26%  Similarity=0.502  Sum_probs=38.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .....++|||+|||+++|+++|+++|++||.|.+|+|+++++
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~   79 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE   79 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC
Confidence            345678999999999999999999999999999999999875

>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=98.43  E-value=2.7e-07  Score=68.72  Aligned_cols=39  Identities=21%  Similarity=0.357  Sum_probs=36.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ....++|||+|||+.+|+++|+++|++||.|.+|+|+++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~   60 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE   60 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            345789999999999999999999999999999999986

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.43  E-value=3.2e-07  Score=67.26  Aligned_cols=38  Identities=29%  Similarity=0.308  Sum_probs=34.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ....++|||+|||+++|+++|+++|++||.|.+|++.+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~   61 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP   61 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec
Confidence            34568999999999999999999999999999999984

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.42  E-value=1.6e-07  Score=71.54  Aligned_cols=38  Identities=29%  Similarity=0.659  Sum_probs=35.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~   73 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF   73 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            57999999999999999999999999999999999853

>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=98.41  E-value=3.2e-07  Score=68.13  Aligned_cols=40  Identities=18%  Similarity=0.229  Sum_probs=36.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCC-eeEEEEe-cCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVA-RKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~-I~~v~v~-~~~~  264 (274)
                      .+.++|||+|||+.+|+++|+++|++||. |.+|.|+ .++.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~   47 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAAD   47 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCT
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCC
Confidence            35689999999999999999999999998 9999998 5554

>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=98.41  E-value=1.9e-07  Score=70.03  Aligned_cols=35  Identities=23%  Similarity=0.407  Sum_probs=33.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      .++|||+|||+++|+++|+++|++||.|.+|.|++
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   44 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE   44 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC
Confidence            57999999999999999999999999999999875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.41  E-value=4.4e-07  Score=69.88  Aligned_cols=44  Identities=20%  Similarity=0.357  Sum_probs=35.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIR----RHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~----~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ..++++|||+|||+.+++++|+    ++|++||.|.+|.+.+  +++..|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG   73 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSG   73 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCC
Confidence            3467899999999999999876    6999999999998864  344444

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.41  E-value=2.5e-07  Score=70.95  Aligned_cols=38  Identities=21%  Similarity=0.271  Sum_probs=36.8

Q ss_pred             ceEEEeCC----CCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         228 TTLYIKNL----NFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       228 ~~lfV~NL----~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      +.|||+||    |+.+++++|+.+|++||+|.+|.++.|+++
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~T   44 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNS   44 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC
Confidence            68999999    999999999999999999999999999985

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.40  E-value=2.7e-07  Score=67.09  Aligned_cols=37  Identities=27%  Similarity=0.535  Sum_probs=33.4

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         224 PEPDTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~-~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..+.++|||+|||+ .+|+++|+++|++||.|.+|.|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~   44 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK   44 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe
Confidence            34678999999999 99999999999999999999986

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.40  E-value=2.5e-07  Score=67.84  Aligned_cols=35  Identities=29%  Similarity=0.566  Sum_probs=33.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|.|+++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~   35 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN   35 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC
Confidence            58999999999999999999999999999999987

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.38  E-value=4.4e-07  Score=65.02  Aligned_cols=36  Identities=22%  Similarity=0.262  Sum_probs=34.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      .+..|||+||++.+|+++|+++|.+||+|.++++..
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~   41 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL   41 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC
Confidence            467999999999999999999999999999999976

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.38  E-value=7.8e-07  Score=64.33  Aligned_cols=32  Identities=19%  Similarity=0.349  Sum_probs=30.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEE
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV  257 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v  257 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v   38 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV   38 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE
Confidence            45799999999999999999999999999987

>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=98.37  E-value=2.7e-07  Score=69.09  Aligned_cols=42  Identities=14%  Similarity=0.229  Sum_probs=38.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH---HHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIR---RHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~---~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+.++|||+|||+++++++|+   ++|++||.|..|+|++++..
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~   56 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSY   56 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSC
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCc
Confidence            3456899999999999999999   99999999999999988753

>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=98.36  E-value=3e-07  Score=77.98  Aligned_cols=39  Identities=21%  Similarity=0.403  Sum_probs=35.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcC--CeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCG--PIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG--~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+.+|+++|+++|++||  .|.+|+|++++.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~  107 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA  107 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCC
Confidence            457999999999999999999999999  999999999864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.36  E-value=3.3e-07  Score=67.17  Aligned_cols=43  Identities=30%  Similarity=0.523  Sum_probs=35.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ..+.++|||+|||+.+|+++|+++|++||.|   +++++..++..|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g   54 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKG   54 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEee
Confidence            3467899999999999999999999999987   566665555444

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.36  E-value=7.3e-07  Score=65.09  Aligned_cols=38  Identities=26%  Similarity=0.521  Sum_probs=34.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhc--CCeeEEEEec
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKC--GPIASVTVAR  261 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~f--G~I~~v~v~~  261 (274)
                      ..+.++|||+|||+.+|+++|+++|++|  |.|.+|++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~   51 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR   51 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeC
Confidence            3467899999999999999999999999  9999998763

>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=98.36  E-value=2.3e-07  Score=70.04  Aligned_cols=37  Identities=14%  Similarity=0.346  Sum_probs=33.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|+.+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~   51 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   51 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence            4579999999999999999999999999999999875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.33  E-value=5.4e-07  Score=67.20  Aligned_cols=37  Identities=19%  Similarity=0.468  Sum_probs=34.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|+|+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~   64 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL   64 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            3467899999999999999999999999999999997

>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=98.33  E-value=7.4e-07  Score=65.04  Aligned_cols=37  Identities=24%  Similarity=0.480  Sum_probs=34.2

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         224 PEPDTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~-~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..++++|||+|||+ .+++++|+++|++||.|.+|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~   56 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK   56 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe
Confidence            44678999999999 99999999999999999999984

>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=98.33  E-value=1.7e-07  Score=67.87  Aligned_cols=39  Identities=18%  Similarity=0.257  Sum_probs=35.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+.+|+++|+++|++||.|..+.++.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~   52 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE   52 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCC
Confidence            458999999999999999999999999999988888754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.32  E-value=3.6e-07  Score=68.70  Aligned_cols=39  Identities=13%  Similarity=0.170  Sum_probs=34.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcC-CeeEEEEecC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCG-PIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG-~I~~v~v~~~  262 (274)
                      +...++|||+|||+++|+++|+++|++|| .|..|.|..+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~   64 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR   64 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC
Confidence            34567999999999999999999999999 9999999643

>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=98.32  E-value=2.2e-07  Score=70.90  Aligned_cols=43  Identities=21%  Similarity=0.334  Sum_probs=35.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec-CCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR-KKDPKS  267 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~-~~~~~~  267 (274)
                      ...++|||+|||+++|+++|+++|++||.|..+.++. +.+++.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~   66 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA   66 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCC
Confidence            3568999999999999999999999999999854444 444443

>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=98.29  E-value=7.6e-07  Score=64.56  Aligned_cols=38  Identities=34%  Similarity=0.642  Sum_probs=34.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHhhhcCCeeEEEEec
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIR----RHFKKCGPIASVTVAR  261 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~----~~F~~fG~I~~v~v~~  261 (274)
                      ..++++|||+|||+++|+++|+    ++|++||.|.+|.|++
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~   46 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR   46 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc
Confidence            3467899999999999999999    9999999999999874

>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=98.28  E-value=3.3e-07  Score=66.74  Aligned_cols=40  Identities=18%  Similarity=0.242  Sum_probs=35.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...++|||+|||+.+|+++|+++|++||.|..+.++.++.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~   52 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE   52 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECC
Confidence            3467999999999999999999999999999888887653

>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=98.27  E-value=6.2e-07  Score=67.65  Aligned_cols=39  Identities=13%  Similarity=0.308  Sum_probs=34.3

Q ss_pred             CCCCceEEE--eCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         224 PEPDTTLYI--KNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       224 ~~~~~~lfV--~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..++++|||  +||++++|+++|+++|++||.|.+|.|+.+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~   62 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN   62 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            346789999  569999999999999999999999988753

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=97.58  E-value=1.2e-07  Score=71.53  Aligned_cols=40  Identities=23%  Similarity=0.453  Sum_probs=36.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeE--------EEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS--------VTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~--------v~v~~~~~  264 (274)
                      .+.++|||+|||+.+|+++|+++|++||.|.+        |+|++++.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~   52 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE   52 (116)
Confidence            35689999999999999999999999999999        89998854

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.24  E-value=9.8e-07  Score=68.10  Aligned_cols=36  Identities=22%  Similarity=0.382  Sum_probs=33.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..|||+||++.+|+++|+++|++||.|.+|+|..+.
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~   64 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN   64 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC
Confidence            478899999999999999999999999999998754

>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=98.23  E-value=1.3e-06  Score=64.96  Aligned_cols=35  Identities=26%  Similarity=0.465  Sum_probs=32.8

Q ss_pred             CCCceEEEeCCCCC-CCHHHHHHHhhhcCCeeEEEE
Q psy3343         225 EPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTV  259 (274)
Q Consensus       225 ~~~~~lfV~NL~~~-~tee~L~~~F~~fG~I~~v~v  259 (274)
                      ...++|||+|||+. +|+++|+++|++||.|..|.|
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i   60 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV   60 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE
Confidence            34689999999999 999999999999999999998

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.23  E-value=1.9e-06  Score=62.61  Aligned_cols=37  Identities=14%  Similarity=0.389  Sum_probs=32.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...++|||+|||+.+|+++|+++|++||.|. ++++.+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~   53 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ   53 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC
Confidence            4568999999999999999999999999997 677654

>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=98.20  E-value=1.5e-06  Score=61.55  Aligned_cols=37  Identities=27%  Similarity=0.591  Sum_probs=34.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhc----C-------CeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKC----G-------PIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~f----G-------~I~~v~v~~~  262 (274)
                      +.++|||+|||+++|+++|+++|++|    |       .|.++++.++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~   52 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD   52 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC
Confidence            45799999999999999999999999    8       9999999865

>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=98.17  E-value=2.9e-06  Score=63.45  Aligned_cols=37  Identities=27%  Similarity=0.398  Sum_probs=32.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCe----eEEEEe
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPI----ASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I----~~v~v~  260 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|    ..+++.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~   62 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM   62 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC
Confidence            3467899999999999999999999999999    566655

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.16  E-value=2.7e-06  Score=65.16  Aligned_cols=34  Identities=18%  Similarity=0.273  Sum_probs=31.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .|||+||++.+|+++|+++|++||.|.+|+|..+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~   60 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR   60 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC
Confidence            5789999999999999999999999999999763

>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=98.16  E-value=1.4e-06  Score=62.74  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=31.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCC-eeEEEEe
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVA  260 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~-I~~v~v~  260 (274)
                      .+.++|||+|||+++|+++|+++|++||. |..+.+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~   42 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL   42 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc
Confidence            45689999999999999999999999999 6666664

>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=98.16  E-value=2.4e-06  Score=68.47  Aligned_cols=37  Identities=22%  Similarity=0.345  Sum_probs=33.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+|||+||++.+|+++|+++|++||.|.+|+|..+.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~   82 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN   82 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC
Confidence            3579999999999999999999999999999997654

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.11  E-value=2.6e-05  Score=57.01  Aligned_cols=71  Identities=20%  Similarity=0.142  Sum_probs=59.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHcccc-----CCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEP-----FGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~-----~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....+|.|.|||+.+.++-|.-+|+.     -|.|..+...+  +-|+|+|.+...|++.++. ....|++.+|.|...
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~   81 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPA   81 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEEC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcC
Confidence            34589999999999999999999987     26788888776  6799999999999999862 367788888888654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.11  E-value=2.9e-07  Score=67.44  Aligned_cols=37  Identities=16%  Similarity=0.136  Sum_probs=32.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .+.++|||+|||+++|+++|+++|++||.|.. .++++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~   51 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVD   51 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEec
Confidence            35689999999999999999999999999888 55554

>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=98.10  E-value=8.2e-07  Score=69.36  Aligned_cols=34  Identities=26%  Similarity=0.442  Sum_probs=30.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEE
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV  257 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v  257 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|.+|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~   75 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSE   75 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccc
Confidence            3467899999999999999999999999999874

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.05  E-value=8.8e-07  Score=64.14  Aligned_cols=33  Identities=39%  Similarity=0.513  Sum_probs=30.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEE
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV  257 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v  257 (274)
                      .+.++|||+|||+.+|+++|+++|++||.|..+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~   46 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV   46 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe
Confidence            456899999999999999999999999988776

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.05  E-value=4.4e-06  Score=63.51  Aligned_cols=42  Identities=14%  Similarity=0.143  Sum_probs=38.4

Q ss_pred             CCCCCceEEEeCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~-~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ...+++.|||+||+.. +++++|+++|++||+|.+|.++++..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~   56 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK   56 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC
Confidence            4568999999999999 99999999999999999999987653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.01  E-value=1.1e-05  Score=58.49  Aligned_cols=35  Identities=26%  Similarity=0.449  Sum_probs=31.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..+.++|||+||  ++|+++|+++|++||.|.+|.|.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~   46 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD   46 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec
Confidence            346789999996  89999999999999999999995

>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=97.99  E-value=5e-06  Score=59.26  Aligned_cols=34  Identities=18%  Similarity=0.231  Sum_probs=31.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..++|||+|||+++|+++|+++|++| .|.+|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~   37 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD   37 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe
Confidence            45799999999999999999999999 99999985

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=97.93  E-value=6.7e-06  Score=70.00  Aligned_cols=38  Identities=24%  Similarity=0.386  Sum_probs=34.9

Q ss_pred             CCCceEEEeCCCCCC---------CHHHHHHHhhhcCCeeEEEEecC
Q psy3343         225 EPDTTLYIKNLNFNS---------TEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~---------tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...++|||+||++.+         ++++|+++|++||.|.+|+|+..
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~  178 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES  178 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC
Confidence            356899999999998         79999999999999999999865

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.84  E-value=2e-05  Score=56.98  Aligned_cols=30  Identities=40%  Similarity=0.644  Sum_probs=26.4

Q ss_pred             ceEEEeCCCCCCCHHH----HHHHhhhc-CCeeEE
Q psy3343         228 TTLYIKNLNFNSTEDS----IRRHFKKC-GPIASV  257 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~----L~~~F~~f-G~I~~v  257 (274)
                      +.|||+|||+.+++++    |+++|++| |+|.+|
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V   44 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI   44 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE
Confidence            3499999999999988    55899999 599988

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=97.76  E-value=3.9e-05  Score=56.78  Aligned_cols=40  Identities=13%  Similarity=0.223  Sum_probs=33.9

Q ss_pred             CCCceEEEeCCCC-----CCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNF-----NSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~-----~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++++|+|+||..     +.++++|++.|++||.|.+|.|+++++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~   50 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPG   50 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSS
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCC
Confidence            4678999999963     237899999999999999999999865

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.75  E-value=3.3e-05  Score=56.32  Aligned_cols=38  Identities=21%  Similarity=0.537  Sum_probs=32.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+.++|||+|||+.+|+++|+++|++|+   .|++++++.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~   49 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRE   49 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSS
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCC
Confidence            44678999999999999999999999874   677777753

>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=97.72  E-value=7.6e-05  Score=54.69  Aligned_cols=73  Identities=14%  Similarity=0.010  Sum_probs=64.0

Q ss_pred             CcEEEEeCCCCCC-C----HHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          96 KRIILVKNLPYRT-L----PTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~-t----e~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .++|+|.||+..+ .    .+.++.+|..|+++......++=.=..|.|.++++|.+|-..|++..+.|+.++|-+++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            5889999998865 2    25789999999999888877765567999999999999999999999999999999986

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=97.59  E-value=4.6e-05  Score=68.26  Aligned_cols=39  Identities=15%  Similarity=0.320  Sum_probs=34.2

Q ss_pred             CCCCCceEEEeC--CCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         223 EPEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       223 ~~~~~~~lfV~N--L~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ...++.+|||+|  |++.+|+++|+++|++||.|.+|.+..
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~   54 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP   54 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC
Confidence            345778999999  578999999999999999999988754

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.55  E-value=0.00058  Score=49.01  Aligned_cols=74  Identities=14%  Similarity=0.211  Sum_probs=60.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC--------eEEEEEecCHHHHHHHHHHhCCCeeCC-----eEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--------ITGLVEFLQKNQAKAAFNSLAYTKFKE-----VPLY  163 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~--------~~afV~F~~~~~A~~A~~~l~~~~~~g-----~~l~  163 (274)
                      +.|.|++||+.+|++++.+.++....+......+.+        .-|||.|.+.+++..-.+.++|..|.+     .+-.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            578899999999999999999999887766664421        469999999999999999999988753     2346


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |++|+-.
T Consensus        82 VE~AP~q   88 (91)
T 1uw4_A           82 VEFAPFQ   88 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEcCCC
Confidence            7887643

>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=97.20  E-value=0.0011  Score=47.79  Aligned_cols=55  Identities=24%  Similarity=0.381  Sum_probs=45.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA  153 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~  153 (274)
                      ..+++| ++|+.....||.++|+.||.| .|... +-..|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~Wi-dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEE-ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEE-cCCeEEEEecCHHHHHHHHHhcc
Confidence            366666 999999999999999999954 33333 34589999999999999998764

>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=97.16  E-value=0.0013  Score=49.38  Aligned_cols=71  Identities=15%  Similarity=0.197  Sum_probs=59.4

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC-eEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE-VPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g-~~l~v~~a  167 (274)
                      ..+.|.|-++|+.. ...+...|++||.|.+...+..+.+-.|.|.++.+|++|+. .||..+.| ..|-|.+.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            45889999999885 66788899999999999887677899999999999999997 69999985 44555543

>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=97.12  E-value=0.00063  Score=50.47  Aligned_cols=41  Identities=17%  Similarity=0.270  Sum_probs=31.9

Q ss_pred             CCCCCceEEEeCCCCCCC-----------HHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         223 EPEPDTTLYIKNLNFNST-----------EDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~t-----------ee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+.++++|+|+||.....           +++|+++|++||.|.+|.| .++.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~   62 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH   62 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC
Confidence            445678999999944332           5899999999999999966 4443

>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=97.12  E-value=0.00066  Score=49.13  Aligned_cols=54  Identities=26%  Similarity=0.351  Sum_probs=45.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA  153 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~  153 (274)
                      .+++| ++|++....||.++|+.||. ..|... +-..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~Wi-dDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWI-DDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEE-ETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEE-cCCeEEEEecCHHHHHHHHHhcc
Confidence            55666 99999999999999999993 344444 34689999999999999999875

>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=97.09  E-value=0.00049  Score=50.74  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=33.6

Q ss_pred             CCCceEEEeCC--CCCCC--------HHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         225 EPDTTLYIKNL--NFNST--------EDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       225 ~~~~~lfV~NL--~~~~t--------ee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .|+++|.++|+  |....        +++|++.|++||.|.+|+|++++++
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~   53 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG   53 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTT
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCC
Confidence            36789999998  33333        3799999999999999999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.69  E-value=0.0041  Score=45.35  Aligned_cols=35  Identities=17%  Similarity=0.224  Sum_probs=29.4

Q ss_pred             CceEEEeCCC-------CCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         227 DTTLYIKNLN-------FNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       227 ~~~lfV~NL~-------~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ..+|.|....       ..+|+++|+++|++||.|..|+|+.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~   51 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS   51 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc
Confidence            3577777654       5689999999999999999999984

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.68  E-value=0.0051  Score=44.41  Aligned_cols=74  Identities=14%  Similarity=0.203  Sum_probs=55.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC--------eEEEEEecCHHHHHHHHHHhCCCeeCC-----eEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--------ITGLVEFLQKNQAKAAFNSLAYTKFKE-----VPL  162 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~--------~~afV~F~~~~~A~~A~~~l~~~~~~g-----~~l  162 (274)
                      .-.|.|+.||+.+|++++.+.++..=.+......+.+        .-|||.|.+.++...-.+.++|..|.+     -+-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            3578899999999999999888876444333332211        358999999999999999999987743     245


Q ss_pred             EEEEecC
Q psy3343         163 YLEWAPE  169 (274)
Q Consensus       163 ~v~~a~~  169 (274)
                      .|++||-
T Consensus        89 ~VE~APy   95 (97)
T 2l08_A           89 VVEFAPF   95 (97)
T ss_dssp             EEEECCC
T ss_pred             EEEecCC
Confidence            6788763

>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=96.67  E-value=0.00021  Score=52.67  Aligned_cols=38  Identities=16%  Similarity=0.332  Sum_probs=30.7

Q ss_pred             EeCCCCCCCHHHHHHHh------------hhcCCeeEEEEecCCCCCCCC
Q psy3343         232 IKNLNFNSTEDSIRRHF------------KKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       232 V~NL~~~~tee~L~~~F------------~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +.|||+.+++++|+++|            ++||.|.+|+|++++.+++.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G   69 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG   69 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccE
Confidence            56788888888888777            999999999999987765544

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.58  E-value=0.00097  Score=61.78  Aligned_cols=54  Identities=20%  Similarity=0.307  Sum_probs=42.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC-eEEEEEecCHHHHHHHHH
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG-ITGLVEFLQKNQAKAAFN  150 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~-~~afV~F~~~~~A~~A~~  150 (274)
                      .++|+|. .|..+++.+|.++|++||+|.++.+..++ .||+|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            3789997 79999999999999999999999998865 599999999999997765

>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=96.42  E-value=0.0027  Score=47.81  Aligned_cols=39  Identities=18%  Similarity=0.316  Sum_probs=32.9

Q ss_pred             CCceEEEeCCCC--CC---CHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNF--NS---TEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~--~~---tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++++|+++|+-.  ++   -+++|++.|++||.|.+|.|++++.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~   62 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQ   62 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCC
Confidence            578999999942  22   3699999999999999999999865

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.43  E-value=0.017  Score=43.91  Aligned_cols=71  Identities=20%  Similarity=0.075  Sum_probs=54.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeE-EEee-----------------C--CCeEEEEEecCHHHHHHHHHHhCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGR-VLVP-----------------P--YGITGLVEFLQKNQAKAAFNSLAY  154 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~l~-----------------~--~~~~afV~F~~~~~A~~A~~~l~~  154 (274)
                      ..+.|.|-+.|+... ..+...|++||.|.+ +...                 .  .+++..|+|.++.+|.+|+. .||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            347788889987654 566679999999866 2111                 1  24688999999999999997 699


Q ss_pred             CeeCCeEEEEEEe
Q psy3343         155 TKFKEVPLYLEWA  167 (274)
Q Consensus       155 ~~~~g~~l~v~~a  167 (274)
                      ..|.|..|-|.+.
T Consensus        84 ~ii~G~mIGV~Py   96 (132)
T 3p3d_A           84 AVFNGVLLGVIPY   96 (132)
T ss_dssp             CEETTEECEEEEC
T ss_pred             eEeCcEEEEEEEC
Confidence            9999998788765

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.41  E-value=0.017  Score=41.24  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=31.3

Q ss_pred             CCCceEEEeCCC----CCCCH----HHHHHHhhhcCCeeEEEEecCC
Q psy3343         225 EPDTTLYIKNLN----FNSTE----DSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       225 ~~~~~lfV~NL~----~~~te----e~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ++..||+|...+    ..+-+    .+|.+.|++||.|..++|+.++
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~   51 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK   51 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC
Confidence            466788888876    23444    7899999999999999998765

>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=94.80  E-value=0.049  Score=40.47  Aligned_cols=40  Identities=15%  Similarity=0.266  Sum_probs=31.2

Q ss_pred             CCCCceEEEeCCCCCC----------CHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFNS----------TEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~----------tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +.++++|.++|+=..-          .+++|++.|++||.|.+|.|.++.
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~   53 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS   53 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC
Confidence            3567899999983321          236899999999999999997764

>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=94.05  E-value=0.044  Score=39.29  Aligned_cols=41  Identities=12%  Similarity=0.163  Sum_probs=32.6

Q ss_pred             CCCCCceEEEeCCCCC-----CCH----HHHHHHhhhcCCeeEEEEecCC
Q psy3343         223 EPEPDTTLYIKNLNFN-----STE----DSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~-----~te----e~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+|..||+|..++..     +-+    .+|.+.|++||.|..+++..++
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~   60 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ   60 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc
Confidence            3457789999988743     333    6799999999999999998774

>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=89.96  E-value=0.38  Score=34.58  Aligned_cols=27  Identities=19%  Similarity=0.278  Sum_probs=23.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCe
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPI  254 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I  254 (274)
                      ...++| ++|..+.-.+|.++|++||.|
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv   42 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI   42 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE
Confidence            346777 999999999999999999965

>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=89.43  E-value=0.69  Score=32.79  Aligned_cols=36  Identities=11%  Similarity=0.175  Sum_probs=31.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +.|.|++||+..|++++.+..+..+.+.+...+.-+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~   37 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND   37 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCc
Confidence            478999999999999999999999988887776544

>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=89.02  E-value=0.91  Score=42.44  Aligned_cols=56  Identities=25%  Similarity=0.418  Sum_probs=46.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAY  154 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~  154 (274)
                      ...++|+ +|..+...+|.++|+.||.+ +|+.. +...|||.|.+++.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHHHh
Confidence            3677776 99999999999999999954 44433 456899999999999999998854

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=87.90  E-value=0.73  Score=33.88  Aligned_cols=39  Identities=10%  Similarity=0.107  Sum_probs=35.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhc-----CCeeEEEEecCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKC-----GPIASVTVARKKDP  265 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~f-----G~I~~v~v~~~~~~  265 (274)
                      .++|-+-|||..+++..++.+.+++     |.|..+.+..|-.|
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~G   64 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG   64 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCc
Confidence            5789999999999999999999999     99999999887654

>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=85.92  E-value=0.46  Score=34.23  Aligned_cols=25  Identities=16%  Similarity=0.242  Sum_probs=22.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCe
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPI  254 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I  254 (274)
                      .++| ++|..+.-.+|.++|++||.|
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv   32 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI   32 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE
Confidence            5666 999999999999999999954

---

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	274
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	0.004
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-05
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.003
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.002
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.004
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	0.002
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	0.004
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.001
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:) 5e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	0.002
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.004
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.001
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.001
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.001
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.001
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.002
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.003
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.003
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.003
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.004
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.004

>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 = 61.5 bits (148), Expect = 7e-13
 Identities = 51/100 (51%), Positives = 66/100 (66%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
             RSK +IL KNLP  TL  +++  F  FG LGRVL+P  GIT +VEFL+  +A+ AF  
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRH 65

Query: 152 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGE 191
           LAY+KF  VPLYLEWAP GVF  A +K   + ++  E+ E
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 16/72 (22%), Positives = 28/72 (38%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           + V NLP      +++ LFE +G  G V +      G +    +  A+ A   L     +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 70

Query: 159 EVPLYLEWAPEG 170
              L + +A   
Sbjct: 71  GKQLRVRFACHS 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 = 36.9 bits (85), Expect = 3e-04
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
           E+     + L++ NL  + TE+ +R+ F+K G    V
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV 38

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 16/83 (19%), Positives = 26/83 (31%), Gaps = 2/83 (2%)

Query: 87  FNQVVE--ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQ 144
           F  VV   +     +    +        ++  F PFG +  + V P      V F     
Sbjct: 7   FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHES 66

Query: 145 AKAAFNSLAYTKFKEVPLYLEWA 167
           A  A  S+  T  +   +   W 
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWG 89

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 9/47 (19%), Positives = 18/47 (38%)

Query: 215 NVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
             E+   +    + T+Y   +    T+  +R+ F   G I  + V  
Sbjct: 6   RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP 52

>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 = 50.8 bits (120), Expect = 2e-08
 Identities = 13/36 (36%), Positives = 23/36 (63%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
           +EPE    L+I  L+F +T++S+R HF++ G +   
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDC 36

>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 = 35.4 bits (80), Expect = 0.004
 Identities = 18/175 (10%), Positives = 42/175 (24%), Gaps = 40/175 (22%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
           E    R + +  L + T    L++ FE +G L   +V     T                 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTK---------------- 45

Query: 152 LAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPE 211
                                   + +  G       E             +        
Sbjct: 46  ------------------------RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR 81

Query: 212 VEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
                +            +++  +  ++ E  +R +F++ G I  + +   +   
Sbjct: 82  AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSG 136

>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 = 47.2 bits (112), Expect = 4e-08
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
           + V +L        L   F P G +  + V    IT        V F Q   A+ A +++
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 153 AYTKFKEVPLYLEWA 167
            +   K  P+ + W+
Sbjct: 63  NFDVIKGKPVRIMWS 77

>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 = 41.8 bits (98), Expect = 4e-06
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           +LY+ +L+ + TE  +   F   GPI S+ V R    +  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRS 41

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 46.1 bits (109), Expect = 1e-07
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
           S   ++V  LP      +L ALF   G +    +     TG       V+F  +  ++ A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 149 FNSLAYTKFKEVPLYLEWAPEG 170
              L     +   L + +A  G
Sbjct: 61  IKVLNGITVRNKRLKVSYARPG 82

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.6 bits (105), Expect = 5e-07
 Identities = 9/48 (18%), Positives = 19/48 (39%)

Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +T L +  L  + T+  +   F+  GPI +  + R         +  +
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFV 49

>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 = 46.9 bits (111), Expect = 1e-07
 Identities = 20/105 (19%), Positives = 43/105 (40%), Gaps = 10/105 (9%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI---TGLVEFLQKNQAKAAFNSLA 153
           RI+ ++NLPY+    ++  +F  +G + ++ V        T  V +     AK A + L+
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 154 YTKFKEVPLYLEWAPEGVFAEAKEKSKGKEKEKNEEGEGEEEKKE 198
                   L + +           ++  K   K +E + +  K++
Sbjct: 68  GFNVCNRYLVVLYYNA-------NRAFQKMDTKKKEEQLKLLKEK 105

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
           PE +  LYI+NL +  T + +   F K GPI  + V    + +
Sbjct: 4   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR 46

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (108), Expect = 3e-07
 Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 8/87 (9%)

Query: 89  QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQ 141
           QV + ++   ILV+N+P++    +++ LF  FG+L  V +P        +   G V+F+ 
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 142 KNQAKAAFNSLAY-TKFKEVPLYLEWA 167
           K  AK AFN+L + T      L LEWA
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWA 87

>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 = 41.8 bits (98), Expect = 6e-06
 Identities = 8/44 (18%), Positives = 21/44 (47%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
           + +  + + ++N+ F + +  IR  F   G + +V + +K    
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGT 47

>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 = 44.7 bits (105), Expect = 4e-07
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 6/79 (7%)

Query: 95  SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAA 148
           SK  ++V  LP      + ++LF   G++    +    ITG       V ++    A+ A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 149 FNSLAYTKFKEVPLYLEWA 167
            N+L   + +   + + +A
Sbjct: 61  INTLNGLRLQTKTIKVSYA 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 = 37.0 bits (85), Expect = 2e-04
 Identities = 8/26 (30%), Positives = 11/26 (42%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGP 253
           T L +  L  N T++  R  F   G 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGE 28

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.6 bits (105), Expect = 6e-07
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-TGLVEFLQKNQAKAAFN 150
           + R+ R +L KNL +     +LK +FE   ++  V           +EF  +  A+    
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 151 SLAYTKFKEVPLYLEWA 167
                +     + L + 
Sbjct: 72  EKQGAEIDGRSVSLYYT 88

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 15/50 (30%), Positives = 24/50 (48%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           ++     TL  KNL+FN TED ++  F+    I  V+   K    +  +F
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEF 60

>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 = 43.4 bits (102), Expect = 1e-06
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-----PYGITGLVEFLQKNQAKAAFNSLA 153
           +LV NL +     D++ LF  FG L +  V          T  V F +K  A  A     
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 154 YTKFKEVPLYLEWAP 168
                  P+ ++   
Sbjct: 63  GVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (88), Expect = 8e-05
 Identities = 8/32 (25%), Positives = 15/32 (46%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
           L + NL+F  ++  I+  F + G +    V  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY 34

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 93  ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAK 146
           A +KR++ V  L        L A F PFGD+  + +P    T        VEF     A 
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 147 AAFNSLAYTKFKEVPLYLEWA 167
           AA +++  ++     + +  A
Sbjct: 62  AAIDNMNESELFGRTIRVNLA 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 = 6/31 (19%), Positives = 9/31 (29%)

Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
               LY+  L     +  +   F   G I  
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITD 34

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 13/34 (38%), Positives = 19/34 (55%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
            P+P+  L +  L+  +TE  +R  F K GPIA 
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIAD 38

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 6/73 (8%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFN 150
             + V  L   T   DL+ +F  +G +  V +     +        V F   + AK A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 151 SLAYTKFKEVPLY 163
                +     + 
Sbjct: 70  RANGMELDGRRIR 82

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.2 bits (99), Expect = 3e-06
 Identities = 16/49 (32%), Positives = 20/49 (40%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           E   DT LY+ NL    T+D +   F K G I    + R K    P   
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 50

>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 = 41.1 bits (96), Expect = 9e-06
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 145
           E+     + V NLP       L  +F  +G + +  +    +T        V + ++ +A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 146 KAAFNSLAYTKFK--EVPLYLEWA 167
           + A ++L     +    PL +  A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>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 = 41.9 bits (98), Expect = 4e-06
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
           E   D T+Y+  L+   +E  +   F + GP+ +
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVN 38

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 19/82 (23%), Positives = 28/82 (34%), Gaps = 6/82 (7%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 145
           E      + V  L  +     L  LF   G +    +P   +T      G VEFL +  A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 146 KAAFNSLAYTKFKEVPLYLEWA 167
             A   +   K    P+ +  A
Sbjct: 65  DYAIKIMDMIKLYGKPIRVNKA 86

>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 = 41.6 bits (97), Expect = 5e-06
 Identities = 8/45 (17%), Positives = 16/45 (35%)

Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           D  LY+  L    T+  + + F + G I +  +   +        
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 50

>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 = 35.8 bits (82), Expect = 5e-04
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 8/77 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
           + V  LP      +L+ LF  +G +    +    +T      G + F ++ +A+ A   L
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 153 AYTKF--KEVPLYLEWA 167
              K      P+ +++A
Sbjct: 69  NGQKPSGATEPITVKFA 85

>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 = 6e-06
 Identities = 9/49 (18%), Positives = 16/49 (32%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
               D  +Y+ NL  +     I   F K G I  + +  ++        
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFV 58

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP---PYGITGLVEFLQKNQAKAAFNSLAYT 155
           I V NLP      D++ +F  +G +  + +           VEF     A+ A       
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 156 KFKEVPLYLEWAPEG 170
            +    L +E+   G
Sbjct: 77  DYDGYRLRVEFPRSG 91

>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 = 42.0 bits (98), Expect = 6e-06
 Identities = 14/43 (32%), Positives = 26/43 (60%)

Query: 211 EVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGP 253
            +E    E ++RE E    L+I  L+F +TE+S+R ++++ G 
Sbjct: 4   TLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGK 46

>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 = 41.2 bits (96), Expect = 8e-06
 Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 9/78 (11%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP---------PYGITGLVEFLQKNQAKAAF 149
           + +KNL + T    LK +F   G +    +               G VE+ +  QA+ A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 150 NSLAYTKFKEVPLYLEWA 167
             L         L +  +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 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 = 40.0 bits (93), Expect = 2e-05
 Identities = 17/42 (40%), Positives = 28/42 (66%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           L+IKNLNF++TE++++  F K G I S T+++KK+       
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLS 42

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.9 bits (95), Expect = 9e-06
 Identities = 6/28 (21%), Positives = 14/28 (50%)

Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPI 254
           + TL++ N   + T+ +IR   +    +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVV 28

>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 = 41.3 bits (96), Expect = 9e-06
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 1/70 (1%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           ILVKNLP  +   ++  L + +      +         V  L   QA+ A        F+
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAF-VTLLNGEQAQNAIQMFHQYSFR 66

Query: 159 EVPLYLEWAP 168
              L ++  P
Sbjct: 67  GKDLIVQLQP 76

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.6 bits (94), Expect = 1e-05
 Identities = 14/47 (29%), Positives = 23/47 (48%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           TT+ +KNL  +  ++ + ++FK CGPI  V VA           +  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEF 47

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           +EPE    L+I  L+F +T++S+R HF++ G +    V R  + K    F
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 50

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSL 152
           + V NL + T    +  LF   GD+ ++++              VE+  +  A+ A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 153 AYTKFKEVPLYLEWAP 168
             T+  +  +  +W  
Sbjct: 70  NGTRLDDRIIRTDWDA 85

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 17/51 (33%), Positives = 26/51 (50%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           E+  +   TLY+ NL+F +TE+ I   F K G I  + +   K  K+   F
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF 51

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 11/53 (20%), Positives = 26/53 (49%)

Query: 222 REPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           R  + + T+ + NL+ ++ E  ++  F+  G I+ + +A+ K       F  +
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 55

>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQA 145
            A     I V NL   T  TDL+ LF PFG + R+ +     T        + F ++  A
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 146 KAAFNSLAYTKFKEVPLYLEWA 167
             A   ++   +  + L +EWA
Sbjct: 64  ARAIAGVSGFGYDHLILNVEWA 85

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 99  ILVKNL-PYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
           + + NL       +D++A+F  +G +    V        V+++ +  A+AA         
Sbjct: 18  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--FAFVQYVNERNARAAVAGEDGRMI 75

Query: 158 KEVPLYLEWAPE 169
               L +  A E
Sbjct: 76  AGQVLDINLAAE 87

>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 = 37.5 bits (87), Expect = 2e-04
 Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 1/38 (2%)

Query: 223 EPEPDTTLYIKNLNFNSTEDS-IRRHFKKCGPIASVTV 259
               ++ ++I NLN    + S +   F K G I   +V
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV 48

>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +     TLY+ NL+ + TE  I + F + GP  S  +  +     P  F+  
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEF 55

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 8e-05
 Identities = 16/80 (20%), Positives = 25/80 (31%), Gaps = 4/80 (5%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP----PYGITGLVEFLQKNQAKA 147
           +    R + V NL        +  LF   G      +            VEF +   A A
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 148 AFNSLAYTKFKEVPLYLEWA 167
           A  ++   K     + + WA
Sbjct: 64  ALAAMNGRKILGKEVKVNWA 83

>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 = 40.2 bits (93), Expect = 3e-05
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
            ++ V+ L    +  DL    E FG +  V++ P+    LVEF   + AK      A   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVP 75

Query: 157 F--KEVPLYLEWA 167
                   +  ++
Sbjct: 76  VYIAGQQAFFNYS 88

>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 = 34.4 bits (78), Expect = 0.003
 Identities = 6/40 (15%), Positives = 15/40 (37%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
              +      ++++ L  +  E  +    +K G I  V +
Sbjct: 8   SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM 47

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 9/38 (23%), Positives = 16/38 (42%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
            LY+ N+ F  TE+++   F     +  +T A      
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVL 40

>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 = 39.6 bits (92), Expect = 4e-05
 Identities = 6/48 (12%), Positives = 15/48 (31%)

Query: 217 EEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
            ++   E     T++   L        +   F   G +  V +   ++
Sbjct: 8   VDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 55

>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 = 39.2 bits (91), Expect = 5e-05
 Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 4/73 (5%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG----LVEFLQKNQAKAAFNSLAY 154
           I +KNL        L   F  FG++    V            V F  +  A+ A   +  
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 155 TKFKEVPLYLEWA 167
               +  +++   
Sbjct: 71  MLLNDRKVFVGRF 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 = 36.9 bits (85), Expect = 3e-04
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
             ++IKNL+ +    ++   F   G I S  V  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 42

>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 = 39.4 bits (91), Expect = 5e-05
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           E   ++ +Y++ LN + T D +   FK+CG +       + 
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQP 44

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (77), Expect = 0.004
 Identities = 16/90 (17%), Positives = 22/90 (24%), Gaps = 14/90 (15%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY--------------GITGLV 137
           E      I V+ L       DL   F+  G +                           V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWA 167
            +     AKAA        F+   L +  A
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>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 = 38.5 bits (89), Expect = 7e-05
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFN 150
            I+ V ++       +++  F  +G++  + +             LVE+    QA AA  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 151 SLAYTKFKEVPLYLEWA 167
           +L   +     + ++W 
Sbjct: 68  ALNGAEIMGQTIQVDWC 84

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 6/26 (23%), Positives = 13/26 (50%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGP 253
             L++ +++  + ED I+  F   G 
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGE 33

>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 = 37.7 bits (87), Expect = 1e-04
 Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
           + +  LP       +K L   FG L    +     T         E++  N    A   L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 153 AYTKFKEVPLYLEWAPEG 170
              +  +  L ++ A  G
Sbjct: 64  NGMQLGDKKLLVQRASVG 81

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 14/71 (19%), Positives = 23/71 (32%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
           +I+ V+NL   T    ++  F          V        V F  +  A  A  +L    
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 157 FKEVPLYLEWA 167
               P+ +  A
Sbjct: 69  LDGSPIEVTLA 79

>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 = 33.5 bits (76), Expect = 0.004
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
           +E        LY++NL  +++E+ I + F    P A   V + +
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR 44

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 12/55 (21%), Positives = 21/55 (38%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
                 P  T ++ NL ++ TE+SI+  F+     A        +P+    F   
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62

>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 = 37.0 bits (85), Expect = 2e-04
 Identities = 12/76 (15%), Positives = 23/76 (30%), Gaps = 7/76 (9%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGI-------TGLVEFLQKNQAKAAFNS 151
           I + NL        L   F  FG + +                  + F   + + AA  +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 152 LAYTKFKEVPLYLEWA 167
           +        P+ + +A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>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 = 36.3 bits (83), Expect = 5e-04
 Identities = 7/25 (28%), Positives = 11/25 (44%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPI 254
           ++I NL+    E  +   F   G I
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVI 25

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 10/51 (19%), Positives = 21/51 (41%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           +R  +  + L +  L + +TE  ++ +F   G +  V V +         F
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGF 52

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 36.9 bits (84), Expect = 3e-04
 Identities = 9/48 (18%), Positives = 17/48 (35%)

Query: 220 EEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           E  E      L+I NLN N +   ++    +      + V   +   +
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN 53

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.1 bits (85), Expect = 3e-04
 Identities = 10/74 (13%), Positives = 19/74 (25%), Gaps = 5/74 (6%)

Query: 99  ILVKNLP-----YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
           ++                  ++LF  +                + F     A  A   L 
Sbjct: 8   LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLH 67

Query: 154 YTKFKEVPLYLEWA 167
            T+F    + L +A
Sbjct: 68  KTEFLGKEMKLYFA 81

>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 = 36.9 bits (85), Expect = 4e-04
 Identities = 9/41 (21%), Positives = 18/41 (43%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
             P   + ++NL +  T D + + F K G +  +    K +
Sbjct: 4   QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 44

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
             + V  L   T    L   F+ FG +  +          +++   + A+AA   +    
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 157 F--KEVPLYLEWA 167
               +  L +++A
Sbjct: 78  LGGPDRRLRVDFA 90

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 7e-04
 Identities = 9/35 (25%), Positives = 19/35 (54%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
           +  P T L++  L  N++  ++ R F + G I ++
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI 47

>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 = 36.1 bits (83), Expect = 5e-04
 Identities = 6/25 (24%), Positives = 17/25 (68%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPI 254
           ++I  L++ +T++ +R +F + G +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEV 27

>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 = 34.6 bits (79), Expect = 0.001
 Identities = 11/58 (18%), Positives = 21/58 (36%), Gaps = 6/58 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFN 150
           + +  L ++T    L+  F  FG++   LV    +T        V F+ +        
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 5e-04
 Identities = 5/54 (9%), Positives = 16/54 (29%)

Query: 214 ENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
           +N  +  +      + + ++       E+      +K G +  + V        
Sbjct: 14  QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHL 67

>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 = 6e-04
 Identities = 10/50 (20%), Positives = 18/50 (36%)

Query: 225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           EP+  LY+KNL+   TE  +   F +        +  +           +
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 65

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 7e-04
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSL 152
           + V+NL Y +   DL+ LF  +G L  +  P             V F+    A  A+  +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 153 AYTKFKEVPLYLEWA 167
               F+   L++  +
Sbjct: 71  DGQVFQGRMLHVLPS 85

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 11/51 (21%), Positives = 24/51 (47%)

Query: 224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
                 L+++NL++ S+E+ + + F   GP++ +        K P  F  +
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFV 55

>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 = 35.8 bits (82), Expect = 7e-04
 Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 219 DEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           + E +  P   L++ N+ F   +  +R+ F + G I  V +   +       F++ 
Sbjct: 4   NSESKSTP-KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 58

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 4/78 (5%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG----LVEFLQKNQAKAAF 149
            + + + V N+P+R    DL+ +F  FG +  V +            V F     A  A 
Sbjct: 9   STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAR 68

Query: 150 NSLAYTKFKEVPLYLEWA 167
             L  T  +   + +  A
Sbjct: 69  EKLHGTVVEGRKIEVNNA 86

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (80), Expect = 9e-04
 Identities = 8/42 (19%), Positives = 19/42 (45%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           +++  L+ ++ E+ IR +F   G + S+ +           F
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGF 43

>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 = 33.4 bits (76), Expect = 0.004
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 6/58 (10%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFN 150
           I V  L   T    ++  F  FG++  + +P    T        + F ++   K    
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 9e-04
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 15/98 (15%)

Query: 94  RSKRIILVKNLPYRTLPTDLK----ALFEPFGDLGRVLVPPYGIT---GLVEFLQKNQAK 146
           R    I + NL  +    +LK    A+F  FG +  +LV           V F + + A 
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 147 AAFNSLAYTKFKEVPLYLEWAPEGVFAEAKEKSKGKEK 184
            A  S+    F + P+ +++        AK  S    K
Sbjct: 61  NALRSMQGFPFYDKPMRIQY--------AKTDSDIIAK 90

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 5/76 (6%)

Query: 97  RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTK 156
            ++    L        L  + E  G +  +L+PP        +    ++K A+ +L   +
Sbjct: 21  LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKE 80

Query: 157 FKE-----VPLYLEWA 167
             +     + LYL + 
Sbjct: 81  VVDDLGQKITLYLNFV 96

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 7/36 (19%), Positives = 15/36 (41%)

Query: 221 EREPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS 256
           ++E      L+I +L     +  + + F   G + S
Sbjct: 12  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVS 47

>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 = 34.5 bits (78), Expect = 0.001
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
           IL++ LP      ++  L   +       V  Y  T  V  L   QA+AA N+   ++ +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-KYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 159 EVPLYLEWAP 168
           E  L ++  P
Sbjct: 60  ERELSVQLQP 69

>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 = 34.6 bits (79), Expect = 0.001
 Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 94  RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
           R    + V        PT L+  F PFG++  + + P      V + +   A  A   L 
Sbjct: 3   RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELN 60

Query: 154 YTKFKEVPLYLEWA 167
            T+ + V L +  A
Sbjct: 61  GTQVESVQLKVNIA 74

>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 = 34.7 bits (79), Expect = 0.001
 Identities = 7/29 (24%), Positives = 16/29 (55%)

Query: 226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPI 254
           P  TL++ N+  + +E+ ++  F   G +
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGV 37

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 97  RIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN--SLA 153
           R++ + +    + L   L  L EPFG +   L+        +E      A+AA +  +  
Sbjct: 9   RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 154 YTKFKEVPLYLEWA 167
                  P+ +  +
Sbjct: 69  PALVFGKPVRVHLS 82

>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 = 34.1 bits (77), Expect = 0.002
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 92  EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNS 151
           +    R++ ++ LP     T++ AL  PFG +  +L+        +E   +  A    N 
Sbjct: 4   DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 152 LAY--TKFKEVPLYLEWA 167
            +      +  P+Y++++
Sbjct: 64  YSAVTPHLRNQPIYIQYS 81

>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 = 33.9 bits (77), Expect = 0.003
 Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP 268
           +P P T + ++N+ F  + D I   F     I      +  +   P
Sbjct: 6   KPGP-TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMP 50

>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 = 33.8 bits (77), Expect = 0.003
 Identities = 8/42 (19%), Positives = 20/42 (47%)

Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
           ++I  L++++T+  ++ +F K G +   T+           F
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGF 43

>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 = 33.9 bits (77), Expect = 0.003
 Identities = 8/79 (10%), Positives = 22/79 (27%), Gaps = 10/79 (12%)

Query: 99  ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT--------GLVEFLQKNQAKAAFN 150
           + +  +P      ++        +    ++                VE+     A  A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 151 SLAYTKFK--EVPLYLEWA 167
            L   + +     + ++WA
Sbjct: 64  KLMPGRIQLWGHQIAVDWA 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 = 34.9 bits (79), Expect = 0.003
 Identities = 7/53 (13%), Positives = 17/53 (32%)

Query: 199 NTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKKC 251
               +  Q    + +         EP+    L +  +     E  +R+ F++ 
Sbjct: 14  GQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERY 66

>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 = 34.0 bits (77), Expect = 0.003
 Identities = 11/52 (21%), Positives = 24/52 (46%)

Query: 223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
           +     T++I+NL+F+S E+++    ++ G +  V V    D +        
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 55

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.5 bits (76), Expect = 0.004
 Identities = 11/35 (31%), Positives = 15/35 (42%)

Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
            LYI NL+   T D +R+ F       +  V  K 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS 37

>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 = 33.5 bits (76), Expect = 0.004
 Identities = 7/30 (23%), Positives = 15/30 (50%)

Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASV 257
           + +++     + TED +R  F + G +  V
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDV 35

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	274
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.76
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.75
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.75
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.74
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.72
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.72
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.7
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.7
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.69
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.69
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.69
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.69
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.69
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.68
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.64
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.64
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.5
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
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	99.48
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.45
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.44
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.29
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.02
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.98
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.96
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.96
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.94
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	98.93
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.92
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.91
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.9
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.89
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.88
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.88
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.87
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.87
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.86
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.85
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.81
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.74
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.72
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.71
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.69
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.69
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.67
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.67
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.66
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.66
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.65
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.65
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.65
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.62
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.62
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.6
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.59
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.58
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.58
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.58
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.57
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.53
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.53
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.51
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.49
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.48
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.48
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.46
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.45
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.45
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.44
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.44
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.44
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.4
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.37
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.32
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.31
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.28
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.27
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.27
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.24
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.24
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.15
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.01
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	97.74
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.62
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	97.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	97.34
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.11
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.9
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.74
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	95.82
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.17
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	91.69

>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=99.87  E-value=1.5e-21  Score=158.67  Aligned_cols=122  Identities=17%  Similarity=0.279  Sum_probs=101.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ++|||+|||+++|+++|+++|++||.|.++.++.      .+|||||+|.+.++|..|+. +.+..+.++.+.+.+....
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            7899999999999999999999999999999875      24799999999999999997 5777888888887765433


Q ss_pred             CCcccccccccccccccccccchhhhhccchhhcccCCCCcccccccccccCCCCCCceEEEeCCCCCCCHHHHHHHhhh
Q psy3343         171 VFAEAKEKSKGKEKEKNEEGEGEEEKKENTAEEDNQQGVPEVEENVEEDEEREPEPDTTLYIKNLNFNSTEDSIRRHFKK  250 (274)
Q Consensus       171 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~tee~L~~~F~~  250 (274)
                      .    ...         .                                .......++|||+|||+.+|+++|+++|+.
T Consensus        86 ~----~~~---------~--------------------------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~  120 (183)
T d1u1qa_          86 E----DSQ---------R--------------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ  120 (183)
T ss_dssp             T----GGG---------S--------------------------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGG
T ss_pred             c----ccc---------c--------------------------------cccccccceeEEccCCCcCCHHHHhhhhcc
Confidence            0    000         0                                012234579999999999999999999999


Q ss_pred             cCCeeEEEEecCCC
Q psy3343         251 CGPIASVTVARKKD  264 (274)
Q Consensus       251 fG~I~~v~v~~~~~  264 (274)
                      ||.|..+.|+++..
T Consensus       121 ~G~v~~~~i~~~~~  134 (183)
T d1u1qa_         121 YGKIEVIEIMTDRG  134 (183)
T ss_dssp             GSCEEEEEEEECTT
T ss_pred             CCceeeeeeecccc
Confidence            99999999999865

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=9e-21  Score=142.16  Aligned_cols=81  Identities=58%  Similarity=0.997  Sum_probs=76.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGV  171 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~~  171 (274)
                      ..++.++|||+|||+.+++++|+++|++||.|..|.|++.++||||+|.+.++|.+|++.|||..|.|++|+|+|++...
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            45677999999999999999999999999999999999999999999999999999999999999999999999998664


Q ss_pred             C
Q psy3343         172 F  172 (274)
Q Consensus       172 f  172 (274)
                      +
T Consensus        86 ~   86 (111)
T d1whxa_          86 F   86 (111)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=4.9e-20  Score=130.66  Aligned_cols=75  Identities=20%  Similarity=0.259  Sum_probs=69.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ++++|||+|||+++++++|+++|++||.|.+|.+.+      .+|||||+|.++++|..|++.|+|..+.|++|+|.||.
T Consensus         1 s~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           1 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999865      24799999999999999999999999999999999986


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=1.5e-19  Score=129.43  Aligned_cols=76  Identities=21%  Similarity=0.339  Sum_probs=72.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..++|||+|||+++++++|+++|++||.|.+|.+.++++||||+|.+.++|..|+..|+|..|.|++|.|+||...
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            3478999999999999999999999999999999999999999999999999999999999999999999999754

>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=99.79  E-value=2.6e-19  Score=126.77  Aligned_cols=74  Identities=20%  Similarity=0.359  Sum_probs=69.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|||+|||+++++++|+++|++||.|.+|.++++      +|||||+|.++++|..|++.|+|..+.|++|.|.||.
T Consensus         1 s~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            3578999999999999999999999999999998752      3799999999999999999999999999999999985

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.8e-19  Score=131.66  Aligned_cols=77  Identities=18%  Similarity=0.227  Sum_probs=72.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ...++|||+|||+++++++|+++|++||.|.+|.+++++|||||+|.+.++|..|+..|+|..|.|++|+|.|+...
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 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            44589999999999999999999999999999999999999999999999999999999999999999999998543

>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=99.78  E-value=5.8e-19  Score=128.13  Aligned_cols=77  Identities=18%  Similarity=0.308  Sum_probs=71.0

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +.+++|||+|||+++|+++|+++|++||.|.+|.++++      +|||||+|.+.++|..|++.|+|..+.|++|.|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45689999999999999999999999999999999763      379999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      +..
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.77  E-value=5.8e-19  Score=128.38  Aligned_cols=78  Identities=36%  Similarity=0.626  Sum_probs=71.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-------CCeEEEEEecCHHHHHHHHHHh-CCCeeCCeEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNSL-AYTKFKEVPLYL  164 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l-~~~~~~g~~l~v  164 (274)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++       .+|||||+|.+.++|..|+..| +|..+.|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            45668999999999999999999999999999999965       2579999999999999999998 899999999999


Q ss_pred             EEecCC
Q psy3343         165 EWAPEG  170 (274)
Q Consensus       165 ~~a~~~  170 (274)
                      +||..+
T Consensus        85 ~~A~~~   90 (94)
T d2cpha1          85 EWADSE   90 (94)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999654

>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=99.77  E-value=9.3e-19  Score=126.22  Aligned_cols=77  Identities=21%  Similarity=0.253  Sum_probs=71.1

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...+++|||+|||+++|+++|+++|++||.|.+|.+++    .++||||+|.+.++|..|+..|+|..+.|++|+|.||.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34568999999999999999999999999999999976    35799999999999999999999999999999999985


Q ss_pred             C
Q psy3343         169 E  169 (274)
Q Consensus       169 ~  169 (274)
                      .
T Consensus        85 ~   85 (90)
T d2cqia1          85 T   85 (90)
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=99.77  E-value=5.5e-19  Score=127.16  Aligned_cols=77  Identities=25%  Similarity=0.319  Sum_probs=70.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .+.++|||+|||+++++++|+++|++||.|.+|.++.      .+|||||+|.+.++|..|+..|+|..+.|++|.|.||
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3568999999999999999999999999999999975      3589999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      .+.
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.77  E-value=8.4e-19  Score=125.94  Aligned_cols=77  Identities=17%  Similarity=0.248  Sum_probs=70.2

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ...+++|||+|||+++|+++|+++|++||.|.+|.++++      +|||||+|.+.++|..|+..|+|..+.|++|.|+|
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~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999998753      47999999999999999999999999999999999


Q ss_pred             ecC
Q psy3343         167 APE  169 (274)
Q Consensus       167 a~~  169 (274)
                      |..
T Consensus        84 a~~   86 (88)
T d1rk8a_          84 CFV   86 (88)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            853

>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=99.77  E-value=1.9e-18  Score=125.37  Aligned_cols=78  Identities=23%  Similarity=0.270  Sum_probs=72.0

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ....++|||+|||+++++++|+++|++||.|.+|.+..+    +|||||+|.+.++|..|+..|+|..+.|+.|.|+||.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            445689999999999999999999999999999998763    5899999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      .+
T Consensus        88 ~r   89 (93)
T d2cq3a1          88 AR   89 (93)
T ss_dssp             SS
T ss_pred             cC
Confidence            54

>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=99.76  E-value=1e-18  Score=122.67  Aligned_cols=71  Identities=25%  Similarity=0.317  Sum_probs=67.3

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +|||+|||+++++++|+++|++||.|.+|.++.+     +|||||+|.+.++|..|++.|||..+.|++|.|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999999999999999999999999999763     4799999999999999999999999999999999985

>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=99.76  E-value=1e-18  Score=123.24  Aligned_cols=71  Identities=21%  Similarity=0.279  Sum_probs=67.3

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +|||+|||+++|+++|+++|++||.|.+|+|+++      +|||||+|.++++|..|++.|+|..+.|++|.|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            6999999999999999999999999999999862      3799999999999999999999999999999999984

>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=99.76  E-value=8.3e-19  Score=123.40  Aligned_cols=76  Identities=24%  Similarity=0.315  Sum_probs=71.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .+++++|||+|||  +|+++|+++|++||.|.+|.+.++++||||+|.+.++|..|+..|||..+.|++|.|.|+..+
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            4567899999996  899999999999999999999999999999999999999999999999999999999999543

>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=99.76  E-value=1.7e-18  Score=130.27  Aligned_cols=74  Identities=22%  Similarity=0.314  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .+++|||+|||+++++++|+++|++||.|.+|+++.   ++|||||+|.+.++|..|++.|+|..|.|++|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999986   46899999999999999999999999999999999984

>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=99.76  E-value=3e-18  Score=123.51  Aligned_cols=76  Identities=28%  Similarity=0.460  Sum_probs=70.3

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|..|++.|+|..+.|+.|.|+||.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4589999999999999999999999999999999763      4799999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      +.
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.75  E-value=2.6e-18  Score=119.63  Aligned_cols=71  Identities=27%  Similarity=0.448  Sum_probs=67.5

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      |||+|||+++++++|+++|++|| +..+.+.+.+|||||+|.+.++|.+|+..|||..+.|++|.|+|++.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 777888889999999999999999999999999999999999999755

>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=99.75  E-value=1.2e-18  Score=126.41  Aligned_cols=77  Identities=22%  Similarity=0.239  Sum_probs=70.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|.++.      .+|||||+|.+.++|..|++.|+|..+.|++|.|.||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3458999999999999999999999999999999875      2479999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        87 ~~~   89 (93)
T d1x5ua1          87 SAH   89 (93)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            644

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.9e-19  Score=125.41  Aligned_cols=74  Identities=16%  Similarity=0.114  Sum_probs=68.7

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCC-eeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT-KFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~-~~~g~~l~v~~a~~~  170 (274)
                      ++|||+|||+++|+++|+++|++||.|..+.+...+|||||+|.+.++|..|++.|+|. .++|++|.|+|+.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            47999999999999999999999999988877778899999999999999999999996 699999999999644

>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=99.75  E-value=1.2e-18  Score=125.40  Aligned_cols=75  Identities=19%  Similarity=0.189  Sum_probs=69.9

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..+|||+|||+++++++|+++|++||.|.++.++.    ++|||||+|.+.++|..|++.|+|..+.|++|.|.|+..+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            46899999999999999999999999999999987    3589999999999999999999999999999999998643

>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=99.75  E-value=2.5e-18  Score=122.61  Aligned_cols=74  Identities=19%  Similarity=0.273  Sum_probs=68.2

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLE  165 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~  165 (274)
                      .++++|||+|||+++++++|+++|++||.|.+++++++      +|||||+|.+.++|..|++.|+|..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            45688999999999999999999999999999998763      3799999999999999999999999976  899999


Q ss_pred             Ee
Q psy3343         166 WA  167 (274)
Q Consensus       166 ~a  167 (274)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.75  E-value=1.7e-18  Score=123.44  Aligned_cols=71  Identities=23%  Similarity=0.323  Sum_probs=66.4

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      |||+|||+++|+++|+++|++||.|.+|.|++         ++|||||+|.+.++|..|++.|+|..++|++|.|.|+..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999875         247999999999999999999999999999999999853

>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=99.75  E-value=2.9e-18  Score=124.85  Aligned_cols=77  Identities=19%  Similarity=0.239  Sum_probs=71.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...+++|||+|||+++|+++|+++|++||.|..+.+..   .++||||+|.+.++|..|++.|+|..|.|++|.|+||..
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            45668999999999999999999999999999998865   468999999999999999999999999999999999854

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.9e-18  Score=124.04  Aligned_cols=75  Identities=25%  Similarity=0.336  Sum_probs=68.5

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ..++|||+|||++++++||+++|++|| +..+.+.+.++||||+|.+.++|..|++.|++..|.|++|.|+|++.+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            457899999999999999999999999 445666677899999999999999999999999999999999999755

>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=99.75  E-value=3e-18  Score=125.72  Aligned_cols=77  Identities=22%  Similarity=0.291  Sum_probs=71.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|..|++.|++..|.|++|.|.|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44688999999999999999999999999999999763      479999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        86 ~~~   88 (99)
T d1whwa_          86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.75  E-value=1.4e-18  Score=123.97  Aligned_cols=74  Identities=19%  Similarity=0.260  Sum_probs=69.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .+|||+|||+++|+++|+++|++||+|.+|.|++      ++|||||+|.++++|..|++.|+|..+.|++|.|.||...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999999976      3589999999999999999999999999999999999644

>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=99.75  E-value=2.3e-18  Score=121.65  Aligned_cols=72  Identities=13%  Similarity=0.165  Sum_probs=66.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ++|||+|||+++|+++|+++|++||.|..+.+.+      .+|||||+|.+.++|.+|++.|+|..+.|++|.|.++.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            7999999999999999999999999998776654      35899999999999999999999999999999999984

>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=99.74  E-value=3.1e-18  Score=122.14  Aligned_cols=73  Identities=21%  Similarity=0.307  Sum_probs=66.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~  166 (274)
                      .+++|||+|||+.+|+++|+++|++||.|.++.++++      +|||||+|.+.++|..|++.|||..+.|  ++|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            3588999999999999999999999999999998752      3799999999999999999999999987  5699998


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.74  E-value=4.1e-18  Score=121.68  Aligned_cols=75  Identities=19%  Similarity=0.163  Sum_probs=70.7

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .++|||+|||+++++++|+++|++||.|..+.+...+|||||+|.+.++|..|+..|+|..|.|+.|.|.|+.+.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            478999999999999999999999999988888888999999999999999999999999999999999998533

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=3.7e-18  Score=121.11  Aligned_cols=76  Identities=26%  Similarity=0.327  Sum_probs=69.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeC-CeEEEEEEec
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFK-EVPLYLEWAP  168 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~-g~~l~v~~a~  168 (274)
                      .+++++|||+|||+++++++|+++|++||.|.+|++.+ .+|||||+|.+.++|..|++.|+|..+. |++|.|.||.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            44568999999999999999999999999999999977 4589999999999999999999998884 6899999984

>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=99.74  E-value=2.2e-18  Score=124.18  Aligned_cols=76  Identities=20%  Similarity=0.302  Sum_probs=70.0

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++++++|+++|++||.|..+.+..      .+|||||+|.+.++|..|+..|+|..|.|++|.|.||.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999999998765      35799999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.74  E-value=2.2e-18  Score=127.17  Aligned_cols=77  Identities=21%  Similarity=0.210  Sum_probs=70.3

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .+.++|||+|||+++++++|+++|++||.|.++.+..+      +|||||+|.+.++|..|++.|+|..|.|++|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999988652      479999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        96 ~~k   98 (102)
T d2cpza1          96 RSK   98 (102)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            644

>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=99.73  E-value=2.2e-17  Score=118.35  Aligned_cols=78  Identities=19%  Similarity=0.377  Sum_probs=71.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh--CCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL--AYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l--~~~~~~g~~l~v~~a~~~  170 (274)
                      ..++++|||+|||+++++++|+++|++||.|..+.+.++++||||+|.+.++|..|+..+  ++..+.|++|.|.|+..+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            456799999999999999999999999999999999999999999999999999999865  578999999999998644

>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=99.72  E-value=7.1e-18  Score=121.75  Aligned_cols=77  Identities=25%  Similarity=0.399  Sum_probs=69.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHH----ccccCCCeeEEEeeC---CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKA----LFEPFGDLGRVLVPP---YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~----~F~~~G~i~~v~l~~---~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      +++++|||+|||+.+++++|++    +|++||.|.+|.+..   .+|||||+|.+.++|..|+..|+|..+.|++|.|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4578999999999999999864    689999999999876   468999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      |..+
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9643

>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=1.7e-18  Score=127.46  Aligned_cols=76  Identities=14%  Similarity=0.197  Sum_probs=68.8

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....++|||+|||+++++++|+++|++||.|..+.+..+     +|||||+|.+.++|.+|++.|||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            445689999999999999999999999999998887652     479999999999999999999999999999988776


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.72  E-value=1.4e-18  Score=128.67  Aligned_cols=77  Identities=25%  Similarity=0.341  Sum_probs=69.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ++.++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|..|++.|+|..|.|++|.|.|+
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            33478999999999999999999999999999998752      379999999999999999999999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        86 ~~~   88 (104)
T d1p1ta_          86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCC
Confidence            543

>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=99.72  E-value=1e-17  Score=118.72  Aligned_cols=70  Identities=19%  Similarity=0.165  Sum_probs=65.1

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      +.++|||+|||+++|+++|+++|++||.|.+|.|+.+      +|||||+|.+.++|..|+..|+|..|.|++|.|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4579999999999999999999999999999998752      479999999999999999999999999999986

>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=99.72  E-value=6.9e-18  Score=119.65  Aligned_cols=72  Identities=17%  Similarity=0.180  Sum_probs=65.0

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEE-EeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRV-LVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v-~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      |||+|||+++|+++|+++|++||.|.++ .+++      ++|||||+|.+.++|..|++.|+|..+.|++|.|.||..+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998654 5554      3589999999999999999999999999999999998644

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.2e-17  Score=119.70  Aligned_cols=76  Identities=17%  Similarity=0.188  Sum_probs=68.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCee-CCeEEEEEEecC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKF-KEVPLYLEWAPE  169 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~-~g~~l~v~~a~~  169 (274)
                      .++++|||+|||+++++++|+++|++||.|..+.+..  +++||||+|.+.++|..|+..|+|..+ +|++|+|.|+..
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            3468999999999999999999999999998776654  578999999999999999999999988 589999999854

>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=99.72  E-value=1.1e-17  Score=122.16  Aligned_cols=77  Identities=17%  Similarity=0.172  Sum_probs=71.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCC--eEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKE--VPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g--~~l~v~~a~~~  170 (274)
                      .+.++|||+|||+++++++|+++|++||.|..|.+.++++||||+|.+.++|..|++.|++..|.|  ++|+|+|+...
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            346899999999999999999999999999999999999999999999999999999999999986  58999998644

>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=99.72  E-value=1.1e-17  Score=122.42  Aligned_cols=75  Identities=19%  Similarity=0.247  Sum_probs=68.2

Q ss_pred             cCCCcEEEEeCCC-CCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLP-YRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp-~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ....++|||+||| ..+++++|+++|++||.|.+|.|.  +|||||+|.+.++|.+|++.|+|..|.|++|.|+|+..
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3445789999997 568899999999999999999995  68999999999999999999999999999999999853

>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=99.71  E-value=1.5e-17  Score=122.86  Aligned_cols=76  Identities=25%  Similarity=0.307  Sum_probs=68.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++      ++|||||+|.+.++|..|++.+++ .|.|++|.|.|+
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3457899999999999999999999999999999976      358999999999999999998876 799999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            643

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.3e-18  Score=125.62  Aligned_cols=75  Identities=29%  Similarity=0.401  Sum_probs=69.3

Q ss_pred             CcEEEEeCCCC-CCCHHHHHHccccCCCeeEEEeeCC-CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          96 KRIILVKNLPY-RTLPTDLKALFEPFGDLGRVLVPPY-GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        96 ~~~l~V~nLp~-~~te~~l~~~F~~~G~i~~v~l~~~-~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      +++|||+|||+ .+|+++|+++|++||.|.+|.|.++ +|||||+|.+.++|.+|++.|+|..|.|++|.|.|+...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            58999999965 5999999999999999999999875 589999999999999999999999999999999998533

>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=99.71  E-value=1.3e-17  Score=123.16  Aligned_cols=74  Identities=19%  Similarity=0.225  Sum_probs=68.1

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      .++|||+|||+++++++|+++|++||.|..+.|+.      .+|||||+|.+.++|..|++ +++..|.|++|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            37899999999999999999999999999999976      35899999999999999996 799999999999999864


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      +
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.71  E-value=9.8e-18  Score=119.73  Aligned_cols=74  Identities=22%  Similarity=0.385  Sum_probs=66.5

Q ss_pred             CCcEEEEeCCCCCCC-HHHHHHccccCCCeeEEEeeC-------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          95 SKRIILVKNLPYRTL-PTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        95 ~~~~l~V~nLp~~~t-e~~l~~~F~~~G~i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..++|||+|||++++ +++|+++|++||.|.+|.|+.       .+|||||+|.+.++|..|++ |+|..+.|++|.|.|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            358999999999976 566999999999999999865       35799999999999999995 999999999999999


Q ss_pred             ecC
Q psy3343         167 APE  169 (274)
Q Consensus       167 a~~  169 (274)
                      +..
T Consensus        82 a~~   84 (86)
T d2ghpa3          82 ADK   84 (86)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.71  E-value=1e-17  Score=116.54  Aligned_cols=69  Identities=19%  Similarity=0.252  Sum_probs=63.8

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +|||+|||+++|+++|+++|++||.|..|.|+.      ++|||||+|.++++|.+|++ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            489999999999999999999999999999976      35899999999999999997 7999999999998754

>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=99.71  E-value=1.8e-17  Score=121.00  Aligned_cols=78  Identities=18%  Similarity=0.294  Sum_probs=69.5

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhC------CCeeCCe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLA------YTKFKEV  160 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~------~~~~~g~  160 (274)
                      ....++|||+|||+++|+++|+++|++||.|.++.+..      .+|||||+|.+.++|..|++.|+      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            34568999999999999999999999999999998876      35899999999999999999887      5678999


Q ss_pred             EEEEEEecCC
Q psy3343         161 PLYLEWAPEG  170 (274)
Q Consensus       161 ~l~v~~a~~~  170 (274)
                      +|.|+|+..+
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999998644

>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=99.70  E-value=3.5e-17  Score=114.77  Aligned_cols=71  Identities=15%  Similarity=0.165  Sum_probs=65.6

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      -++|||+|||+++|+++|+++|++||.|..+.++.+      +|||||+|.++++|.+|+. ++|..|+|++|.|.+|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            378999999999999999999999999999988762      4799999999999999996 8999999999999986

>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=99.70  E-value=5.1e-18  Score=118.70  Aligned_cols=70  Identities=17%  Similarity=0.294  Sum_probs=65.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ++|||+|||+++|+++|+++|++||.|.++.|+.      ++|||||+|.+.++|.+|+. +++..++|++|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            5799999999999999999999999999999876      35899999999999999997 7999999999999876

>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=99.70  E-value=1.9e-17  Score=121.79  Aligned_cols=72  Identities=22%  Similarity=0.336  Sum_probs=67.2

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .++|||+|||+++++++|+++|+.||.|.+|.|++      ++|||||+|.+.++|.+|+. |+|..|.|++|.|.++.
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 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            47899999999999999999999999999999986      35799999999999999995 99999999999999874

>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=99.70  E-value=4e-17  Score=120.65  Aligned_cols=78  Identities=19%  Similarity=0.302  Sum_probs=71.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh--CCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL--AYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l--~~~~~~g~~l~v~~a~~~  170 (274)
                      ....++|||+|||+.+|+++|+++|++||.|..|.+.+.+++|||+|.+.++|..|+..|  ++..+.|++|+|.|+..+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            345689999999999999999999999999999999999999999999999999999987  556788999999999644

>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=99.70  E-value=1.1e-17  Score=116.15  Aligned_cols=69  Identities=20%  Similarity=0.274  Sum_probs=64.2

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +|||+|||+++|+++|+++|++||.|..+.++.      .++||||+|.+.++|..|++ ++|..|+|++|.|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            589999999999999999999999999998865      24799999999999999996 9999999999999986

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.70  E-value=9.6e-18  Score=122.25  Aligned_cols=78  Identities=21%  Similarity=0.254  Sum_probs=70.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      .++.++|||+|||+++|+++|+++|++||.|..+.... .++||||+|.+.++|..|+..|+|..|.|++|.|.|+..+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            44568999999999999999999999999988776542 5689999999999999999999999999999999999654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.9e-18  Score=122.09  Aligned_cols=71  Identities=28%  Similarity=0.264  Sum_probs=66.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ++|||+|||+++++++|+++|++||.|.++.+.++ |||||+|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            36999999999999999999999999999998765 799999999999999999999999999999988763

>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=99.70  E-value=2.5e-17  Score=114.55  Aligned_cols=70  Identities=21%  Similarity=0.172  Sum_probs=64.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ++|||+|||+++++++|+++|+.||.|..|.|+++    .+||||+|.+.++|.+|+. +++..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999763    3699999999999999995 8999999999999865

>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=99.70  E-value=1.5e-17  Score=129.29  Aligned_cols=76  Identities=24%  Similarity=0.305  Sum_probs=69.9

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|.+      .+|||||+|.+.++|..|++.|+|..|.|+.|.|.|+.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            347899999999999999999999999999998865      24799999999999999999999999999999999986


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus       121 ~~  122 (139)
T d1u6fa1         121 SG  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.70  E-value=2.5e-17  Score=120.75  Aligned_cols=78  Identities=17%  Similarity=0.222  Sum_probs=71.1

Q ss_pred             cCCCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHH--HhCCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFN--SLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~--~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...+++|||+|||.+ +|+++|.++|++||.|.+|.+.++++||||+|.+.++|..|++  .+++..++|++|.|.|+..
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            445689999999985 8999999999999999999999999999999999999999997  4788899999999999954


Q ss_pred             C
Q psy3343         170 G  170 (274)
Q Consensus       170 ~  170 (274)
                      .
T Consensus        95 ~   95 (99)
T d1x4fa1          95 Y   95 (99)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.70  E-value=4.1e-17  Score=115.94  Aligned_cols=72  Identities=22%  Similarity=0.268  Sum_probs=66.4

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .++|||+|||+++|+++|+++|++||.|..+.|+.+      +|||||+|.++++|.+|++ +++..|+|+.|.|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            478999999999999999999999999999998752      4799999999999999997 69999999999999874

>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=4.8e-17  Score=116.85  Aligned_cols=77  Identities=18%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             cCCCcEEEEeCCCCC-CCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHh--CCCeeCCeEEEEEEecC
Q psy3343          93 ARSKRIILVKNLPYR-TLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSL--AYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l--~~~~~~g~~l~v~~a~~  169 (274)
                      ...+++|||+|||.. +|++||.++|++||.|.+|.+.+++++|||+|.+.++|..|++.|  ++..+.|++|+|.|+..
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            345689999999986 889999999999999999999999999999999999999999966  67889999999999853

>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=99.69  E-value=3.8e-17  Score=117.60  Aligned_cols=75  Identities=20%  Similarity=0.229  Sum_probs=66.9

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.+      +|||||+|.+.++|.+|++.  +..|+|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            34688999999999999999999999999999999763      47999999999999999984  45899999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.3e-17  Score=119.65  Aligned_cols=75  Identities=16%  Similarity=0.267  Sum_probs=68.5

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEecCC
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEG  170 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~~~  170 (274)
                      ...++|||+|||+++|+++|+++|++||.|.+|.++. .++||||+|.+.++|+.|+.  ++..|+|++|.|.|+..+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            4568999999999999999999999999999998876 57899999999999999985  788999999999998544

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=2.8e-17  Score=118.09  Aligned_cols=70  Identities=17%  Similarity=0.322  Sum_probs=64.4

Q ss_pred             CcEEEEeCCCCCCCHHHH---HHccccCCCeeEEEeeCC---------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEE
Q psy3343          96 KRIILVKNLPYRTLPTDL---KALFEPFGDLGRVLVPPY---------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLY  163 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l---~~~F~~~G~i~~v~l~~~---------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~  163 (274)
                      .++|||+|||+++++++|   +++|++||.|..|.++++         +|||||+|.++++|..|++.|||..+.|++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            478999999999999999   778999999999999762         27999999999999999999999999999998


Q ss_pred             EE
Q psy3343         164 LE  165 (274)
Q Consensus       164 v~  165 (274)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>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=99.69  E-value=2.8e-17  Score=120.23  Aligned_cols=76  Identities=29%  Similarity=0.297  Sum_probs=70.8

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ..++..+|||+|||+++++++|+++|++||.|..+.+.+ +|||||+|.+.++|..|++.|||..|.|+.|.|.|+.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            455678999999999999999999999999999999885 4799999999999999999999999999999999974

>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=99.69  E-value=4.2e-17  Score=119.72  Aligned_cols=79  Identities=20%  Similarity=0.175  Sum_probs=68.3

Q ss_pred             hcCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE--------EEeeC------CCeEEEEEecCHHHHHHHHHHhCCCee
Q psy3343          92 EARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR--------VLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKF  157 (274)
Q Consensus        92 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~--------v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~  157 (274)
                      .....++|||+|||+++|+++|+++|++||.|..        +.+..      .+|||||+|.+.++|..|++.|+|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            3456789999999999999999999999998743        33332      247999999999999999999999999


Q ss_pred             CCeEEEEEEecCC
Q psy3343         158 KEVPLYLEWAPEG  170 (274)
Q Consensus       158 ~g~~l~v~~a~~~  170 (274)
                      .|++|.|.||..+
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999998643

>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=99.68  E-value=5.8e-17  Score=115.39  Aligned_cols=72  Identities=21%  Similarity=0.241  Sum_probs=66.7

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ..++|||+|||+++|+++|+++|+.||.|..|.|+.+     +|||||+|.++++|.+|++ +++..+.|++|.|.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            3579999999999999999999999999999999762     4799999999999999996 7999999999999986

>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=99.68  E-value=7.5e-18  Score=121.65  Aligned_cols=76  Identities=17%  Similarity=0.113  Sum_probs=67.9

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .....+|||+|||+++|+++|+++|++||.|..+.+..     ++|||||+|.+.++|.+|++ |+|..+.|++|.|+||
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34557999999999999999999999999987776643     56899999999999999996 9999999999999998


Q ss_pred             cC
Q psy3343         168 PE  169 (274)
Q Consensus       168 ~~  169 (274)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.67  E-value=1.7e-17  Score=122.19  Aligned_cols=77  Identities=21%  Similarity=0.246  Sum_probs=69.6

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .++++|||+|||+++++++|+++|++||.|..+.+..      .+|||||+|.+.++|..|++.|+|..|.|++|.|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            3468999999999999999999999999998777653      4589999999999999999999999999999999999


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ..+
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=4.2e-17  Score=121.38  Aligned_cols=76  Identities=20%  Similarity=0.247  Sum_probs=68.2

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC--CCeEEEEEecCHHHHHHHHHHhCCCee--CCeEEEEEEecCC
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP--YGITGLVEFLQKNQAKAAFNSLAYTKF--KEVPLYLEWAPEG  170 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~--~~~~afV~F~~~~~A~~A~~~l~~~~~--~g~~l~v~~a~~~  170 (274)
                      ...+|||+|||+.+|+++|+++|++||.|.+|.+..  ++|||||+|.+.++|..|+..|+|..|  .++.|.|.|+...
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            347899999999999999999999999999998866  568999999999999999999999988  4788999987543

>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=99.66  E-value=6.8e-17  Score=117.62  Aligned_cols=74  Identities=14%  Similarity=0.161  Sum_probs=66.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCC-eeEEEeeC-------CCeEEEEEecCHHHHHHHHHHhCC--CeeCCeEEEEE
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGD-LGRVLVPP-------YGITGLVEFLQKNQAKAAFNSLAY--TKFKEVPLYLE  165 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~-i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l~~--~~~~g~~l~v~  165 (274)
                      +++|||+|||+++++++|+++|++||. |..+.+++       ++|||||+|.+.++|..|++.|++  ..+.|++|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 89999865       347999999999999999999965  45679999999


Q ss_pred             EecC
Q psy3343         166 WAPE  169 (274)
Q Consensus       166 ~a~~  169 (274)
                      ||.+
T Consensus        81 ~A~p   84 (96)
T d2disa1          81 WAEP   84 (96)
T ss_dssp             ESCS
T ss_pred             EcCC
Confidence            9953

>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=99.66  E-value=3.6e-17  Score=113.69  Aligned_cols=69  Identities=17%  Similarity=0.237  Sum_probs=62.9

Q ss_pred             EEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        98 ~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +|||+|||+++|+++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+|++ .++..+.|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            589999999999999999999999999999976      35899999999999999997 5778899999988754

>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=4.4e-17  Score=112.25  Aligned_cols=64  Identities=20%  Similarity=0.256  Sum_probs=59.9

Q ss_pred             EEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEE
Q psy3343          99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPL  162 (274)
Q Consensus        99 l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l  162 (274)
                      |||+|||+++|+++|+++|++||.|..+.+.+      .+|||||+|.+.++|..|+..|||..|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            79999999999999999999999999998865      35899999999999999999999999999875

>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=99.64  E-value=1e-16  Score=114.21  Aligned_cols=75  Identities=19%  Similarity=0.206  Sum_probs=65.6

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeE-EEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ..+.++|||+|||++++++||+++|+.||.+.. +.+..     .+|+|||+|.+.++|.+|+..|++..+.|++|+|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            455688999999999999999999999999854 33432     247999999999999999999999999999999987


Q ss_pred             e
Q psy3343         167 A  167 (274)
Q Consensus       167 a  167 (274)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.64  E-value=3.8e-16  Score=115.20  Aligned_cols=74  Identities=20%  Similarity=0.310  Sum_probs=64.8

Q ss_pred             CCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        95 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      +.++|||+|||+++|+++|+++|+.|| +..+.++.       .+|||||+|.+.++|++|+ .|++..|.|+.|.|.||
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            458999999999999999999999999 66776654       2479999999999998777 59999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        92 ~~~   94 (104)
T d1wi8a_          92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=9.3e-17  Score=118.63  Aligned_cols=77  Identities=13%  Similarity=-0.009  Sum_probs=70.4

Q ss_pred             CCCcEEEEeCCCCCC-C----HHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          94 RSKRIILVKNLPYRT-L----PTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~-t----e~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      ...++|||+||+..+ +    +++|+.+|++||.|.++.+.++++||||+|.+.++|.+|+..|||..|.|++|.|.|+.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~   82 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecc
Confidence            456899999999986 3    35799999999999999999999999999999999999999999999999999999996


Q ss_pred             CC
Q psy3343         169 EG  170 (274)
Q Consensus       169 ~~  170 (274)
                      ..
T Consensus        83 ~~   84 (104)
T d1weya_          83 TL   84 (104)
T ss_dssp             CS
T ss_pred             cC
Confidence            44

>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=99.60  E-value=8e-16  Score=113.13  Aligned_cols=76  Identities=21%  Similarity=0.290  Sum_probs=65.3

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC-----CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY-----GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~-----~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      .....+|||+|||+++|+++|+++|+.||.+ .|.++.+     +|||||+|.+.++|.+|++ +++..|.||.|.|.|+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3445799999999999999999999999854 5555442     4799999999999999986 8999999999999998


Q ss_pred             cCC
Q psy3343         168 PEG  170 (274)
Q Consensus       168 ~~~  170 (274)
                      ...
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.59  E-value=2.2e-15  Score=111.06  Aligned_cols=77  Identities=10%  Similarity=0.171  Sum_probs=66.4

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC------CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP------YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~------~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ......|||+|||+++|+++|+++|+.||.+..+.+..      .+|||||+|.++++|.+|++ +++..|.||.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            33457899999999999999999999999987654433      34899999999999999996 899999999999999


Q ss_pred             ecCC
Q psy3343         167 APEG  170 (274)
Q Consensus       167 a~~~  170 (274)
                      +...
T Consensus        91 ~~~~   94 (104)
T d1wg5a_          91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8544

>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=99.58  E-value=1.2e-15  Score=112.39  Aligned_cols=74  Identities=18%  Similarity=0.169  Sum_probs=65.1

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeE-EEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGR-VLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~-v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ...++|||+|||+++|+++|+++|+.||.|.. +.++.     .+|||||+|.+.++|.+|+. |++..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            34578999999999999999999999999865 44433     35899999999999999996 9999999999999987


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=2.7e-15  Score=110.00  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=65.6

Q ss_pred             cCCCcEEEEeC--CCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeC-C--e--EEEEE
Q psy3343          93 ARSKRIILVKN--LPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK-E--V--PLYLE  165 (274)
Q Consensus        93 ~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~-g--~--~l~v~  165 (274)
                      ..+.++|+|.|  ||+++|+++|+++|++||.|..|.+.++++||||+|.+.++|..|+..|+|..+. +  .  ++++.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i~~~~~   94 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEEEEEEE
Confidence            34457888865  9999999999999999999999999999999999999999999999999998873 2  2  45556


Q ss_pred             Eec
Q psy3343         166 WAP  168 (274)
Q Consensus       166 ~a~  168 (274)
                      |..
T Consensus        95 ~~~   97 (101)
T d2cq2a1          95 FVE   97 (101)
T ss_dssp             EES
T ss_pred             eee
Confidence            653

>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=99.55  E-value=7.1e-15  Score=109.96  Aligned_cols=74  Identities=16%  Similarity=0.188  Sum_probs=67.3

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCH-HHHHHHHHHhCCCeeCCeEEEEEEecC
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQK-NQAKAAFNSLAYTKFKEVPLYLEWAPE  169 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~-~~A~~A~~~l~~~~~~g~~l~v~~a~~  169 (274)
                      ...+||+|||+.+|+++|+++|++||+|.+|.|+++++||||.|.++ ++|..|+..|++..+.++.+.|.|+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            35569999999999999999999999999999999999999999996 689999999999999888888888753

>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=99.50  E-value=5.1e-15  Score=110.58  Aligned_cols=74  Identities=15%  Similarity=0.137  Sum_probs=63.7

Q ss_pred             CCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEee-C--C---CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEe
Q psy3343          94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-P--Y---GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWA  167 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~-~--~---~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a  167 (274)
                      ....+|||+|||+++|+++|+++|+.||.+..+.++ .  +   +|||||+|.+.++|.+|+. |+|..|+|+.|.|.++
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            345799999999999999999999999988543222 2  2   3799999999999999996 9999999999999987


Q ss_pred             c
Q psy3343         168 P  168 (274)
Q Consensus       168 ~  168 (274)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.50  E-value=1.9e-16  Score=113.85  Aligned_cols=70  Identities=17%  Similarity=0.251  Sum_probs=62.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEee-----------CCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-----------PYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLE  165 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~-----------~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~  165 (274)
                      ++|||+|||+++|+++|+++|++||.+..+.+.           .++|||||+|.+.++|..|+. |+|..+.|++|.|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999987655543           256899999999999999995 99999999999997


Q ss_pred             Ee
Q psy3343         166 WA  167 (274)
Q Consensus       166 ~a  167 (274)
                      ++
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            64

>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=99.48  E-value=1.5e-15  Score=111.98  Aligned_cols=72  Identities=17%  Similarity=0.171  Sum_probs=66.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeC-----CCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPP-----YGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~-----~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      +.++|++++.++++++|+++|++||.|.+|.|++     .+|||||+|.+.++|.+|+..|+|..|+|++|.|+|.|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            4577888888899999999999999999999976     35899999999999999999999999999999999975

>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=99.45  E-value=6.7e-14  Score=98.17  Aligned_cols=71  Identities=17%  Similarity=0.152  Sum_probs=63.0

Q ss_pred             CcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeE-EEEEEec
Q psy3343          96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVP-LYLEWAP  168 (274)
Q Consensus        96 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~-l~v~~a~  168 (274)
                      .+.|+|.+||++.+++.| ++|++||.|.++.+.++++||||+|.++++|.+|+. +||..|.|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            478999999999886555 579999999999999999999999999999999996 9999999975 5677664

>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=99.44  E-value=1.5e-13  Score=100.20  Aligned_cols=78  Identities=19%  Similarity=0.291  Sum_probs=67.8

Q ss_pred             hcCCCcEEEEeCC--CCCC---------CHHHHHHccccCCCeeEEEeeCC--CeEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3343          92 EARSKRIILVKNL--PYRT---------LPTDLKALFEPFGDLGRVLVPPY--GITGLVEFLQKNQAKAAFNSLAYTKFK  158 (274)
Q Consensus        92 ~~~~~~~l~V~nL--p~~~---------te~~l~~~F~~~G~i~~v~l~~~--~~~afV~F~~~~~A~~A~~~l~~~~~~  158 (274)
                      ..+..++|+|+|+  |.++         .+++|++.|++||.|..|.++..  +|+|||+|.+.++|.+|+..|||..|.
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            4566799999999  5442         23689999999999999998773  589999999999999999999999999


Q ss_pred             CeEEEEEEecC
Q psy3343         159 EVPLYLEWAPE  169 (274)
Q Consensus       159 g~~l~v~~a~~  169 (274)
                      |++|.|+++..
T Consensus        84 gr~i~v~~~~g   94 (99)
T d2dita1          84 GRQITAQAWDG   94 (99)
T ss_dssp             TEECEEEECCS
T ss_pred             CEEEEEEEeCC
Confidence            99999998753

>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=99.41  E-value=3.7e-13  Score=108.24  Aligned_cols=76  Identities=14%  Similarity=0.139  Sum_probs=68.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCC------CeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEE
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPY------GITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEW  166 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~------~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~  166 (274)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.+..+      +|||||+|.+.++|.+|+. +++..+.|++|.|.|
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            455689999999999999999999999999999988752      3799999999999999997 799999999999999


Q ss_pred             ecC
Q psy3343         167 APE  169 (274)
Q Consensus       167 a~~  169 (274)
                      |..
T Consensus       173 A~~  175 (183)
T d1u1qa_         173 ALS  175 (183)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            853

>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=99.29  E-value=1.8e-12  Score=95.16  Aligned_cols=75  Identities=16%  Similarity=0.244  Sum_probs=65.0

Q ss_pred             CCcEEEEeCC--CCCC--------CHHHHHHccccCCCeeEEEeeC--------CCeEEEEEecCHHHHHHHHHHhCCCe
Q psy3343          95 SKRIILVKNL--PYRT--------LPTDLKALFEPFGDLGRVLVPP--------YGITGLVEFLQKNQAKAAFNSLAYTK  156 (274)
Q Consensus        95 ~~~~l~V~nL--p~~~--------te~~l~~~F~~~G~i~~v~l~~--------~~~~afV~F~~~~~A~~A~~~l~~~~  156 (274)
                      ++++|.|+|+  |..+        ..+||++.|++||.|.+|.|++        ..|++||+|.+.++|.+|+..|+|..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  4443        3457999999999999999975        13799999999999999999999999


Q ss_pred             eCCeEEEEEEecC
Q psy3343         157 FKEVPLYLEWAPE  169 (274)
Q Consensus       157 ~~g~~l~v~~a~~  169 (274)
                      |.||+|.+.|.+.
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999863

>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=99.02  E-value=1.6e-10  Score=82.20  Aligned_cols=40  Identities=20%  Similarity=0.405  Sum_probs=37.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..+++|||+|||+++|+++|+++|++||.|.+|+|++|+.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~   45 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK   45 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCC
Confidence            3567999999999999999999999999999999999875

>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=98.98  E-value=1.9e-10  Score=80.40  Aligned_cols=41  Identities=34%  Similarity=0.639  Sum_probs=38.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++++|||+|||+.+|+++|+++|++||.|.+|+|+++++
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~   46 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ   46 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccccc
Confidence            34678999999999999999999999999999999999876

>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=98.96  E-value=2.8e-10  Score=79.82  Aligned_cols=39  Identities=31%  Similarity=0.638  Sum_probs=36.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+++|+++++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~   43 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN   43 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeeccccc
Confidence            346999999999999999999999999999999999886

>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=98.96  E-value=2.1e-10  Score=79.12  Aligned_cols=42  Identities=24%  Similarity=0.494  Sum_probs=37.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      |+|||+|||+++|+++|+++|++||.|.+++|++++. +++.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG   43 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG   43 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccc
Confidence            5799999999999999999999999999999999886 44443

>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=98.94  E-value=4.3e-10  Score=77.09  Aligned_cols=41  Identities=22%  Similarity=0.464  Sum_probs=36.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      .|||+|||+++|+++|+++|++||.|.+|+|++++. +++.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG   42 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG   42 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccccccccccc
Confidence            599999999999999999999999999999999875 44444

>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=98.93  E-value=6.1e-10  Score=76.85  Aligned_cols=41  Identities=24%  Similarity=0.498  Sum_probs=38.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +|||+|||+++|+++|+++|++||.|.+|+|+.+++++++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g   42 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG   42 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccce
Confidence            59999999999999999999999999999999998887765

>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=98.92  E-value=1.1e-09  Score=79.72  Aligned_cols=44  Identities=27%  Similarity=0.508  Sum_probs=38.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ..++|||+|||+.+|+++|+++|++||.|.+|+|++++. +++.|
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg   53 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG   53 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCS
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCC
Confidence            346899999999999999999999999999999999876 34433

>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=98.91  E-value=9.3e-10  Score=77.19  Aligned_cols=39  Identities=21%  Similarity=0.371  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+++|||+|||+.+|+++|+++|++||+|.+|+|++++.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~   43 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV   43 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccc
Confidence            357899999999999999999999999999999999875

>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=98.90  E-value=6.6e-10  Score=77.04  Aligned_cols=38  Identities=32%  Similarity=0.529  Sum_probs=35.6

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ++|||+|||+.+|+++|+++|++||+|.+|+|+++++.
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~t   38 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMIT   38 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccc
Confidence            37999999999999999999999999999999998763

>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=98.89  E-value=7.1e-10  Score=75.94  Aligned_cols=36  Identities=19%  Similarity=0.448  Sum_probs=34.4

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .|||+|||+++|+++|+++|++||+|.+|+|+++++
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~   36 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI   36 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTT
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCC
Confidence            489999999999999999999999999999999876

>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=98.88  E-value=7.3e-10  Score=78.41  Aligned_cols=44  Identities=18%  Similarity=0.354  Sum_probs=38.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++++. ++..|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg   48 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG   48 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccc
Confidence            347999999999999999999999999999999999876 34443

>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=98.88  E-value=1.1e-09  Score=77.34  Aligned_cols=41  Identities=17%  Similarity=0.360  Sum_probs=37.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~   44 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR   44 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccccc
Confidence            34578999999999999999999999999999999999865

>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=98.87  E-value=1.1e-09  Score=74.97  Aligned_cols=39  Identities=36%  Similarity=0.591  Sum_probs=36.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                      ++|||+|||+++++++|+++|++||+|..|+++.++++.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~   39 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN   39 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc
Confidence            589999999999999999999999999999999988754

>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=98.87  E-value=1.9e-09  Score=76.38  Aligned_cols=41  Identities=29%  Similarity=0.412  Sum_probs=37.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|++++.+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~   47 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN   47 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc
Confidence            45799999999999999999999999999999999987643

>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=98.86  E-value=2.1e-09  Score=76.61  Aligned_cols=41  Identities=34%  Similarity=0.528  Sum_probs=37.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .++++|||+|||+.+|+++|+++|++||+|.+|+|++++..
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~   45 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK   45 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceecccccccc
Confidence            35689999999999999999999999999999999998763

>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=98.86  E-value=1.8e-09  Score=75.60  Aligned_cols=39  Identities=36%  Similarity=0.511  Sum_probs=36.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++++.
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~   43 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL   43 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccc
Confidence            457899999999999999999999999999999999875

>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=98.86  E-value=1.5e-09  Score=77.54  Aligned_cols=39  Identities=21%  Similarity=0.516  Sum_probs=36.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+++++
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~   45 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT   45 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccc
Confidence            567999999999999999999999999999999998764

>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=98.85  E-value=1.2e-09  Score=76.60  Aligned_cols=43  Identities=21%  Similarity=0.417  Sum_probs=38.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      .++|||+|||+++|+++|+++|++||+|.+|+|+++++++..|
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG   48 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG   48 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcce
Confidence            4699999999999999999999999999999999887765443

>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=98.85  E-value=1.4e-09  Score=76.30  Aligned_cols=42  Identities=19%  Similarity=0.400  Sum_probs=37.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      .+|||+|||+.+|+++|+++|++||+|.+|+|++++. |++.|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg   44 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG   44 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccce
Confidence            3799999999999999999999999999999999876 44433

>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=98.84  E-value=2.1e-09  Score=76.61  Aligned_cols=39  Identities=21%  Similarity=0.458  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~   46 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV   46 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeeccc
Confidence            457999999999999999999999999999999999865

>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=98.84  E-value=1.5e-09  Score=75.48  Aligned_cols=38  Identities=24%  Similarity=0.434  Sum_probs=35.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~   39 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK   39 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecc
Confidence            47899999999999999999999999999999998764

>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=98.84  E-value=3.9e-09  Score=75.19  Aligned_cols=41  Identities=20%  Similarity=0.352  Sum_probs=37.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ...++|||+|||+.+|+++|+++|++||+|.+|+|+.++++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~   49 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG   49 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC
Confidence            34678999999999999999999999999999999998765

>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=98.82  E-value=2.9e-09  Score=73.90  Aligned_cols=37  Identities=32%  Similarity=0.417  Sum_probs=35.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~   39 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI   39 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeecc
Confidence            6899999999999999999999999999999998754

>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=98.82  E-value=3.3e-09  Score=73.88  Aligned_cols=40  Identities=18%  Similarity=0.321  Sum_probs=36.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+|+++|||+|||.++|+++|+++|++||+|.+|++++++
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~   44 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR   44 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc
Confidence            4567899999999999999999999999999999998764

>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=98.81  E-value=2.9e-09  Score=77.15  Aligned_cols=42  Identities=17%  Similarity=0.366  Sum_probs=38.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC-CCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD-PKSPG  269 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~-~~~~g  269 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|+|+++++ |++.|
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG   61 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG   61 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccc
Confidence            6899999999999999999999999999999999875 55554

>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=98.77  E-value=4e-09  Score=76.31  Aligned_cols=43  Identities=28%  Similarity=0.426  Sum_probs=38.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSP  268 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~  268 (274)
                      ..++|||+|||+++|+++|+++|++||.|.++++..+..+++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~   59 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR   59 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccc
Confidence            3579999999999999999999999999999999988765543

>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=98.77  E-value=3.1e-09  Score=74.31  Aligned_cols=38  Identities=45%  Similarity=0.794  Sum_probs=35.4

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      |||+|||+++|+++|+++|++||+|.+|+|++++++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~   38 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAG   38 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccccccc
Confidence            89999999999999999999999999999999887543

>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=98.75  E-value=8.8e-09  Score=74.57  Aligned_cols=42  Identities=19%  Similarity=0.256  Sum_probs=38.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .+++++|||+|||+++|+++|+++|++||.|.+++++.++.+
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~   56 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT   56 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeeccc
Confidence            346789999999999999999999999999999999988653

>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=98.75  E-value=6.9e-09  Score=76.57  Aligned_cols=39  Identities=31%  Similarity=0.585  Sum_probs=36.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+++|||+|||+.+|+++|+++|++||.|.+|++..+..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~   44 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE   44 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCC
Confidence            467999999999999999999999999999999987654

>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=98.75  E-value=3.2e-09  Score=75.13  Aligned_cols=39  Identities=23%  Similarity=0.480  Sum_probs=36.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+++++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~   45 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT   45 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccccccccccc
Confidence            457999999999999999999999999999999999875

>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=98.74  E-value=5e-09  Score=76.11  Aligned_cols=39  Identities=28%  Similarity=0.537  Sum_probs=36.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      .++|||+|||+++|+++|+++|++||.|..+.|++++.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~   58 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPAS   58 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccC
Confidence            368999999999999999999999999999999998764

>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=98.74  E-value=6.2e-09  Score=71.62  Aligned_cols=38  Identities=13%  Similarity=0.437  Sum_probs=36.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+++.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~   40 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS   40 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTT
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCC
Confidence            58999999999999999999999999999999998764

>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=98.73  E-value=5.3e-09  Score=73.69  Aligned_cols=38  Identities=18%  Similarity=0.371  Sum_probs=34.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+++|||+|||+++|+++|+++|++||.|.+|+++.+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~   41 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF   41 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeecc
Confidence            46799999999999999999999999999999887543

>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=98.72  E-value=7.3e-09  Score=74.18  Aligned_cols=42  Identities=26%  Similarity=0.512  Sum_probs=37.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK  266 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~  266 (274)
                      ..+++|||+|||+++|+++|+++|++||+|.++.++.++...
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~   47 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTE   47 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccc
Confidence            356899999999999999999999999999999999887543

>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=98.71  E-value=9.2e-09  Score=74.00  Aligned_cols=39  Identities=21%  Similarity=0.520  Sum_probs=36.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ..++|||+|||+.+|+++|+++|++||.|.+|+|++++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~   45 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL   45 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTT
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeeccccc
Confidence            456899999999999999999999999999999998864

>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=98.71  E-value=1e-08  Score=72.29  Aligned_cols=39  Identities=23%  Similarity=0.348  Sum_probs=36.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+|||+|||+++|+++|+++|++||.|.+|+|+.++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~   46 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG   46 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC
Confidence            358999999999999999999999999999999998764

>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=98.69  E-value=7.3e-10  Score=78.81  Aligned_cols=46  Identities=15%  Similarity=0.161  Sum_probs=40.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +...++|||+|||+++|+++|+++|++||.|.+++|+.+.+|++.|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg   55 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK   55 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTT
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccE
Confidence            3456799999999999999999999999999999998877776655

>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=98.69  E-value=1.1e-08  Score=73.20  Aligned_cols=39  Identities=23%  Similarity=0.381  Sum_probs=35.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+.++|||+|||+.+++++|+++|++||.|.+|+|++++
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k   54 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK   54 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc
Confidence            345799999999999999999999999999999999764

>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=98.69  E-value=1.4e-08  Score=71.45  Aligned_cols=41  Identities=20%  Similarity=0.241  Sum_probs=37.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         223 EPEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       223 ~~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +..|+++|||+|||+++|+++|+++|++||.|.++++.+++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~   44 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK   44 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc
Confidence            34578899999999999999999999999999999998654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=1.8e-08  Score=71.90  Aligned_cols=42  Identities=21%  Similarity=0.385  Sum_probs=36.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+.++|||+|||+++|+++|+++|++||.|..+.+..+..+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~   52 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG   52 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccc
Confidence            345679999999999999999999999999999998766543

>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=98.67  E-value=4.6e-09  Score=76.29  Aligned_cols=37  Identities=19%  Similarity=0.620  Sum_probs=35.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++|||+|||+++|+++|+++|++||.|.+|+|+++++
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~   45 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE   45 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccc
Confidence            5899999999999999999999999999999999875

>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=98.66  E-value=1.4e-08  Score=77.48  Aligned_cols=41  Identities=24%  Similarity=0.485  Sum_probs=37.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|++++.
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~   79 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE   79 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccc
Confidence            33457899999999999999999999999999999999876

>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=98.66  E-value=1.6e-08  Score=70.82  Aligned_cols=38  Identities=29%  Similarity=0.519  Sum_probs=35.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +.++|||+|||.++++++|+++|++||.|.+|++.+++
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k   44 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK   44 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc
Confidence            45689999999999999999999999999999998764

>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=98.65  E-value=1.6e-08  Score=71.29  Aligned_cols=39  Identities=28%  Similarity=0.648  Sum_probs=35.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      ..+|||+|||+++|+++|+++|++||.|..|.+++++++
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~   43 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRET   43 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSS
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeecccccc
Confidence            468999999999999999999999999999999887653

>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=98.65  E-value=6.9e-09  Score=72.73  Aligned_cols=38  Identities=18%  Similarity=0.416  Sum_probs=33.1

Q ss_pred             CCceEEEeCCCCCCCH-HHHHHHhhhcCCeeEEEEecCC
Q psy3343         226 PDTTLYIKNLNFNSTE-DSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       226 ~~~~lfV~NL~~~~te-e~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+++|||+|||+++|+ +.|+++|++||.|.+|+|+++.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~   41 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ   41 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeeccc
Confidence            4679999999999865 5699999999999999998753

>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=98.65  E-value=1.7e-08  Score=72.26  Aligned_cols=40  Identities=23%  Similarity=0.492  Sum_probs=36.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..|.++|||+|||+++|+++|+++|++||.|..|++.+++
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~   53 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD   53 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc
Confidence            3567899999999999999999999999999999998764

>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=98.65  E-value=1.3e-08  Score=68.76  Aligned_cols=36  Identities=25%  Similarity=0.397  Sum_probs=34.0

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      |||+|||+++|+++|+++|++||.|..+++.+++.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~   36 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTT   36 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSS
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccccc
Confidence            799999999999999999999999999999988753

>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=98.63  E-value=9.7e-09  Score=69.81  Aligned_cols=37  Identities=16%  Similarity=0.434  Sum_probs=34.5

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP  265 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~  265 (274)
                      +|||+|||+++|+++|+++|++||.|..+.+++++++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~   37 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTT   37 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccc
Confidence            4999999999999999999999999999999988764

>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=98.62  E-value=1.8e-08  Score=71.99  Aligned_cols=38  Identities=16%  Similarity=0.211  Sum_probs=34.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCC-eeEEEEecCCC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGP-IASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~-I~~v~v~~~~~  264 (274)
                      +|+|||+|||..+|+++|+++|++||+ |.+++|+++..
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~   39 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA   39 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeecc
Confidence            368999999999999999999999996 99999998864

>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=98.62  E-value=9.4e-09  Score=72.55  Aligned_cols=42  Identities=14%  Similarity=0.268  Sum_probs=37.2

Q ss_pred             CCceEEEeCCCCCCCHHHH---HHHhhhcCCeeEEEEecCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSI---RRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L---~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      +.++|||+|||+++++++|   +++|++||+|.+|.|++++....
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~   51 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG   51 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCC
Confidence            4568999999999999999   77899999999999999876543

>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=98.60  E-value=1.2e-08  Score=71.67  Aligned_cols=34  Identities=15%  Similarity=0.341  Sum_probs=32.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       229 ~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      +|||+|||+++|+++|+++|++||.|.+|+|.++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~   35 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   35 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc
Confidence            6999999999999999999999999999998765

>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=98.59  E-value=1.6e-08  Score=74.05  Aligned_cols=35  Identities=23%  Similarity=0.407  Sum_probs=32.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      .++|||+|||+.+|+++|+++|++||.|..|.|..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~   44 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE   44 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec
Confidence            47999999999999999999999999999998854

>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=98.59  E-value=1.5e-08  Score=74.00  Aligned_cols=40  Identities=23%  Similarity=0.403  Sum_probs=36.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .+..+|||+|||+.+|+++|+++|++||.|.+|.|+++++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~   44 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN   44 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETT
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCC
Confidence            4567999999999999999999999999999999998754

>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=98.58  E-value=1.6e-08  Score=69.80  Aligned_cols=37  Identities=19%  Similarity=0.191  Sum_probs=32.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~   38 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR   38 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC---
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccc
Confidence            6999999999999999999999999999888776543

>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=98.58  E-value=2.7e-08  Score=72.55  Aligned_cols=38  Identities=26%  Similarity=0.329  Sum_probs=34.2

Q ss_pred             CceEEEeCCCC-CCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         227 DTTLYIKNLNF-NSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       227 ~~~lfV~NL~~-~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +++|||+|||+ .+|+++|+++|++||.|.+|+|++++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~k   40 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK   40 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEeccc
Confidence            47999999965 599999999999999999999998753

>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=98.58  E-value=4.3e-08  Score=71.04  Aligned_cols=40  Identities=18%  Similarity=0.193  Sum_probs=36.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..++.+|||+|||+.+|+++|+++|++||.|..|++.+++
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k   51 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK   51 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc
Confidence            3467899999999999999999999999999999998654

>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=98.57  E-value=4.4e-08  Score=68.68  Aligned_cols=40  Identities=23%  Similarity=0.314  Sum_probs=35.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +|+++|||+|||+++|+++|+++|++||.|..+.+...++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~   47 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD   47 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecc
Confidence            4678999999999999999999999999999988776543

>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=98.53  E-value=2.6e-08  Score=69.06  Aligned_cols=35  Identities=26%  Similarity=0.420  Sum_probs=31.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEE-EEecCCC
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASV-TVARKKD  264 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v-~v~~~~~  264 (274)
                      |||+|||+++|+++|+++|++||.|.++ +|++++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~   36 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPD   36 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTT
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeecc
Confidence            7999999999999999999999999764 7887765

>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=98.53  E-value=4.3e-08  Score=72.17  Aligned_cols=39  Identities=13%  Similarity=0.214  Sum_probs=34.5

Q ss_pred             CCCc-eEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         225 EPDT-TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       225 ~~~~-~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      +.|+ .+||+|||+.+|+++|+++|++||+|.+|+|++++
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k   47 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA   47 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC
Confidence            3455 55999999999999999999999999999998653

>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=98.51  E-value=4.4e-08  Score=70.41  Aligned_cols=40  Identities=18%  Similarity=0.268  Sum_probs=35.7

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~-~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..++++|||+|||.+ +|+++|.++|++||.|.++++++++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k   55 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK   55 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC
Confidence            346789999999985 8999999999999999999998765

>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=98.49  E-value=1e-07  Score=68.24  Aligned_cols=37  Identities=14%  Similarity=0.349  Sum_probs=34.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ...+|||+|||+.+++++|+++|++||.|.+|.|.++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~   50 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD   50 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc
Confidence            4568999999999999999999999999999999754

>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=98.48  E-value=4.4e-08  Score=70.74  Aligned_cols=45  Identities=18%  Similarity=0.307  Sum_probs=37.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         224 PEPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       224 ~~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      ...+.+|||+|||+++|+++|+++|+.|| +..|.++++.+++..|
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G   56 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTG   56 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceE
Confidence            34567999999999999999999999997 5678888888765543

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=6.9e-08  Score=66.30  Aligned_cols=37  Identities=22%  Similarity=0.367  Sum_probs=33.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+++|||+|||  +|+++|+++|++||.|.+|++.+++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~   39 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR   39 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC
Confidence            357899999986  8999999999999999999998654

>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=98.46  E-value=9.5e-08  Score=69.14  Aligned_cols=44  Identities=16%  Similarity=0.255  Sum_probs=35.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec-CCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR-KKDPKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~-~~~~~~~g  269 (274)
                      ...+|||+|||+++|+++|+++|++||.|..+.++. +.+++..|
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG   58 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTG   58 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcce
Confidence            456899999999999999999999999988755544 44544444

>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=98.45  E-value=7.4e-08  Score=67.78  Aligned_cols=40  Identities=13%  Similarity=0.152  Sum_probs=35.7

Q ss_pred             CCCceEEEeCCCCC-CCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFN-STEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~-~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++++|||+|||.. +|+++|.++|++||.|.+|.++.+++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~   46 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN   46 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSS
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccce
Confidence            45689999999986 78999999999999999999987654

>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=98.45  E-value=9.9e-08  Score=68.86  Aligned_cols=44  Identities=16%  Similarity=0.172  Sum_probs=37.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS-VTVARKKDPKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~-v~v~~~~~~~~~g  269 (274)
                      ..++|||+|||+++|+++|+++|+.||.|.. +.+..+..|+..|
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G   51 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLG   51 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSS
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCc
Confidence            3468999999999999999999999999986 5566666776666

>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=98.44  E-value=1.1e-07  Score=68.79  Aligned_cols=38  Identities=32%  Similarity=0.607  Sum_probs=34.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.++|||+|||+++|+++|+++|++|| |..+++++++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~   51 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS   51 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeec
Confidence            568999999999999999999999998 88888887754

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=1.5e-07  Score=65.62  Aligned_cols=37  Identities=27%  Similarity=0.460  Sum_probs=33.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      ..++|||+|||+++|+++|+++|++||.|..+.+.+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~   43 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI   43 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc
Confidence            4579999999999999999999999999998888554

>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=98.44  E-value=1e-07  Score=68.41  Aligned_cols=31  Identities=29%  Similarity=0.645  Sum_probs=28.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCee
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIA  255 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~  255 (274)
                      ...++|||+|||+.+|+++|+++|++||.|.
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~   36 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVK   36 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEE
Confidence            4568999999999999999999999999985

>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=98.40  E-value=4.7e-08  Score=67.36  Aligned_cols=36  Identities=31%  Similarity=0.296  Sum_probs=32.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+|||+|||+++|+++|+++|++||.|.++++.+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~r   37 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS   37 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEET
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEeccc
Confidence            379999999999999999999999999988887653

>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=98.37  E-value=8.6e-08  Score=66.80  Aligned_cols=44  Identities=20%  Similarity=0.278  Sum_probs=36.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeE-EEEecCCCCCCCC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIAS-VTVARKKDPKSPG  269 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~-v~v~~~~~~~~~g  269 (274)
                      ..++|||+|||+++++++|+++|+.||.|.. +.+..+..+++.|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G   52 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTG   52 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcce
Confidence            4568999999999999999999999999976 5666666665544

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.32  E-value=2.7e-07  Score=65.00  Aligned_cols=37  Identities=35%  Similarity=0.686  Sum_probs=32.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHH----HhhhcCCeeEEEEecC
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRR----HFKKCGPIASVTVARK  262 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~----~F~~fG~I~~v~v~~~  262 (274)
                      |+++|||+|||+.+|+++|++    +|++||+|.+|++...
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~   42 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS   42 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee
Confidence            468999999999999999865    6899999999998653

>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=98.31  E-value=1.7e-07  Score=68.77  Aligned_cols=45  Identities=24%  Similarity=0.405  Sum_probs=36.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEE-EEecCCCCCCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASV-TVARKKDPKSPG  269 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v-~v~~~~~~~~~g  269 (274)
                      .++.+|||+|||+++|+++|+++|+.||.+..+ .+..+.+|+..|
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G   61 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG   61 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceee
Confidence            356799999999999999999999999998764 445556665544

>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=98.28  E-value=3e-07  Score=66.15  Aligned_cols=40  Identities=18%  Similarity=0.361  Sum_probs=35.3

Q ss_pred             CCCCceEEEeC--CCCCCCHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         224 PEPDTTLYIKN--LNFNSTEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       224 ~~~~~~lfV~N--L~~~~tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..++.+|||.|  ||+++|+++|+++|++||.|..|++++++
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k   56 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK   56 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc
Confidence            34667899966  99999999999999999999999988764

>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=98.27  E-value=5.3e-08  Score=70.12  Aligned_cols=40  Identities=25%  Similarity=0.349  Sum_probs=36.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      .++++|||+|||.++|+++|+++|++||.|..+.++.+..
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~   55 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM   55 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccc
Confidence            3578999999999999999999999999999999887653

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=3.3e-07  Score=64.14  Aligned_cols=35  Identities=20%  Similarity=0.277  Sum_probs=29.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         226 PDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       226 ~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ..++|||+|||+++|+++|+++|++|| +..+.+.+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~   38 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR   38 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec
Confidence            357999999999999999999999999 44455443

>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=98.24  E-value=2.6e-07  Score=65.69  Aligned_cols=35  Identities=37%  Similarity=0.484  Sum_probs=31.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEE
Q psy3343         225 EPDTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV  259 (274)
Q Consensus       225 ~~~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v  259 (274)
                      .+.++|||+|||+++|+++|+++|++||.|..++.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~   48 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ   48 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee
Confidence            34679999999999999999999999999877753

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=4.2e-07  Score=64.92  Aligned_cols=35  Identities=26%  Similarity=0.465  Sum_probs=31.2

Q ss_pred             CCceEEEeCCC-CCCCHHHHHHHhhhcCCeeEEEEe
Q psy3343         226 PDTTLYIKNLN-FNSTEDSIRRHFKKCGPIASVTVA  260 (274)
Q Consensus       226 ~~~~lfV~NL~-~~~tee~L~~~F~~fG~I~~v~v~  260 (274)
                      ..++|||+||| ..+++++|+++|++||.|.+|+|.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~   49 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH   49 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe
Confidence            45689999997 578899999999999999999985

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.15  E-value=1.3e-06  Score=59.15  Aligned_cols=31  Identities=13%  Similarity=0.221  Sum_probs=27.5

Q ss_pred             EEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       230 lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      |||+|||+++|+++|+++|++|| +..+.+.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~   31 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK   31 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc
Confidence            79999999999999999999999 66666644

>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=98.01  E-value=2.6e-07  Score=64.86  Aligned_cols=34  Identities=26%  Similarity=0.429  Sum_probs=30.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEec
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR  261 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~  261 (274)
                      ++|||+|||+++|+++|+++|++||.|..+.+..
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~   35 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAP   35 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEec
Confidence            5899999999999999999999999988777653

>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=97.74  E-value=7.3e-06  Score=58.92  Aligned_cols=38  Identities=11%  Similarity=0.034  Sum_probs=32.0

Q ss_pred             CCceEEEeCCCCCC-CH----HHHHHHhhhcCCeeEEEEecCC
Q psy3343         226 PDTTLYIKNLNFNS-TE----DSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       226 ~~~~lfV~NL~~~~-te----e~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      .+++|||+||+.++ ++    ++|+++|++||.|.++++.+.+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~   46 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF   46 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC
Confidence            46799999999886 33    6799999999999999998643

>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=97.62  E-value=0.00019  Score=49.72  Aligned_cols=74  Identities=14%  Similarity=0.211  Sum_probs=61.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCC--------eEEEEEecCHHHHHHHHHHhCCCeeCC-----eEEE
Q psy3343          97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYG--------ITGLVEFLQKNQAKAAFNSLAYTKFKE-----VPLY  163 (274)
Q Consensus        97 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~--------~~afV~F~~~~~A~~A~~~l~~~~~~g-----~~l~  163 (274)
                      +.|.|++||+.+|++++.+.++..|.+......+.+        .-|+|.|.+.++...-.+.++|..|.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            678999999999999999999999998887775522        369999999999999999999988753     2347


Q ss_pred             EEEecCC
Q psy3343         164 LEWAPEG  170 (274)
Q Consensus       164 v~~a~~~  170 (274)
                      |++||-.
T Consensus        82 VE~AP~q   88 (91)
T d1uw4a_          82 VEFAPFQ   88 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEcCcc
Confidence            7888644

>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=97.39  E-value=2.5e-06  Score=61.44  Aligned_cols=42  Identities=12%  Similarity=0.124  Sum_probs=37.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCCCCCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG  269 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~~~~~g  269 (274)
                      +.++|++++.+++++.|+++|++||.|.+|+|+++..++..|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G   69 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG   69 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEee
Confidence            468899999999999999999999999999999887766655

>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=97.34  E-value=7.3e-05  Score=50.91  Aligned_cols=35  Identities=17%  Similarity=0.188  Sum_probs=29.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecC
Q psy3343         227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARK  262 (274)
Q Consensus       227 ~~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~  262 (274)
                      .+.|+|.++|++++++.| ++|++||.|.++++.+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~   38 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT   38 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC
Confidence            367999999999987666 57999999999998654

>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=97.11  E-value=0.00083  Score=43.65  Aligned_cols=62  Identities=23%  Similarity=0.273  Sum_probs=52.5

Q ss_pred             CCCHHHH----HHccccCCCeeEEEeeC--CC-eEEEEEecCHHHHHHHHHHhCCCeeCCeEEEEEEec
Q psy3343         107 RTLPTDL----KALFEPFGDLGRVLVPP--YG-ITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYLEWAP  168 (274)
Q Consensus       107 ~~te~~l----~~~F~~~G~i~~v~l~~--~~-~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v~~a~  168 (274)
                      .+.+.+|    ...|.++|.|.++.+.+  ++ -.|-|...+..+|..|+..|+..++++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3445554    46799999999999966  32 479999999999999999999999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.90  E-value=0.00083  Score=45.90  Aligned_cols=70  Identities=16%  Similarity=0.127  Sum_probs=55.0

Q ss_pred             CCCcEEEEeCCCCCCC---------HHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhCCCeeCCeEEEE
Q psy3343          94 RSKRIILVKNLPYRTL---------PTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFKEVPLYL  164 (274)
Q Consensus        94 ~~~~~l~V~nLp~~~t---------e~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~~~~~~g~~l~v  164 (274)
                      +...+|.|.=..+...         -.+|.+.|..||+|.-|++..+  -..|+|.+-++|-+|+. ++|.++.|+.|.|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--~mwVTF~dG~SAL~al~-l~g~~v~G~~l~I   89 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--QMLVTFADSHSALSVLD-VDGMKVKGRAVKI   89 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--EEEEECSCSHHHHHHHH-GGGSEETTEEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--eEEEEECCcHHHHHHhc-cCCeEEcceEEEE
Confidence            3456677743332222         2468889999999998888754  68999999999999997 9999999999998


Q ss_pred             EE
Q psy3343         165 EW  166 (274)
Q Consensus       165 ~~  166 (274)
                      .-
T Consensus        90 t~   91 (95)
T d1ufwa_          90 SG   91 (95)
T ss_dssp             EC
T ss_pred             ec
Confidence            74

>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=96.74  E-value=0.00034  Score=49.71  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=34.1

Q ss_pred             CCCceEEEeCC--CCCC--------CHHHHHHHhhhcCCeeEEEEecCCCCCC
Q psy3343         225 EPDTTLYIKNL--NFNS--------TEDSIRRHFKKCGPIASVTVARKKDPKS  267 (274)
Q Consensus       225 ~~~~~lfV~NL--~~~~--------tee~L~~~F~~fG~I~~v~v~~~~~~~~  267 (274)
                      .|+.+|.|+||  |...        ..++|++.|++||.|.+|.|++++++..
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~   54 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVE   54 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCc
Confidence            36789999999  4433        3467999999999999999998776543

>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=95.82  E-value=0.0041  Score=43.37  Aligned_cols=39  Identities=18%  Similarity=0.346  Sum_probs=31.1

Q ss_pred             CCCceEEEeCC--CCCC---------CHHHHHHHhhhcCCeeEEEEecCC
Q psy3343         225 EPDTTLYIKNL--NFNS---------TEDSIRRHFKKCGPIASVTVARKK  263 (274)
Q Consensus       225 ~~~~~lfV~NL--~~~~---------tee~L~~~F~~fG~I~~v~v~~~~  263 (274)
                      ..+.+|+|+||  |.++         ..++|++.|++||.|..|.+..+.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~   55 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH   55 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC
Confidence            45689999999  5432         237899999999999999988764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.17  E-value=0.083  Score=36.23  Aligned_cols=59  Identities=22%  Similarity=0.326  Sum_probs=47.7

Q ss_pred             cCCCcEEEEeCCCCCCCHHHHHHccccCCCeeEEEeeCCCeEEEEEecCHHHHHHHHHHhC
Q psy3343          93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA  153 (274)
Q Consensus        93 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~l~~~~~~afV~F~~~~~A~~A~~~l~  153 (274)
                      ..+...||.-.+|......||.++|++||.|.---|  +-.-|||...+.++|+.++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI--ddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE--ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe--cCceEEEEecCHHHHHHHHHHhc
Confidence            334567888899999999999999999998744444  33479999999999999987554

>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=91.69  E-value=0.16  Score=34.45  Aligned_cols=37  Identities=11%  Similarity=0.170  Sum_probs=32.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhhcCCeeEEEEecCCC
Q psy3343         228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD  264 (274)
Q Consensus       228 ~~lfV~NL~~~~tee~L~~~F~~fG~I~~v~v~~~~~  264 (274)
                      +.|.|++||++.|++++.+.++..|.+.+......+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~   38 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDT   38 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCc
Confidence            5799999999999999999999999999887776543