Citrus Sinensis ID: 014384

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-----
Protein Sequence
MSKSVSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPAED
Secondary Structure (PSIPRED)
ccccEEEEEEEEEEEEEcccHHHHHHHccccEEEEcccccccccccHHHHHHccccEEEEcccccccHHHHHHHHccccccEEEEEEccEEEEEEccHHHHHHHHHHccccccccccEEEEEEcccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEEEEEEEEccEEcEcccccccEEEEEcEEEHHHHHHHccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcEEEEEcccHHHHHHHHHHHcccccccccEEEEEEEccccHHHHHcccHHHHccccccccccEEEEEEccccccccHHHHHHHHcccccEEEEEEEcccEEEEcccHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccc
Coil and Loop (DISEMBL)
MSKSVSVYQCHYLLIVYSHsvwpvqkkylprrlyVLGFRRSHSQLSIAAFEAMMRpifcgnfeydarQSDLERLFRRygkvdrvdmKSGFAFIYMDDERDAEDAIRgldrtefgrkgrRLRVEWtkhergirrpgggssarrpstntrpsktlfvinfdpyhtrtrdlerhfepygKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEyavrddddrrnghspdrnrdrspdrgrrrspspyrrergspdygrgssrspyrrergspdygrvrspspyrrdrgspdygrnssrspykkeraaighgrgpsrspyrrdrgspenghgsspspyrkgkpspnngrgpsrspyererpspengrggsrspyrrerpspdngrvpspnsmpeprdspgydgadspineryrsrsppaed
Flexible Loop (DISEMBL)
MSKSVSVYQCHYLLIVYshsvwpvqKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRrygkvdrvdmKSGFAfiymdderdaedairgldrtefgrkgrrlrvewtkhergirrpgggssarrpstntrpsktlfvinfdpyhtrtrdlerhfepyGKIISVRIRRNFAFVQYEVQEdatraldatnmskltdrvisveyavrddddrrnghspdrnrdrspdrgrrrspspyrrergspdygrgssrspyrrergspdygrvrspspyrrdrgspdygrnssrspykkeraaighgrgpsrspyrrdrgspenghgsspspyrkgkpspnngrgpsrspyererpspengrggsrspyrrerpspdngrvpspnsmpeprdspgydgadspineryrsrsppaed
Low Complexity Region (SEG)
MSKSVSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHErgirrpgggssarrpsTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHspdrnrdrspdrgrrrspspyrrergspDygrgssrspyrrergspDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENgrggsrspyrrerpspDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPAED
Disordered region (IsUnstruct)
*****SVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDE******IRGL*************V*****************************TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA*************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
****VSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVL********************IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE*****************************LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDAT***KLTD*********************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MSKSVSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE*******************RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD************************************************************************************************************************************************************************************YDGADSPINER**********
Disordered Region (DISPRO)
***SVSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE*************RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDY********************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKSVSVYQCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPAED
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	425	2.2.26 [Sep-21-2011]
P92965	350	Arginine/serine-rich-spli	yes	no	0.8	0.971	0.615	1e-101
P92966	356	Arginine/serine-rich-spli	no	no	0.797	0.952	0.616	1e-93
P92964	264	Arginine/serine-rich-spli	no	no	0.6	0.965	0.593	4e-73
Q6IQ97	419	RNA-binding protein 4.1 O	no	no	0.338	0.343	0.278	4e-14
Q3MHX3	362	RNA-binding protein 4 OS=	yes	no	0.338	0.397	0.284	9e-14
Q4R979	364	RNA-binding protein 4 OS=	N/A	no	0.301	0.351	0.308	1e-13
Q9BWF3	364	RNA-binding protein 4 OS=	yes	no	0.301	0.351	0.308	1e-13
Q8C7Q4	361	RNA-binding protein 4 OS=	yes	no	0.338	0.398	0.284	1e-13
Q06AT9	359	RNA-binding protein 4B OS	yes	no	0.338	0.401	0.284	2e-13
Q9BDY9	359	RNA-binding protein 4 OS=	no	no	0.338	0.401	0.284	2e-13

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

 Score =  370 bits (949), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 235/382 (61%), Positives = 280/382 (73%), Gaps = 42/382 (10%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M+P+FCGNFEYDAR+ DLERLFR+YGKV+RVDMK+GFAF+YM+DERDAEDAIR LDR EF
Sbjct: 1   MKPVFCGNFEYDAREGDLERLFRKYGKVERVDMKAGFAFVYMEDERDAEDAIRALDRFEF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GRKGRRLRVEWTK ERG  +  GG S R  S++ RPSKTLFVINFD  +TRTRDLE+HFE
Sbjct: 61  GRKGRRLRVEWTKSERGGDKRSGGGSRRS-SSSMRPSKTLFVINFDADNTRTRDLEKHFE 119

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGKI++VRIRRNFAF+QYE QEDATRALDA+N SKL D+VISVEYAV+DDD R NGHSP
Sbjct: 120 PYGKIVNVRIRRNFAFIQYEAQEDATRALDASNNSKLMDKVISVEYAVKDDDARGNGHSP 179

Query: 234 DRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSS-RSPYRRERGSPDYGRVRSPSPYRRD- 291
           +R RDRS    RRRSPSPY+RERGSPDYGRG+S  + YR+ER SPDYGR RSPSPY++  
Sbjct: 180 ERRRDRS-PERRRRSPSPYKRERGSPDYGRGASPVAAYRKERTSPDYGRRRSPSPYKKSR 238

Query: 292 RGSPDYGRN--SSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSP 349
           RGSP+YGR+   + SP ++ER A                         SP+ Y +   SP
Sbjct: 239 RGSPEYGRDRRGNDSPRRRERVA-------------------------SPTKYSR---SP 270

Query: 350 NNGR---GPSRSPYERERPSPENGRGGSRSPY---RRERPSPDNGRVPSPNSMPEPRDSP 403
           NN R    P+ SP+++E  SP NG G   SP     R R SP+NG+V SP S+       
Sbjct: 271 NNKRERMSPNHSPFKKE--SPRNGVGEVESPIERRERSRSSPENGQVESPGSIGRRDSDG 328

Query: 404 GYDGADSPINERYRSRSPPAED 425
           GYDGA+SP+ +    RSPPA++
Sbjct: 329 GYDGAESPMQKSRSPRSPPADE 350

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

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

 Score =  344 bits (882), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 240/389 (61%), Positives = 275/389 (70%), Gaps = 50/389 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M+P+FCGNFEYDAR+SDLERLFR+YGKV+RVDMK+GFAF+YM+DERDAEDAIR LDR E+
Sbjct: 1   MKPVFCGNFEYDARESDLERLFRKYGKVERVDMKAGFAFVYMEDERDAEDAIRALDRFEY 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GR GRRLRVEWTK++RG         +RR S+  RPSKTLFVINFD  +TRTRDLERHFE
Sbjct: 61  GRTGRRLRVEWTKNDRGGAG--RSGGSRRSSSGLRPSKTLFVINFDAQNTRTRDLERHFE 118

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGKI++VRIRRNFAF+QYE QEDATRALDATN SKL D+VISVEYAV+DDD R NG+SP
Sbjct: 119 PYGKIVNVRIRRNFAFIQYEAQEDATRALDATNSSKLMDKVISVEYAVKDDDSRGNGYSP 178

Query: 234 DRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRV-RSPSPYRRDR 292
           +R RDRS    RRRSPSPYRRERGSPDYGRG+S   ++RER SPDYGR  RSPSPY+R R
Sbjct: 179 ERRRDRS-PDRRRRSPSPYRRERGSPDYGRGASPVAHKRERTSPDYGRGRRSPSPYKRAR 237

Query: 293 GSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNG 352
            SPDY R+  R    +ER A                 SPENG   + SP +        G
Sbjct: 238 LSPDYKRDDRR----RERVA-----------------SPENGAVRNRSPRK--------G 268

Query: 353 RGPSRS--PYERER----PSPENGRGGSRSP----------YRRERPSPDNGRVPSPNSM 396
           RG SRS  PYE+ R    P P   R  SRSP            R + SP+NG+V SP  +
Sbjct: 269 RGESRSPPPYEKRRESRSPPPYEKRRESRSPPPYEKRRERSRSRSKSSPENGQVESPGQI 328

Query: 397 PEPRDSPGYDGADSPINERYRSRSPPAED 425
            E     GYDGADSPI E   SRSPPAE+
Sbjct: 329 MEVEAGRGYDGADSPIRES-PSRSPPAEE 356

Required for constitutive and alternative pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  275 bits (703), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 168/283 (59%), Positives = 200/283 (70%), Gaps = 28/283 (9%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           MRP+F GNFEY+ RQSDLERLF +YG+VDRVDMKSG+AF+Y +DERDAEDAIR LD   F
Sbjct: 1   MRPVFVGNFEYETRQSDLERLFDKYGRVDRVDMKSGYAFVYFEDERDAEDAIRKLDNFPF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           G + RRL VEW K ERG  RP G + A    +N +P+KTLFVINFDP  T+  D+E+HFE
Sbjct: 61  GYEKRRLSVEWAKGERG--RPRGDAKA---PSNLKPTKTLFVINFDPIRTKEHDIEKHFE 115

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGK+ +VRIRRNF+FVQ+E QEDAT+AL+AT  SK+ DRV+SVEYA++DDD+R      
Sbjct: 116 PYGKVTNVRIRRNFSFVQFETQEDATKALEATQRSKILDRVVSVEYALKDDDER-----D 170

Query: 234 DRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRG 293
           DRN  RSP    RRS SP  R R SPDYGR    SP +  R SPDYGR RSP  Y R +G
Sbjct: 171 DRNGGRSP----RRSLSPVYRRRPSPDYGRRP--SPGQGRRPSPDYGRARSPE-YDRYKG 223

Query: 294 --------SPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDR 328
                   SPDYGR S  S Y ++R+  G+ R  SRSP  R R
Sbjct: 224 PAAYERRRSPDYGRRS--SDYGRQRSP-GYDRYRSRSPVPRGR 263

Required for constitutive and alternative pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 79.7 bits (195), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 79/165 (47%), Gaps = 21/165 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  IF GN   +    ++  LF +YGK+   D+   F F++MD + +A++AI+ L    +
Sbjct: 1   MVKIFVGNLSPNTTAEEIRSLFSQYGKISECDIVKNFGFVHMDSKSEADEAIQNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K               +P T+T+    L V N     T  ++L   FE
Sbjct: 59  MLNGMAMNVEMSK--------------GKPKTSTK----LHVGNISSSCT-NQELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            YG ++   I +++AFV  E  EDA  A+   + +    +++SV+
Sbjct: 100 EYGPVVECDIVKDYAFVHMERVEDAMEAISGLDNTAFQGKLMSVK 144

Danio rerio (taxid: 7955)

>sp|Q3MHX3|RBM4_BOVIN RNA-binding protein 4 OS=Bos taurus GN=RBM4 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 21/165 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKTSTKLHVGNISPTCT-NKELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            YG +I   I +++AFV  E  EDA  A+   + ++   + + V+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ 144

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Bos taurus (taxid: 9913)

>sp|Q4R979|RBM4_MACFA RNA-binding protein 4 OS=Macaca fascicularis GN=RBM4 PE=2 SV=1

 Score = 78.2 bits (191), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 73/149 (48%), Gaps = 21/149 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKTSTKLHVGNISPTCT-NKELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRAL 202
            YG +I   I +++AFV  E  EDA  A+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAI 128

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Macaca fascicularis (taxid: 9541)

>sp|Q9BWF3|RBM4_HUMAN RNA-binding protein 4 OS=Homo sapiens GN=RBM4 PE=1 SV=1

 Score = 78.2 bits (191), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 73/149 (48%), Gaps = 21/149 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKTSTKLHVGNISPTCT-NKELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRAL 202
            YG +I   I +++AFV  E  EDA  A+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAI 128

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Homo sapiens (taxid: 9606)

>sp|Q8C7Q4|RBM4_MOUSE RNA-binding protein 4 OS=Mus musculus GN=Rbm4 PE=1 SV=1

 Score = 77.8 bits (190), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 21/165 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKASTKLHVGNISPTCT-NQELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            YG +I   I +++AFV  E  EDA  A+   + ++   + + V+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ 144

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Mus musculus (taxid: 10090)

>sp|Q06AT9|RBM4B_PIG RNA-binding protein 4B OS=Sus scrofa GN=RBM4B PE=2 SV=1

 Score = 77.4 bits (189), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 21/165 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKASTKLHVGNISPTCT-NQELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            YG +I   I +++AFV  E  EDA  A+   + ++   + + V+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ 144

Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA.

Sus scrofa (taxid: 9823)

>sp|Q9BDY9|RBM4_RABIT RNA-binding protein 4 OS=Oryctolagus cuniculus GN=RBM4 PE=2 SV=1

 Score = 77.4 bits (189), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 21/165 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L    +
Sbjct: 1   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHH--Y 58

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
              G  + VE +K++                  ++ S  L V N  P  T  ++L   FE
Sbjct: 59  KLHGVNINVEASKNK------------------SKASTKLHVGNISPTCT-NQELRAKFE 99

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            YG +I   I +++AFV  E  EDA  A+   + ++   + + V+
Sbjct: 100 EYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ 144

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Oryctolagus cuniculus (taxid: 9986)

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	425
255539555	331	arginine/serine-rich splicing factor, pu	0.771	0.990	0.754	1e-129
356575923	376	PREDICTED: arginine/serine-rich-splicing	0.825	0.933	0.668	1e-126
449463727	376	PREDICTED: arginine/serine-rich-splicing	0.837	0.946	0.683	1e-123
358248400	374	uncharacterized protein LOC100796509 [Gl	0.825	0.938	0.666	1e-120
449463729	367	PREDICTED: arginine/serine-rich-splicing	0.835	0.967	0.679	1e-120
357444075	430	Arginine/serine-rich-splicing factor RSP	0.92	0.909	0.629	1e-119
388508248	388	unknown [Medicago truncatula]	0.861	0.943	0.652	1e-118
224136870	343	predicted protein [Populus trichocarpa]	0.788	0.976	0.732	1e-117
41323931	478	splicing factor-like protein [Vitis ripa	0.863	0.767	0.574	1e-115
359490360	480	PREDICTED: arginine/serine-rich-splicing	0.863	0.764	0.574	1e-114

>gi|255539555|ref|XP_002510842.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223549957|gb|EEF51444.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  467 bits (1202), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 252/334 (75%), Positives = 285/334 (85%), Gaps = 6/334 (1%)

Query: 95  MDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLF 154
           M+DERDAEDAIRGLDR EFGRKGRRLRVEWTK ERGIRRPG   ++RR STNTRPSKTLF
Sbjct: 1   MEDERDAEDAIRGLDRIEFGRKGRRLRVEWTKQERGIRRPG---NSRRSSTNTRPSKTLF 57

Query: 155 VINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRV 214
           VINFDP+HTRT+DLERHFEPYG+I+SVRIRRNFAFVQYE Q+DAT+AL+ATNMSKL DRV
Sbjct: 58  VINFDPHHTRTKDLERHFEPYGRIVSVRIRRNFAFVQYESQDDATKALEATNMSKLMDRV 117

Query: 215 ISVEYAVRDDDDRRNGHSPDRNRDRSPDR---GRRRSPSPYRRERGSPDYGRGSSRSPYR 271
           ISVEYAVRDDD+RRNG+SPDR RDRSPDR    R+RS SPYRRERGSPDYGRG S  PYR
Sbjct: 118 ISVEYAVRDDDERRNGYSPDRGRDRSPDRRSHDRKRSSSPYRRERGSPDYGRGPSPGPYR 177

Query: 272 RERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSP 331
           RER SPDYGR RSPSPY+RDR SPDYGR SSRSPY++ER    HGRG SRSPY R+R SP
Sbjct: 178 RERASPDYGRRRSPSPYKRDRASPDYGRASSRSPYRRERPGSDHGRGSSRSPYHRERASP 237

Query: 332 ENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVP 391
           +NG G S SPY++ K SP+NGR  SRSPY RER +P+NGRG SRSPY ++  SP+NGR  
Sbjct: 238 DNGRGHSASPYQREKASPDNGRDRSRSPYGRERTNPDNGRGSSRSPYEKDVNSPENGRRT 297

Query: 392 SPNSMPEPRDSPGYDGADSPINERYRSRSPPAED 425
           SPNSM E RDSP   G +SP++ER++SRSPPA++
Sbjct: 298 SPNSMHEERDSPNEGGIESPMHERFQSRSPPADE 331

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575923|ref|XP_003556085.1| PREDICTED: arginine/serine-rich-splicing factor RSP40-like [Glycine max]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 266/398 (66%), Positives = 300/398 (75%), Gaps = 47/398 (11%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR 110
           +  MRPIFCGNFEYDARQS+LERLFRRYGKVDRVDMKSGFAFIYM+DERDAE AIR LDR
Sbjct: 3   QGKMRPIFCGNFEYDARQSELERLFRRYGKVDRVDMKSGFAFIYMEDERDAEAAIRALDR 62

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLER 170
            EFGRKGRRLRVEWTKHERG+R+P   +S+RR S N RPSKTLFVINFD YHTRTRDLER
Sbjct: 63  VEFGRKGRRLRVEWTKHERGVRKP---ASSRRSSANGRPSKTLFVINFDTYHTRTRDLER 119

Query: 171 HFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNG 230
           HFEPYGKI+SVRIRRNFAFVQYE ++DA+RAL+ATNMSKL DRVISVE+AV+DDDDRRNG
Sbjct: 120 HFEPYGKIVSVRIRRNFAFVQYESEDDASRALEATNMSKLLDRVISVEFAVKDDDDRRNG 179

Query: 231 HSPD--RNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRV------ 282
           +SP+  R+R R   R  RRSPSPYRRERGSPDYGRG   SPY+RERGSPDYGR       
Sbjct: 180 YSPERGRDRHRDRSRDGRRSPSPYRRERGSPDYGRGP--SPYQRERGSPDYGRDRDRSRS 237

Query: 283 ---------------RSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRD 327
                          RS SP+RR+R   +  R+SSRSPY KER    HG  PS+SP  R 
Sbjct: 238 RSPPRRERASPAYGRRSLSPHRREREGSEPVRDSSRSPYHKERGRTDHGISPSQSPEGRG 297

Query: 328 RGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDN 387
           + SP+NGHGSS SP+  GK SP NG G S SP E+  PSP NG GG              
Sbjct: 298 KKSPQNGHGSSRSPHDTGKTSPENGLG-SGSPDEKGNPSPYNGYGG-------------- 342

Query: 388 GRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPAED 425
               SPN+MP+PRDSP Y G +SP++ERYRS+SPPAE+
Sbjct: 343 ----SPNNMPDPRDSPNYGGPESPMHERYRSQSPPAEE 376

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463727|ref|XP_004149583.1| PREDICTED: arginine/serine-rich-splicing factor RSP40-like [Cucumis sativus]

 Score =  448 bits (1153), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 268/392 (68%), Positives = 298/392 (76%), Gaps = 36/392 (9%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M+PIFCGNFEYDARQ DLERLF RYGKVDRVDMKSGFAFIYM+DERDAEDAIR LDR EF
Sbjct: 1   MKPIFCGNFEYDARQPDLERLFSRYGKVDRVDMKSGFAFIYMEDERDAEDAIRALDRREF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSS-----------ARRPSTNTRPSKTLFVINFDPYH 162
           GRKGRRLRVEWTK ERGIRRPG G             +RR STNTRPSKTLFVINFDPYH
Sbjct: 61  GRKGRRLRVEWTKQERGIRRPGPGGGGGGGGGGGGGGSRRSSTNTRPSKTLFVINFDPYH 120

Query: 163 TRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR 222
           TRTRDLERHF+PYGKI+SVRIRRNFAFVQYE+QEDATRAL+ TNMSKL DRVISVEYAVR
Sbjct: 121 TRTRDLERHFDPYGKILSVRIRRNFAFVQYELQEDATRALELTNMSKLMDRVISVEYAVR 180

Query: 223 DDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRV 282
           DDDD+RNG+SPDRNRDRSPDR +RRS SPYRRERGSPDYG G SRSPYRR+R SPDYG  
Sbjct: 181 DDDDKRNGYSPDRNRDRSPDR-KRRSSSPYRRERGSPDYGNGISRSPYRRQRASPDYGSR 239

Query: 283 RSPSPYR--RDRGSPDYGRNSS--RSPYKKERA-AIGHGRGPSRSP-YRRDRGSPENGHG 336
           RSPSPY+  R+RGSPDYGR  S   SPY++ER  +  H R PS  P ++R+R + +    
Sbjct: 240 RSPSPYQRERERGSPDYGRGRSPNHSPYRRERERSSDHVRTPSHRPSHQRERPNDDRVPN 299

Query: 337 SSPSPYRKG--KPSPNNGRGPSRSPYERERPS-PENGRGGSRSPYRRERPSPDNGRVPSP 393
            SPSPY +G  K SP +GRG S SP +RER S P+NG               D+G     
Sbjct: 300 RSPSPYGRGREKGSP-DGRGTSYSPRDRERSSNPDNGH--------------DHGHDQQQ 344

Query: 394 NSMPEPRDSPGYDGADSPINERYRSRSPPAED 425
            ++PEP +SP Y G  SP    Y SRSP AE+
Sbjct: 345 TTIPEPGESPNYGGTQSPKRRGYGSRSPQAEE 376

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248400|ref|NP_001240131.1| uncharacterized protein LOC100796509 [Glycine max] gi|255636874|gb|ACU18770.1| unknown [Glycine max]

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 264/396 (66%), Positives = 296/396 (74%), Gaps = 45/396 (11%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR 110
           +  MRPIFCGNFEYDARQS+LERLFRRYGKVDRVDMKSGFAFIYM+DERDAE AIR LDR
Sbjct: 3   QGKMRPIFCGNFEYDARQSELERLFRRYGKVDRVDMKSGFAFIYMEDERDAEAAIRALDR 62

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLER 170
            EFGRKGRRLRVEWTKHERG+RR    +S+RR S   RPSKTLFVINFD YHTRTRDLER
Sbjct: 63  VEFGRKGRRLRVEWTKHERGVRR---PASSRRSSAIGRPSKTLFVINFDTYHTRTRDLER 119

Query: 171 HFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNG 230
           HFEPYGKI+SVRIRRNFAFVQYE ++DA+RAL+ATNMSKL DRVISVE+AV+DDDDRRNG
Sbjct: 120 HFEPYGKIVSVRIRRNFAFVQYESEDDASRALEATNMSKLLDRVISVEFAVKDDDDRRNG 179

Query: 231 HSPD--RNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRV------ 282
           +SP+  R+R R   R  RRSPSPYR+ERGSPDYGRG   SPY+RERGSPDYGR       
Sbjct: 180 YSPERGRDRQRDRSRDGRRSPSPYRKERGSPDYGRGP--SPYQRERGSPDYGRDRSRSRS 237

Query: 283 -------------RSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRG 329
                        RS SPYRR+R   +  R+SSRSPY KER    HG  PS+SP  R R 
Sbjct: 238 PPRRERASPAYGRRSISPYRREREGSEPVRDSSRSPYHKERGRTDHGISPSQSPEGRGRK 297

Query: 330 SPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGR 389
           SP+NGHGSS SP   GK SP NG G S SP E+  PSP NG GG                
Sbjct: 298 SPQNGHGSSRSPRDTGKTSPENGHG-SGSPDEKGNPSPYNGYGG---------------- 340

Query: 390 VPSPNSMPEPRDSPGYDGADSPINERYRSRSPPAED 425
             SPN++P+PRDSP Y G +SP++ERY S+SPPAE+
Sbjct: 341 --SPNTVPDPRDSPNYGGPESPMHERYHSQSPPAEE 374

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463729|ref|XP_004149584.1| PREDICTED: arginine/serine-rich-splicing factor RSP40-like [Cucumis sativus] gi|449528505|ref|XP_004171244.1| PREDICTED: arginine/serine-rich-splicing factor RSP40-like [Cucumis sativus]

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 261/384 (67%), Positives = 292/384 (76%), Gaps = 29/384 (7%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M+PIFCGNFEYDARQ DLERLF RYGKVDRVDMKSGFAFIYM+DER+AEDAI  LDR EF
Sbjct: 1   MKPIFCGNFEYDARQPDLERLFSRYGKVDRVDMKSGFAFIYMEDEREAEDAIHALDRREF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPS-----TNTRPSKTLFVINFDPYHTRTRDL 168
           GRKGRRLRVEWTK ERGIRRP GG            TNTRPSKTLFVINFDPYHTR RDL
Sbjct: 61  GRKGRRLRVEWTKQERGIRRPSGGGGGSGGGSRRSSTNTRPSKTLFVINFDPYHTRIRDL 120

Query: 169 ERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRR 228
           ERHF+PYGKI++VRIRRNFAFVQYE+QEDATRAL+ TNMSKL DRVISVEYAVRDDD++R
Sbjct: 121 ERHFDPYGKILNVRIRRNFAFVQYELQEDATRALEVTNMSKLMDRVISVEYAVRDDDEKR 180

Query: 229 NGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPY 288
           NG+SPDRNRDRSPDR +RRSPSPYRRERGSPDYG G SRSPYRR+R SPDYG  RSPSPY
Sbjct: 181 NGYSPDRNRDRSPDR-KRRSPSPYRRERGSPDYGNGISRSPYRRQRASPDYGSRRSPSPY 239

Query: 289 R--RDRGSPDY--GRNSSRSPYKKERA-AIGHGRGPSRS-PYRRDRGSPENGHGSSPSPY 342
           +  R+RGSPDY  GR+   SPY++ER  +  H R PS S P++R+R + +     SPSPY
Sbjct: 240 QRERERGSPDYSRGRSPKHSPYRRERERSSDHIRAPSHSPPHQRERPNDDRIPNRSPSPY 299

Query: 343 RKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDS 402
           R+                ERER SP  GRG S SP  RER +PDNG     N++ EP + 
Sbjct: 300 RR----------------ERERGSPIGGRGRSYSPRDRERLNPDNGHDHQENTVAEPGEC 343

Query: 403 PGYDGADSPINERYR-SRSPPAED 425
           P Y G  SP +  Y  SRSP AE+
Sbjct: 344 PSYSGTQSPKHRGYNSSRSPQAEE 367

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357444075|ref|XP_003592315.1| Arginine/serine-rich-splicing factor RSP40 [Medicago truncatula] gi|355481363|gb|AES62566.1| Arginine/serine-rich-splicing factor RSP40 [Medicago truncatula]

 Score =  436 bits (1121), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 265/421 (62%), Positives = 300/421 (71%), Gaps = 30/421 (7%)

Query: 27  KYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM 86
           ++L   L  LGF    + L   A    M+ IFCGNFEYD R+S+LERLFRRYGKVDRVDM
Sbjct: 18  EFLSSPLLRLGF--LPNSLPSYAHPLKMKAIFCGNFEYDCRESELERLFRRYGKVDRVDM 75

Query: 87  KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTN 146
           K+GFAFIYM+DERDAE AIR LDR EFGRKGRRLRVEWTK ERG+RRP      +R S N
Sbjct: 76  KAGFAFIYMEDERDAEAAIRALDRIEFGRKGRRLRVEWTKQERGVRRP--AERPKRSSAN 133

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN 206
            RPSKTLFVINFD Y TRTRDLERHFEPYGKI+SVRIR+NFAFVQYE ++DA +AL+ATN
Sbjct: 134 ARPSKTLFVINFDTYQTRTRDLERHFEPYGKIVSVRIRKNFAFVQYESEDDACKALEATN 193

Query: 207 MSKLTDRVISVEYAVRDDDDRRNGHSP--DRNRDRSPDRGRRRSPSPYRRERGSPDYGRG 264
            SKL DRVISVE+A R DDDRRNGHSP   R+R R   R  RRSPSPYRRERGSPDYGRG
Sbjct: 194 NSKLMDRVISVEFAAR-DDDRRNGHSPDRGRDRQRDRSRDGRRSPSPYRRERGSPDYGRG 252

Query: 265 SSRSPYRRERGSPDYGR--VRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRS 322
              SPY+RER SPDYGR   RS SP+RR+RGSP YGR +  SPY++ER      R  SRS
Sbjct: 253 P--SPYKRERSSPDYGRGNSRSRSPHRRERGSPAYGRRNP-SPYRRERDGAEAVRDTSRS 309

Query: 323 PYRR----------------DRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPS 366
           PY +                +R  P+ GHGS PSPY   K SP NG    RSP  +  PS
Sbjct: 310 PYHKERRRTDRSRSHSLEEGERIEPQKGHGSDPSPYGTVKDSPENGHDRRRSPDAKRNPS 369

Query: 367 PENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYR--SRSPPAE 424
           P NG  GS SP  +  PSP N    SPN+MPEPRDSP Y G +SP+NE+YR  S+SPPAE
Sbjct: 370 PFNGSRGSPSPDAKGNPSPYNDYGGSPNTMPEPRDSPNYGGPESPMNEQYRSQSQSPPAE 429

Query: 425 D 425
           +
Sbjct: 430 E 430

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508248|gb|AFK42190.1| unknown [Medicago truncatula]

 Score =  431 bits (1107), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 257/394 (65%), Positives = 289/394 (73%), Gaps = 28/394 (7%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M+ IFCGNFEYD R+S+LERLFRRYGKVDRVDMK+GFAFIYM+DERDAE  IR LDR EF
Sbjct: 1   MKAIFCGNFEYDCRESELERLFRRYGKVDRVDMKAGFAFIYMEDERDAEAVIRALDRIEF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GRKGRRLRVEWTK ERG+RRP      +R S N RPSKTLFVINFD Y TRTRDLERHFE
Sbjct: 61  GRKGRRLRVEWTKQERGVRRP--AERPKRSSANARPSKTLFVINFDTYQTRTRDLERHFE 118

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGKI+SVRIR+NFAFVQYE ++DA +AL+ATN SKL DRVISVE+A R DDDRRNGHSP
Sbjct: 119 PYGKIVSVRIRKNFAFVQYESEDDACKALEATNNSKLMDRVISVEFAAR-DDDRRNGHSP 177

Query: 234 --DRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGR--VRSPSPYR 289
              R+R R   R  RRSPSPYRRERGSPDYGRG   SPY+RER SPDYGR   RS SP+R
Sbjct: 178 DRGRDRQRDRSRDGRRSPSPYRRERGSPDYGRGP--SPYKRERSSPDYGRGNSRSRSPHR 235

Query: 290 RDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRR----------------DRGSPEN 333
           R+RGSP YGR +  SPY++ER      R  SRSPY +                +R  P+ 
Sbjct: 236 RERGSPAYGRRNP-SPYRRERDGAEAVRDTSRSPYHKERRRTDRSRSHSLEEGERIEPQK 294

Query: 334 GHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSP 393
           GHGS PSPY   K SP NG    RSP  +  PSP NG  GS SP  +  PSP N    SP
Sbjct: 295 GHGSDPSPYGTVKDSPENGHDRRRSPDAKRNPSPFNGSRGSPSPDAKGNPSPYNDYGGSP 354

Query: 394 NSMPEPRDSPGYDGADSPINERYR--SRSPPAED 425
           N+MPEPRDSP Y G +SP+NE+YR  S+SPPAE+
Sbjct: 355 NTMPEPRDSPNYGGPESPMNEQYRSQSQSPPAEE 388

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136870|ref|XP_002322436.1| predicted protein [Populus trichocarpa] gi|222869432|gb|EEF06563.1| predicted protein [Populus trichocarpa]

 Score =  429 bits (1104), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 268/366 (73%), Positives = 305/366 (83%), Gaps = 31/366 (8%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           MRPIFCGNFEYDARQ++LERLF+RYG+V+RVDMKSGFAFIYM+DERDAEDAIRGLDR EF
Sbjct: 1   MRPIFCGNFEYDARQTELERLFKRYGRVERVDMKSGFAFIYMEDERDAEDAIRGLDRVEF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GRKGRRLRVEWTK ERGIRRPGG S   R STNTRPSKTLFVINFDP+HTRT+DLERHFE
Sbjct: 61  GRKGRRLRVEWTKQERGIRRPGGTS---RRSTNTRPSKTLFVINFDPHHTRTKDLERHFE 117

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYG+I+SVRIRRNFAFVQYE QEDAT+ALDATN+SKL DRVISVEYAVRDDD+R++G+SP
Sbjct: 118 PYGRIVSVRIRRNFAFVQYEAQEDATKALDATNLSKLLDRVISVEYAVRDDDERKDGYSP 177

Query: 234 DRNRDRSPD---RGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRR 290
           DR+RDRSPD     RRRSPSPYRRERGSPDYGRG   SPYR+ERGSPDYGR RSPSPYRR
Sbjct: 178 DRSRDRSPDRRGHDRRRSPSPYRRERGSPDYGRGP--SPYRKERGSPDYGRRRSPSPYRR 235

Query: 291 DRGSPDYGRNSSRSPYKKERAAI----GHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGK 346
           DR SPDYGR +SRSPY++ERA       +GRGPSRSPYRR+R +  +G GSS SPY + +
Sbjct: 236 DRASPDYGRGTSRSPYRRERAGKRISPENGRGPSRSPYRRERSNQGHGRGSSHSPYGRER 295

Query: 347 PSPNNGRGPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYD 406
           P+P+NGRG SRSP ER+  SPE                  NG++ SP+S+P+ RDSP   
Sbjct: 296 PNPDNGRGSSRSPTERDGDSPE------------------NGQLRSPSSIPDERDSPN-G 336

Query: 407 GADSPI 412
           GA+SP+
Sbjct: 337 GAESPM 342

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|41323931|gb|AAS00039.1| splicing factor-like protein [Vitis riparia]

 Score =  421 bits (1082), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 273/475 (57%), Positives = 308/475 (64%), Gaps = 108/475 (22%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           MRPIFCGNF+YDARQSDLERLFRRYGKVDRVDMK+GFAFIYM+DERDAEDAIRGLDRT F
Sbjct: 1   MRPIFCGNFDYDARQSDLERLFRRYGKVDRVDMKTGFAFIYMEDERDAEDAIRGLDRTGF 60

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GRKGRRLRVEWTK ERGIRR    S +RR STN RP+KTLFVINFDPY+TRTRDLERHF+
Sbjct: 61  GRKGRRLRVEWTKQERGIRR---PSGSRRSSTNLRPAKTLFVINFDPYNTRTRDLERHFD 117

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGKI+++RIRRNFAF+QYE QEDATRAL+ATNMSKL DRVISVEYAVRDDD+RRNG+SP
Sbjct: 118 PYGKILNIRIRRNFAFIQYESQEDATRALEATNMSKLMDRVISVEYAVRDDDERRNGYSP 177

Query: 234 D-RNRDRSPDRG--RRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYG---------- 280
           D R RD+S +R   + RS SPYRRERGSPDYGRGSS S YRRER SPDYG          
Sbjct: 178 DGRRRDKSSERSYDKGRSLSPYRRERGSPDYGRGSSPSAYRRERASPDYGRDPSPSPRRR 237

Query: 281 --------RVRSPSPYRR---------------------DRGSPDYGRNSSRSPYKKER- 310
                   R RSPS +RR                     DR  PDYGR  S SP ++E+ 
Sbjct: 238 DRAMPDHGRSRSPSHHRRERTSHDSARGPSRSPYRSERSDRAIPDYGRGRSPSPGRREKI 297

Query: 311 -----------------------AAIGHGRGPSRSPYRRDRGS----------------- 330
                                  A   +GRG S S  RR+R +                 
Sbjct: 298 MPDYPDRPSLSPERKEKTGRSEKAIPDYGRGASPSSPRRERTNSDYVRANSRSRSRSQSQ 357

Query: 331 ---------PENGHGSSPSPYRKGKPSPNNGRGPSRS-------------PYERERPSPE 368
                    P+ GH  S SP ++ K +P++GRGPSRS             P + ER  P+
Sbjct: 358 SPRQRERTKPDYGHERSVSPEQREKANPDHGRGPSRSSPRREYDRGPSQSPQQGERALPD 417

Query: 369 NGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPA 423
             RG S SPY+RE  SPD  R PSPNS  E RDSP Y G+ SP+N RYRSRSPPA
Sbjct: 418 YARGPSDSPYQRESISPDYDRGPSPNSKREERDSPNYGGSASPMNGRYRSRSPPA 472

Source: Vitis riparia

Species: Vitis riparia

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359490360|ref|XP_002279907.2| PREDICTED: arginine/serine-rich-splicing factor RSP40-like [Vitis vinifera]

 Score =  419 bits (1077), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 273/475 (57%), Positives = 307/475 (64%), Gaps = 108/475 (22%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           MRPIFCGNF+YDARQSDLERLFRRYGKVDRVDMK+GFAFIYM+DERDAEDAIRGLDRT F
Sbjct: 3   MRPIFCGNFDYDARQSDLERLFRRYGKVDRVDMKTGFAFIYMEDERDAEDAIRGLDRTGF 62

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           GRKGRRLRVEWTK ERGIRR    S +RR STN RP+KTLFVINFDPY+TRTRDLERHF+
Sbjct: 63  GRKGRRLRVEWTKQERGIRR---PSGSRRSSTNLRPAKTLFVINFDPYNTRTRDLERHFD 119

Query: 174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           PYGKI+++RIRRNFAF+QYE QEDATRAL+ATNMSKL DRVISVEYAVRDDD+RRNG+SP
Sbjct: 120 PYGKILNIRIRRNFAFIQYESQEDATRALEATNMSKLMDRVISVEYAVRDDDERRNGYSP 179

Query: 234 D-RNRDRSPDRG--RRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGR--------- 281
           D R RD+S +R   + RS SPYRRERGSPDYGRGSS S YRRER SPDYGR         
Sbjct: 180 DGRRRDKSSERSYDKGRSLSPYRRERGSPDYGRGSSPSAYRRERASPDYGRDPSPSPRRR 239

Query: 282 ---------VRSPSPYRR---------------------DRGSPDYGRNSSRSPYKKER- 310
                     RSPS +RR                     DR  PDYGR  S SP ++E+ 
Sbjct: 240 DRAIPDHGRSRSPSHHRRERTSHDSARGPSRSPYRSERSDRAIPDYGRGRSPSPGRREKI 299

Query: 311 -----------------------AAIGHGRGPSRSPYRRDRGS----------------- 330
                                  A   +GRG S S  RR+R +                 
Sbjct: 300 MPDYPDRPSLSPERKEKTGRSEKAIPDYGRGASPSSPRRERTNSDYVRANSRSRSRSQSQ 359

Query: 331 ---------PENGHGSSPSPYRKGKPSPNNGRGPSRS-------------PYERERPSPE 368
                    P+ GH  S SP ++ K +P+ GRGPSRS             P + ER  P+
Sbjct: 360 SPRQRERTKPDYGHERSVSPEQREKANPDYGRGPSRSSPRREYDRGPSQSPQQGERALPD 419

Query: 369 NGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRSPPA 423
             RG S SPY+RE  SPD  R PSPNS  E RDSP Y G+ SP+N RYRSRSPPA
Sbjct: 420 YSRGPSDSPYQRESISPDYDRGPSPNSKREERDSPNYGGSASPMNGRYRSRSPPA 474

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	425
TAIR|locus:2131864	350	RS40 "arginine/serine-rich spl	0.416	0.505	0.741	1.3e-94
TAIR|locus:2173088	357	RS41 "arginine/serine-rich spl	0.414	0.492	0.735	1.4e-93
TAIR|locus:2079502	264	RS31 "arginine/serine-rich spl	0.404	0.651	0.631	1.1e-66
TAIR|locus:2039975	250	RS31a "arginine/serine-rich sp	0.407	0.692	0.590	6.1e-62
WB|WBGene00004702	208	rsp-5 [Caenorhabditis elegans	0.171	0.350	0.410	6.6e-18
UNIPROTKB|Q10021	208	rsp-5 "Probable splicing facto	0.171	0.350	0.410	6.6e-18
WB|WBGene00004700	258	rsp-3 [Caenorhabditis elegans	0.16	0.263	0.459	1.5e-16
UNIPROTKB|Q9NEW6	258	rsp-3 "Probable splicing facto	0.16	0.263	0.459	1.5e-16
DICTYBASE|DDB_G0275409	737	DDB_G0275409 "RNA-binding regi	0.376	0.217	0.310	5.7e-16
TAIR|locus:2024770	303	SR34 "Serine/Arginine-Rich Pro	0.157	0.221	0.459	1.1e-15

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

 Score = 698 (250.8 bits), Expect = 1.3e-94, Sum P(2) = 1.3e-94
 Identities = 132/178 (74%), Positives = 150/178 (84%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             M+P+FCGNFEYDAR+ DLERLFR+YGKV+RVDMK+GFAF+YM+DERDAEDAIR LDR EF
Sbjct:     1 MKPVFCGNFEYDAREGDLERLFRKYGKVERVDMKAGFAFVYMEDERDAEDAIRALDRFEF 60

Query:   114 GRKGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
             GRKGRRLRVEWTK E                ++ RPSKTLFVINFD  +TRTRDLE+HFE
Sbjct:    61 GRKGRRLRVEWTKSERGGDKRSGGGSRRSS-SSMRPSKTLFVINFDADNTRTRDLEKHFE 119

Query:   174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
             PYGKI++VRIRRNFAF+QYE QEDATRALDA+N SKL D+VISVEYAV+DDD R NGH
Sbjct:   120 PYGKIVNVRIRRNFAFIQYEAQEDATRALDASNNSKLMDKVISVEYAVKDDDARGNGH 177

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

 Score = 697 (250.4 bits), Expect = 1.4e-93, Sum P(2) = 1.4e-93
 Identities = 131/178 (73%), Positives = 150/178 (84%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             M+P+FCGNFEYDAR+SDLERLFR+YGKV+RVDMK+GFAF+YM+DERDAEDAIR LDR E+
Sbjct:     1 MKPVFCGNFEYDARESDLERLFRKYGKVERVDMKAGFAFVYMEDERDAEDAIRALDRFEY 60

Query:   114 GRKGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
             GR GRRLRVEWTK++                +  RPSKTLFVINFD  +TRTRDLERHFE
Sbjct:    61 GRTGRRLRVEWTKNDRGGAGRSGGSRRSS--SGLRPSKTLFVINFDAQNTRTRDLERHFE 118

Query:   174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
             PYGKI++VRIRRNFAF+QYE QEDATRALDATN SKL D+VISVEYAV+DDD R NG+
Sbjct:   119 PYGKIVNVRIRRNFAFIQYEAQEDATRALDATNSSKLMDKVISVEYAVKDDDSRGNGY 176

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008380 "RNA splicing" evidence=NAS

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

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

 Score = 589 (212.4 bits), Expect = 1.1e-66, Sum P(2) = 1.1e-66
 Identities = 113/179 (63%), Positives = 138/179 (77%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             MRP+F GNFEY+ RQSDLERLF +YG+VDRVDMKSG+AF+Y +DERDAEDAIR LD   F
Sbjct:     1 MRPVFVGNFEYETRQSDLERLFDKYGRVDRVDMKSGYAFVYFEDERDAEDAIRKLDNFPF 60

Query:   114 GRKGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
             G + RRL VEW K E                +N +P+KTLFVINFDP  T+  D+E+HFE
Sbjct:    61 GYEKRRLSVEWAKGERGRPRGDAKAP-----SNLKPTKTLFVINFDPIRTKEHDIEKHFE 115

Query:   174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDR--RNG 230
             PYGK+ +VRIRRNF+FVQ+E QEDAT+AL+AT  SK+ DRV+SVEYA++DDD+R  RNG
Sbjct:   116 PYGKVTNVRIRRNFSFVQFETQEDATKALEATQRSKILDRVVSVEYALKDDDERDDRNG 174

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0016607 "nuclear speck" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

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

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

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

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

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

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

GO:0005681 "spliceosomal complex" evidence=TAS

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

 Score = 546 (197.3 bits), Expect = 6.1e-62, Sum P(2) = 6.1e-62
 Identities = 104/176 (59%), Positives = 131/176 (74%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             MR ++ GNF+YD R SDLERLF ++G+V RVDMKSG+AF+Y +DERDAEDAIR  D T F
Sbjct:     1 MRHVYVGNFDYDTRHSDLERLFSKFGRVKRVDMKSGYAFVYFEDERDAEDAIRRTDNTTF 60

Query:   114 GRKGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
             G   R+L VEW K                  +N RP+KTLFVINFDP  TR RD+ERHFE
Sbjct:    61 GYGRRKLSVEWAKD---FQGERGKPRDGKAVSNQRPTKTLFVINFDPIRTRERDMERHFE 117

Query:   174 PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
             PYGK+++VR+RRNFAFVQ+  QEDAT+ALD+T+ SKL D+V+SVEYA+R+  +R +
Sbjct:   118 PYGKVLNVRMRRNFAFVQFATQEDATKALDSTHNSKLLDKVVSVEYALREAGERED 173

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

WB|WBGene00004702 rsp-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 153 (58.9 bits), Expect = 6.6e-18, Sum P(2) = 6.6e-18
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             M  ++ G   Y+AR+ D+ER  + YGK++ + MK GFAF+  +D RDAEDA   LD    
Sbjct:     1 MPRLYLGKIPYNARERDVERFLKGYGKINNISMKYGFAFVDFEDSRDAEDACHDLDGKTM 60

Query:   114 GRKGRRLRVEWTK 126
                  RL VE  +
Sbjct:    61 EGSSMRLVVEMAR 73

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

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

GO:0003723 "RNA binding" evidence=ISS

UNIPROTKB|Q10021 rsp-5 "Probable splicing factor, arginine/serine-rich 5" [Caenorhabditis elegans (taxid:6239)]

 Score = 153 (58.9 bits), Expect = 6.6e-18, Sum P(2) = 6.6e-18
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query:    54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
             M  ++ G   Y+AR+ D+ER  + YGK++ + MK GFAF+  +D RDAEDA   LD    
Sbjct:     1 MPRLYLGKIPYNARERDVERFLKGYGKINNISMKYGFAFVDFEDSRDAEDACHDLDGKTM 60

Query:   114 GRKGRRLRVEWTK 126
                  RL VE  +
Sbjct:    61 EGSSMRLVVEMAR 73

GO:0003723 "RNA binding" evidence=NAS

GO:0008380 "RNA splicing" evidence=NAS

GO:0005634 "nucleus" evidence=IDA

WB|WBGene00004700 rsp-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 170 (64.9 bits), Expect = 1.5e-16, Sum P(3) = 1.5e-16
 Identities = 34/74 (45%), Positives = 50/74 (67%)

Query:    57 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG----FAFIYMDDERDAEDAIRGLDRTE 112
             ++ GN   D R+ ++E +F +YG++  VD+KSG    FAF+  +D RDAEDA+R  D  E
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIKSGRGPAFAFVEFEDHRDAEDAVRARDGYE 70

Query:   113 FGRKGRRLRVEWTK 126
             F   GRR+RVE+T+
Sbjct:    71 FD--GRRIRVEFTR 82

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0006376 "mRNA splice site selection" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

UNIPROTKB|Q9NEW6 rsp-3 "Probable splicing factor, arginine/serine-rich 3" [Caenorhabditis elegans (taxid:6239)]

 Score = 170 (64.9 bits), Expect = 1.5e-16, Sum P(3) = 1.5e-16
 Identities = 34/74 (45%), Positives = 50/74 (67%)

Query:    57 IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG----FAFIYMDDERDAEDAIRGLDRTE 112
             ++ GN   D R+ ++E +F +YG++  VD+KSG    FAF+  +D RDAEDA+R  D  E
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIKSGRGPAFAFVEFEDHRDAEDAVRARDGYE 70

Query:   113 FGRKGRRLRVEWTK 126
             F   GRR+RVE+T+
Sbjct:    71 FD--GRRIRVEFTR 82

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IGI;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0008380 "RNA splicing" evidence=NAS

GO:0003723 "RNA binding" evidence=NAS

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

 Score = 219 (82.2 bits), Expect = 5.7e-16, Sum P(2) = 5.7e-16
 Identities = 54/174 (31%), Positives = 89/174 (51%)

Query:    57 IFCGNFEYDARQSDLERLFRRYGK-VDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
             IF GN   D    D+E LF+ Y K +++VD+K+G+AF+ +    D +  ++ L R EF  
Sbjct:   142 IFVGNLPRDTIVKDIENLFKNYVKSIEKVDIKNGYAFVIVSTN-DPDIVVKELHRKEFLN 200

Query:   116 KGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKTLFVINFDPYHTRTRDLERHFEPY 175
             K   L V+  K E                   +PS+ +F++N++   T T D+     PY
Sbjct:   201 KS--LTVQIAKSESKKKEESE---------EVKPSRAIFIVNYNVSKTTTNDIADWCSPY 249

Query:   176 GKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
             G +  V++ +NF FV++E  + A++AL A ++       ++VEY V    DR N
Sbjct:   250 GNVNRVQMVKNFCFVEFETIDQASKALKALDLKSFDGHSLTVEY-VNGSIDRDN 302

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2024770 SR34 "Serine/Arginine-Rich Protein Splicing Factor 34" [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 1.1e-15, Sum P(2) = 1.1e-15
 Identities = 34/74 (45%), Positives = 46/74 (62%)

Query:    55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLD 109
             R ++ GN   D R+ ++E LF +YG V ++D+K      G+AF+  DD RDAEDAI G D
Sbjct:     7 RTVYVGNLPGDIREREVEDLFSKYGPVVQIDLKVPPRPPGYAFVEFDDARDAEDAIHGRD 66

Query:   110 RTEFGRKGRRLRVE 123
               +F   G RLRVE
Sbjct:    67 GYDFD--GHRLRVE 78

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0035061 "interchromatin granule" evidence=IDA

GO:0016607 "nuclear speck" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P92965	RSP40_ARATH	No assigned EC number	0.6151	0.8	0.9714	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	425
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	7e-40
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	4e-38
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	9e-27
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-16
smart00360	73	smart00360, RRM, RNA recognition motif	2e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-15
smart00360	73	smart00360, RRM, RNA recognition motif	8e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-13
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	6e-13
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-12
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-12
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-12
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-11
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	6e-11
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-11
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	8e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-11
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-10
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-10
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	4e-10
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-09
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-09
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	2e-09
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	4e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-09
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	7e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-08
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-08
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-08
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-08
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	9e-08
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-07
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-07
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	7e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	8e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-06
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-06
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	3e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	6e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-06
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-06
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	8e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	9e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	9e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	9e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	2e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-05
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-05
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	4e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	5e-05
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	6e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-05
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	6e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	7e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	7e-05
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	8e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	9e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	1e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-04
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	2e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	3e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	3e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-04
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	4e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	4e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-04
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	5e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	5e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	5e-04
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	5e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	6e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	7e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	7e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	8e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.001
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.001
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.001
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	0.001
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.001
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.001
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.001
PRK14086	617	PRK14086, dnaA, chromosomal replication initiation	0.001
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.001
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.001
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.001
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.001
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.001
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	0.001
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.001
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	0.001
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.002
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.002
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.002
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.002
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.002
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	0.002
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.002
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.002
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.003
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.003
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.003
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.003
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.003
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.003
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.003
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.003
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.003
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.003
cd12436	76	cd12436, RRM1_2_MATR3_like, RNA recognition motif	0.003
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.003
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.004
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.004
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.004
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.004
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.004

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

 Score =  136 bits (344), Expect = 7e-40
 Identities = 58/70 (82%), Positives = 66/70 (94%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLT 211
           TLFVINFDP +TRTRDLERHFEPYGK+++VRIRRNFAFVQYE QEDAT+AL++TNMSK+ 
Sbjct: 1   TLFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQEDATKALESTNMSKVL 60

Query: 212 DRVISVEYAV 221
           DRVISVEYA 
Sbjct: 61  DRVISVEYAA 70

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

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

 Score =  132 bits (333), Expect = 4e-38
 Identities = 59/72 (81%), Positives = 67/72 (93%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           RP+FCGNFEYDARQS++ERLF +YG+VDRVDMKSGFAF+YM+DERDAEDAIRGLD  EFG
Sbjct: 1   RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDAEDAIRGLDNFEFG 60

Query: 115 RKGRRLRVEWTK 126
           R+ RRLRVEW K
Sbjct: 61  RQRRRLRVEWAK 72

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

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

 Score =  101 bits (254), Expect = 9e-27
 Identities = 33/69 (47%), Positives = 50/69 (72%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLT 211
           TLFV+ FDP  TR  D+E+ FEP+G ++   IR+ FAFV++E  EDAT+AL+A + S++ 
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRID 60

Query: 212 DRVISVEYA 220
             V++VE+ 
Sbjct: 61  GSVLTVEFV 69

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

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

 Score = 71.5 bits (176), Expect = 6e-16
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           +F GN        +L  LF +YG V   D+   + F++M++E DAEDAI+ L+  EF   
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDAEDAIKALNGYEF--M 59

Query: 117 GRRLRVE 123
           G+R+ VE
Sbjct: 60  GKRINVE 66

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

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

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           +F GN   D  + +L  LF ++GKV+ V +          GFAF+  + E DAE A+  L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 109 DRTEFGRKGRRLRV 122
           +  E    GR L+V
Sbjct: 62  NGKELD--GRPLKV 73

Length = 73

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

 Score = 68.9 bits (169), Expect = 7e-15
 Identities = 30/73 (41%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDAT 205
           LFV N  P  T   DL   F  +G+I SVRI        + FAFV++E  EDA +AL+A 
Sbjct: 1   LFVGNL-PPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 206 NMSKLTDRVISVE 218
           N  +L  R + V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 68.8 bits (169), Expect = 8e-15
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 9/74 (12%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
           TLFV N  P  T   +L   F  +GK+ SVR+ R+        FAFV++E +EDA +AL+
Sbjct: 1   TLFVGNL-PPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59

Query: 204 ATNMSKLTDRVISV 217
           A N  +L  R + V
Sbjct: 60  ALNGKELDGRPLKV 73

Length = 73

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

 Score = 68.5 bits (168), Expect = 9e-15
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLD 109
           +F GN   D  + DL  LF ++G+++ V +         GFAF+  +   DAE A+  L+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 110 RTEFGRKGRRLRVE 123
             E    GR+L+V 
Sbjct: 61  GKELD--GRKLKVS 72

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

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

 Score = 66.8 bits (164), Expect = 3e-14
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 9/72 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------GFAFIYMDDERDAEDAIRGLD 109
           +F GN   D  + DL+ LF ++G ++ + +         GFAF+  +DE DAE A+  L+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 110 RTEFGRKGRRLR 121
             E G  GR LR
Sbjct: 61  GKELG--GRELR 70

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

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

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 8/70 (11%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDAT 205
           LFV N  P  T   DL+  F  +G I S+RI        + FAFV++E +EDA +AL+A 
Sbjct: 1   LFVGNL-PPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 206 NMSKLTDRVI 215
           N  +L  R +
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 63.2 bits (154), Expect = 6e-13
 Identities = 33/72 (45%), Positives = 45/72 (62%), Gaps = 7/72 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG-----FAFIYMDDERDAEDAIRGLDRT 111
           I+ GN   D R+ D+E LF +YG +  +D+K+      FAF+  +D RDAEDA+RG D  
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGY 61

Query: 112 EFGRKGRRLRVE 123
           +F   G RLRVE
Sbjct: 62  DFD--GYRLRVE 71

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

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 27/79 (34%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALD 203
            LFV       T  ++LE  F  +G++  V +         R F FV +E  EDA  A+ 
Sbjct: 3   KLFVSGLSTR-TTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 204 ATNMSKLTDRVISVEYAVR 222
             N  +L  RVI VE A R
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 5/74 (6%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           ++ G   Y AR+ D+ER F+ YG++  +++K+GF F+  +D RDA+DA+  L+  E    
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDADDAVYELNGKELC-- 59

Query: 117 GRRLRVEWTKHERG 130
           G R+ VE   H RG
Sbjct: 60  GERVIVE---HARG 70

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

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

 Score = 61.3 bits (149), Expect = 3e-12
 Identities = 33/72 (45%), Positives = 46/72 (63%), Gaps = 7/72 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRT 111
           ++ GN   D R+ ++E LF +YG +  +D+K      G+AFI  +D RDAEDAIRG D  
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGY 61

Query: 112 EFGRKGRRLRVE 123
           +F   G+RLRVE
Sbjct: 62  DF--DGQRLRVE 71

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

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

 Score = 59.5 bits (144), Expect = 1e-11
 Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           IF GN        +L  LF  +G+V   D    +AF++M+ E +A  AI  L+  E   K
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEV--K 60

Query: 117 GRRLRVE 123
           GRR+ VE
Sbjct: 61  GRRINVE 67

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

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

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN    A + +LE  F +YG +  V +     GFAF+  +D RDAEDA+R LD    
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61

Query: 114 GRKGRRLRVE 123
              G R+RVE
Sbjct: 62  --CGNRVRVE 69

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

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F         + +LE LF ++G+V       D    +S GF F+  +   DA+ AIR L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  E   +GR ++VE  K
Sbjct: 64  NGKEL--EGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ GN  Y+  + DL+ LF ++G+V       DR   +S GF F+ M+   +A  AI  L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 109 DRTEFGRKGRRLRV 122
           + T+FG  GR L V
Sbjct: 62  NGTDFG--GRTLTV 73

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

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

 Score = 64.4 bits (157), Expect = 4e-11
 Identities = 67/320 (20%), Positives = 110/320 (34%), Gaps = 43/320 (13%)

Query: 61  NFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           N +    +  L  LF ++G++       D      GFAF+  +   DA  A+  ++  + 
Sbjct: 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKI 244

Query: 114 G--RKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKT----LFVINFDPYHTRTRD 167
           G  ++G++L V   + ++   R              R  K     L+V N D   T    
Sbjct: 245 GLAKEGKKLYVG--RAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVT-DEK 301

Query: 168 LERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           L   F   G+I S ++  +       F FV +   E+A RA+   +   L  + + V  A
Sbjct: 302 LRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361

Query: 221 VRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYG 280
            R +   R  H  D+     P   +    SP     G P Y     + P ++  G P   
Sbjct: 362 QRKEQ--RRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYY---GQGPQQQFNGQPLGW 416

Query: 281 RVRSPSPYRRDRGSPDYGR-----NSSRSPYKKERAAIG-HGRGPSRSPYRRDRGSPENG 334
              S  P     G P         N+ R+P +  + A       P   P           
Sbjct: 417 PRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYP---------PN 467

Query: 335 HGSSPSPYRKGKPSPNNGRG 354
           + S P      +P     +G
Sbjct: 468 YQSLPLSQDLPQPQSTASQG 487

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

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

 Score = 57.5 bits (140), Expect = 6e-11
 Identities = 28/70 (40%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 65  DARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           DA + DL  LFR +G + RV    D ++    GFAF+      DAE AI  L+   FG  
Sbjct: 10  DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG--FGYD 67

Query: 117 GRRLRVEWTK 126
              L VEW K
Sbjct: 68  NLILSVEWAK 77

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

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

 Score = 57.2 bits (139), Expect = 8e-11
 Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           LFV N     T + +L   FE YG +    + +N+ FV  E +EDA  A+ A N  +   
Sbjct: 2   LFVGNLPD-ATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDAEDAIKALNGYEFMG 60

Query: 213 RVISVE 218
           + I+VE
Sbjct: 61  KRINVE 66

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 57.3 bits (138), Expect = 8e-11
 Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           ++ G   Y AR+ D+ER F+ YGK+  VD+K+G+ F+  DD RDA+DA+  L+  +    
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLC-- 59

Query: 117 GRRLRVEWTKHER 129
           G R+ VE  +  R
Sbjct: 60  GERVIVEHARGPR 72

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 57.2 bits (139), Expect = 8e-11
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 8/71 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDR 110
           ++  N      + DL   F  YGKV+ V +        GFAF+      DAE A++ L+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 111 TEFGRKGRRLR 121
                 GR LR
Sbjct: 61  LVL--DGRTLR 69

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

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

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           IF GN + D  Q +L  LF  YG V    +   FAF+++  E  A+ AI  L+  E    
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAADRAIEELNGREL--H 60

Query: 117 GRRLRVE 123
           GR+L VE
Sbjct: 61  GRKLVVE 67

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

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

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 57  IFCGNFEYDA-RQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F   F+    R+ D+E+LF  +G + R D++  FAF+  +D  DA  A+  L  +    
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRID- 60

Query: 116 KGRRLRVEWTK 126
            G  L VE+ K
Sbjct: 61  -GSVLTVEFVK 70

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

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTD 212
           P+     DL++ F P+G +  V I R        FAFVQ+  + DA +A+   N  K+  
Sbjct: 8   PFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67

Query: 213 RVISVEYAV 221
           R ++V++AV
Sbjct: 68  RPVAVDWAV 76

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

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

 Score = 55.2 bits (134), Expect = 3e-10
 Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 5/55 (9%)

Query: 73  RLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW 124
           +LF  +G V+++ +   K GFAF+    E  AE A++ L+   FG  GR LRV++
Sbjct: 3   KLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFG--GRPLRVDY 55

(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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 55.2 bits (134), Expect = 3e-10
 Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 170 RHFEPYGKIISVRIRR---NFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           + F P+G +  +++ +    FAFV++  +E A +A+   N      R + V+Y+
Sbjct: 3   KLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 55.3 bits (133), Expect = 4e-10
 Identities = 20/52 (38%), Positives = 33/52 (63%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGL 108
           +F GN   +A + ++  LF +YGKV   D+   + F++MDD+  A++AIR L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAADEAIRNL 54

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

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

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           ++ G   Y  R+ D++R F  YGK+  +D+K+G+ F+  +D RDA+DA+  L+  +    
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLC-- 59

Query: 117 GRRLRVEWTKHERG 130
           G R+ VE   H RG
Sbjct: 60  GERVIVE---HARG 70

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

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 19/54 (35%), Positives = 30/54 (55%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN 206
           +FV N +       DLE  F  YGKI+ + + + + FVQ++ +EDA  A+   N
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGEN 56

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

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

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           +F G     AR+ D+ER F+ YG++  +D+K GF F+  DD RDA+DA+  LD  E 
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDGKEL 58

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

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 52.5 bits (126), Expect = 4e-09
 Identities = 31/73 (42%), Positives = 47/73 (64%), Gaps = 7/73 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG-----FAFIYMDDERDAEDAIRGLDRT 111
           I+ GN   D R+ DLE LF +YG++  +++K+      FAF+  +D RDAEDA+ G +  
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61

Query: 112 EFGRKGRRLRVEW 124
           +FG+   RLRVE+
Sbjct: 62  DFGQC--RLRVEF 72

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 9/73 (12%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDA 204
           L+V            L   F P+G I  ++I         R FAFV++E  EDA  A+D 
Sbjct: 1   LYVGGLAEEVDEKV-LHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 205 TNMSKLTDRVISV 217
            N S+L  R I V
Sbjct: 60  MNESELFGRTIRV 72

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

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 7/69 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATN 206
           L+V N  P      DL   F PYGK+  VR+       R FAFV++   EDA  AL   N
Sbjct: 1   LYVRNL-PPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLN 59

Query: 207 MSKLTDRVI 215
              L  R +
Sbjct: 60  GLVLDGRTL 68

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

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

 Score = 56.9 bits (136), Expect = 6e-09
 Identities = 49/181 (27%), Positives = 73/181 (40%), Gaps = 27/181 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           +F GN  YD  + DL  LF+++G V RV +          GFAF+  + E  AE AI  L
Sbjct: 118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEEL 177

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGG--------SSARRPSTNTRPSKTLFVINFDP 160
           +  E   +GR LRV+  +     R               +R  +     S  L+V N  P
Sbjct: 178 NGKEL--EGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNL-P 234

Query: 161 YHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTD 212
             T   +L   F+  G I+   +  +         +FV  E  +DA  +    N  K+  
Sbjct: 235 LKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILG 294

Query: 213 R 213
           R
Sbjct: 295 R 295

Length = 306

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

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 3/66 (4%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--NFAFVQYEVQEDATRALDATNMSK 209
           T++V N     T   +L+R F P+G I  VR+ +   +AFV+++  E A  A+ A N + 
Sbjct: 2   TVYVGNLPHGLTEE-ELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 210 LTDRVI 215
           +  + +
Sbjct: 61  INGQTV 66

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

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

 Score = 51.6 bits (123), Expect = 7e-09
 Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 60  GNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
           GN        +L   F  YG V   D+   +AF++M+   DA +AIRGLD TEF  +G+R
Sbjct: 6   GNISSSCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF--QGKR 63

Query: 120 LRVE 123
           + V+
Sbjct: 64  MHVQ 67

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

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

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIIS---VRIR-----RNFAFVQYEVQEDATRALD 203
           TLFV N  PY T    LE  F   G I     V+ +     R F +V + ++EDA RAL+
Sbjct: 1   TLFVRNL-PYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59

Query: 204 ATNMSKLTDRVISVEYAVR 222
               +K   R I VE+A +
Sbjct: 60  EKKKTKFGGRKIHVEFAKK 78

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

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

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 28/77 (36%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F GN  YDA +  L  +F   G V       DR   K  G+ F   +D   A  AIR L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 109 DRTEFGRKGRRLRVEWT 125
           +  EF   GR LRV++ 
Sbjct: 61  NGYEFN--GRALRVDFA 75

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

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVD--RVDMKSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++ GN  +   + +L+R F  +G ++  RV    G+AF+  D    A  AI  ++ T   
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTSIN 62

Query: 115 RKGRRLRVEWTKH 127
             G+ ++  W K 
Sbjct: 63  --GQTVKCSWGKE 73

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDAT 205
           ++FV    P  T+  +L   F  +GKI+ V +         FAF+++E ++ A RA+++ 
Sbjct: 5   SIFVGQLSPDVTKE-ELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 206 NMSKLTDRVISVEY 219
           N S L ++ + V+Y
Sbjct: 64  NHSMLKNKTMHVQY 77

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 6/74 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS----GFAFIYMDDERDAEDAIRGLDRTE 112
           I+ GN   D R  D+E LF +YG +  +D+K+     FAF+  +D RDAEDA+ G D  +
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYD 61

Query: 113 FGRKGRRLRVEWTK 126
           +   G RLRVE+ +
Sbjct: 62  Y--DGYRLRVEFPR 73

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKL 210
           K L+V N  P  T    L   F  YG++  V+  +++AFV +E ++DA +A++  N  +L
Sbjct: 2   KVLYVRNL-PLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKEL 60

Query: 211 TDRVISVEYA 220
               I V  A
Sbjct: 61  EGSPIEVSLA 70

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

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

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALD 203
             LFV    P+     +LE+ F+ +G + SVR+  N        A+V+YE +  A++A+ 
Sbjct: 3   HKLFVSGL-PFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVL 61

Query: 204 ATNMSKLTDRVISV 217
             + +++ ++ ISV
Sbjct: 62  KMDGTEIKEKTISV 75

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

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

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISV----RIRRNFAFVQYEVQEDATRALDATNM 207
           T++   F P      D++R FE  G +  V    R  +  AF+ +E  E A  A++  N 
Sbjct: 1   TVYAGPF-PTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNG 59

Query: 208 SKLTDRVISVEY 219
           + +    I V+ 
Sbjct: 60  ASVDGNCIKVQR 71

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

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

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 10/75 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGL 108
           ++        + +DL++LF +YGKV         R      F F+ M    +A   I+ L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 109 DRTEFGRKGRRLRVE 123
            RTE    GR + VE
Sbjct: 62  HRTELH--GRVISVE 74

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

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           +F GN   D  + + + LF +YG+V  V +    GF FI +D   +AE A   LD     
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIM-- 61

Query: 115 RKGRRLRV 122
           RKGR+LRV
Sbjct: 62  RKGRQLRV 69

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

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 7/67 (10%)

Query: 57  IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F GN   D   + DLE +F +YGK+  + +  G+ F+  D+E DA  A+ G    E GR
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAG----ENGR 58

Query: 116 --KGRRL 120
              G++L
Sbjct: 59  EIAGQKL 65

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

>gnl|CDD|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 = 49.2 bits (118), Expect = 7e-08
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 9/73 (12%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDA 204
           LFV N  P+ T   +L   FE +G+I  V +         + FAFV +   E A +A   
Sbjct: 2   LFVRNL-PFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 205 TNMSKLTDRVISV 217
            + S    R++ V
Sbjct: 61  LDGSIFQGRLLHV 73

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

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

 Score = 48.8 bits (117), Expect = 7e-08
 Identities = 30/70 (42%), Positives = 38/70 (54%), Gaps = 10/70 (14%)

Query: 61  NFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGLDRTE 112
           N  Y     DL R+F +YG+V       DR   +S GFAF+   D+RDAEDA+  +D  E
Sbjct: 5   NLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKE 64

Query: 113 FGRKGRRLRV 122
               GR LRV
Sbjct: 65  LD--GRELRV 72

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

 Score = 48.8 bits (117), Expect = 9e-08
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 61  NFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           N  +   ++DL++LF  +G V            K GFAF+    + DAE AI+G++  + 
Sbjct: 6   NLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKI 65

Query: 114 GRKGRRLRVEW 124
             KGR + V+W
Sbjct: 66  --KGRPVAVDW 74

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

 Score = 48.9 bits (117), Expect = 9e-08
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV------DRVDMKSGFAFIYMDDERDAEDAIRGL 108
             IF G    D  + +L   F R+GK+       R +  + FAFI  + E+ A  A+   
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 109 DRTEFGRKGRRLRVE 123
           + +    K + + V+
Sbjct: 64  NHSML--KNKTMHVQ 76

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 69  SDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK 126
           ++LER F R+G + R+D   G  +A+I  +    A+ A   L     G  GRRLRV++  
Sbjct: 13  AELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRVDFAD 72

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDAT 205
           +F+ N D      + L   F  +G I+S ++        + + FV +E +E A RA++  
Sbjct: 5   IFIKNLDK-SIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 206 NMSKLTDRVISV 217
           N   L D+ + V
Sbjct: 64  NGMLLNDKKVFV 75

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

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDA 204
           TL+V NF P   +  D+   FE YG+I+S+R         R F +VQ+   E A  A+  
Sbjct: 2   TLWVTNFPPSFDQ-SDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 205 TNMSKLTDRVISVEY 219
            N        + V+ 
Sbjct: 61  LNGKLGEGYKLVVKI 75

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

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 10/81 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++  N     R  DL RLF +YG +  V +          GFA++  +D RDAEDA+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 109 DRTEFGRKGRRLRVEWTKHER 129
           DRT F   GR + +++ + +R
Sbjct: 63  DRTRF--LGREIEIQFAQGDR 81

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

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

 Score = 52.5 bits (126), Expect = 3e-07
 Identities = 38/170 (22%), Positives = 66/170 (38%), Gaps = 28/170 (16%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           IF  N +       L   F ++G +       D      G+ F++ + E  A+ AI+ ++
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 110 RTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLE 169
                 K            R I++        R +   +    L+V N DP     + L 
Sbjct: 151 GMLLNDKE-------VYVGRFIKK------HEREAAPLKKFTNLYVKNLDPSVNEDK-LR 196

Query: 170 RHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTD 212
             F  +G+I S  + ++       FAFV +E  EDA +A++  N  K+  
Sbjct: 197 ELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 9/69 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++  N  +    +DL ++F +YGKV       D+   KS G AFI   D  DA   ++ L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 109 DRTE-FGRK 116
           +  E FGR 
Sbjct: 64  NNKELFGRT 72

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

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYEVQEDATRALDATNMSK 209
           ++V N  P     R+LE  FE YG + SV + RN   FAFV++E   DA  A+ A +  +
Sbjct: 2   VYVGNLGPR-ATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 210 LTDRVISVEYAVR 222
           +    + VE +  
Sbjct: 61  ICGNRVRVELSRG 73

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

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

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 12/81 (14%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATR 200
            L++ N D   T    L + F  YGKI                 R + FV +E +E+A +
Sbjct: 1   RLWIGNLDSRLTE-FHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEK 59

Query: 201 ALDATNMSKLTDRVISVEYAV 221
           AL + N      + + V +A 
Sbjct: 60  ALKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 163 TRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRV 214
           T+  DL++ F  YGK++  +I  N        F FV     E+A + +   + ++L  RV
Sbjct: 11  TKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRV 70

Query: 215 ISVE 218
           ISVE
Sbjct: 71  ISVE 74

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

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

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           PY  R RD+ER F+ YG+I  + ++  F FV++E   DA  A+   N  +L    + VE+
Sbjct: 8   PYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEH 67

Query: 220 A 220
           A
Sbjct: 68  A 68

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

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

 Score = 46.1 bits (110), Expect = 8e-07
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 9/77 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALD 203
            L+V N  PY+    DL+  F  +G++ S R+         R F FV+ E  E+A  A++
Sbjct: 1   NLYVGNL-PYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59

Query: 204 ATNMSKLTDRVISVEYA 220
             N +    R ++V  A
Sbjct: 60  KLNGTDFGGRTLTVNEA 76

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

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

 Score = 46.4 bits (111), Expect = 8e-07
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 18/67 (26%)

Query: 151 KTLFV--INFDPYHTRTRDLERHFEPYGKIISVRIRRN-------------FAFVQYEVQ 195
            TLFV  +NF    T    L++HFE  G + SV I +              + FV+++ +
Sbjct: 1   TTLFVKNLNFK---TTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSK 57

Query: 196 EDATRAL 202
           E A +AL
Sbjct: 58  EAAQKAL 64

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

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           +F  N  Y  ++ DLE+LF ++G++  V    D KS    GFA++   D  DA  A + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 109 DRTEFGRKGRRLRV 122
           D   F  +GR + +
Sbjct: 65  DGKVF--QGRLIHI 76

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

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

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           L+V  F P  T    +   F PYG +  V++  NFAFV++E  E A RA D+ +   L +
Sbjct: 2   LYVRPF-PPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAIRAKDSVHGKVLNN 60

Query: 213 RVISVEY 219
             + V Y
Sbjct: 61  NPLYVTY 67

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

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 14/83 (16%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRAL 202
           +T+F+ N  P+     +L+  F  +G++   RI ++         AFV+++ +E A + L
Sbjct: 1   RTVFIRNL-PFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

Query: 203 DATNMS-----KLTDRVISVEYA 220
           +A + +      L  R + V  A
Sbjct: 60  EAADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 13/77 (16%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-----------RRNFAFVQYEVQEDATRA 201
           ++V N D +     DL   F  +G++ S+RI              FAFV ++    A  A
Sbjct: 3   IYVRNLD-FKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 202 LDATNMSKLTDRVISVE 218
           L   N ++L  R ISV 
Sbjct: 62  LQL-NGTELGGRKISVS 77

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

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 162 HTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDR 213
           +T  RDL   F  YG I  V++         R F FV +E  EDA  A +  N  ++  R
Sbjct: 10  YTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGR 69

Query: 214 VISVEYAV 221
            I V+Y++
Sbjct: 70  RIRVDYSI 77

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

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 25/65 (38%), Positives = 34/65 (52%), Gaps = 3/65 (4%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATN 206
           P+K LF+ N     T+   LE  F  +     VR+  RR  AFV++E +E AT AL A  
Sbjct: 1   PNKILFLQNLPEETTKE-MLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQ 59

Query: 207 MSKLT 211
             K+T
Sbjct: 60  GFKIT 64

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

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDA 204
           TLFV N   +     DLE  F+  G+++ VRI ++       F  V++  +E A +AL+ 
Sbjct: 1   TLFVGNL-SWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK 59

Query: 205 TNMSKLTDRVISVEYA 220
           +   +L  R I V+ A
Sbjct: 60  SG-EELLGREIRVDLA 74

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

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDAT 205
           ++V N        + L+  F  YGKI S ++ ++       F FV +E  E A +A++  
Sbjct: 4   VYVKNLGEDMDDEK-LKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 206 NMSKLTDRVISV 217
           N  ++  + + V
Sbjct: 63  NGKEVNGKKLYV 74

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

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

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 16/66 (24%), Positives = 30/66 (45%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           LF+ N         DL R F  YG++  + ++  + FVQ++  E    A++      +  
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFVQFDSPESCANAINCEQGKMIRG 61

Query: 213 RVISVE 218
           R + +E
Sbjct: 62  RKLHLE 67

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

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

 Score = 48.8 bits (116), Expect = 3e-06
 Identities = 39/158 (24%), Positives = 69/158 (43%), Gaps = 35/158 (22%)

Query: 68  QSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
           Q ++  LF   G++       D+V  +S G+ F+      DAE A+  L+       G R
Sbjct: 17  QEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLN-------GLR 69

Query: 120 LRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII 179
           L+ +  K            S  RPS+++     L+V    P      +LE  F P+G+II
Sbjct: 70  LQNKTIK-----------VSYARPSSDSIKGANLYVSGL-PKTMTQHELESIFSPFGQII 117

Query: 180 SVRI--------RRNFAFVQYEVQEDATRALDATNMSK 209
           + RI         +   F++++ +++A RA+   N + 
Sbjct: 118 TSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT 155

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

>gnl|CDD|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 = 44.5 bits (106), Expect = 3e-06
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 9/72 (12%)

Query: 61  NFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEF 113
           N  ++A + +L  LF  +G+V  V +         GFAF+    +++A++A+  L  T  
Sbjct: 7   NVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHL 66

Query: 114 GRKGRRLRVEWT 125
              GR L +E+ 
Sbjct: 67  --YGRHLVLEYA 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 48.6 bits (116), Expect = 4e-06
 Identities = 43/177 (24%), Positives = 79/177 (44%), Gaps = 32/177 (18%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ G+ + D  ++ L  LF+ +G V       D V  +S G+ ++   +  DAE A+  +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
           +    G  G+ +R+ W++ +  +RR G G+              +FV N D      + L
Sbjct: 63  NFKRLG--GKPIRIMWSQRDPSLRRSGVGN--------------IFVKNLDKSVD-NKAL 105

Query: 169 ERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
              F  +G I+S ++        R + FV +E +E A  A+   N   L D+ + V 
Sbjct: 106 FDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVG 162

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

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLD 109
           R +F GN E     SDL   F R+G++  +D+K       +AFI   D      A+R +D
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMD 62

Query: 110 RTEFGRK 116
               G  
Sbjct: 63  GEYLGNN 69

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

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTE 112
           ++ G F      SD++RLF   G V +V M        AFI  ++   A+ AI  L+   
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGAS 61

Query: 113 FGRKGRRLRVE 123
               G  ++V+
Sbjct: 62  V--DGNCIKVQ 70

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

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 14/80 (17%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVD------RVDMKS-----GFAFIYMDDERDAED 103
           R I+  N ++   + DL  +F ++G+V+      + D K      GFAF+   D   AE+
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 104 AIRGLDRTEFGRKGRRLRVE 123
           A++ L+ TE G  GR++ V 
Sbjct: 61  ALQ-LNGTELG--GRKISVS 77

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

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

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 14/85 (16%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGK--IISVRIRRN--------FAFVQYEVQEDA 198
           P+ TL +   D   T   D+ +         I  VR+ R+        FAFV++   EDA
Sbjct: 1   PTNTLILRGLDL-LTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59

Query: 199 TRALDATNMS---KLTDRVISVEYA 220
           T+ +DA N      +  RV+ V YA
Sbjct: 60  TQWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 9/78 (11%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRAL 202
            +L+V N     TR  DL R F  YG I+ V I         R FA+VQ+E   DA  AL
Sbjct: 1   TSLYVRNV-ADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 203 DATNMSKLTDRVISVEYA 220
              + ++   R I +++A
Sbjct: 60  YYLDRTRFLGREIEIQFA 77

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

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDAT 205
           TL+V       T  +DL  HF  +G+I S+ +  R+  AFV +  +E A +A +  
Sbjct: 3   TLYVGGLGERVT-EKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERL 57

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

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

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 161 YHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           YH R +D++R F  YGK++ + ++  + FV++E   DA  A+   N   L    + VE+A
Sbjct: 9   YHVREKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHA 68

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

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

 Score = 43.1 bits (101), Expect = 8e-06
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 57  IFCGNFE-YDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           +F GN      ++SD+E +F +YGK+    +  GFAF+   +ER+A  A+ G D
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGED 57

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

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

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 9/73 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------GFAFIYMDDERDAEDAIRGLD 109
           +F     +   + +LE+LF+++G V  V + +       G A++  ++E  A  A+  +D
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 110 RTEFGRKGRRLRV 122
            TE   K + + V
Sbjct: 65  GTEI--KEKTISV 75

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

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

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRA 201
           +  LFV N  PY  +  DLE+ F  +G++  V +         + FA+V +   EDA +A
Sbjct: 2   TGRLFVRNL-PYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 202 LDATNMSKLTDRVISV 217
               +      R+I +
Sbjct: 61  YKELDGKVFQGRLIHI 76

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

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

 Score = 43.8 bits (104), Expect = 9e-06
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 9/79 (11%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           P  TLFV       T    L   F  YG I  +R+ R+        +AFV+YE + DA R
Sbjct: 2   PYLTLFVGRLSL-QTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 201 ALDATNMSKLTDRVISVEY 219
           A    +   +    I V++
Sbjct: 61  AYRDAHKLVIDGSEIFVDF 79

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

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

 Score = 43.1 bits (101), Expect = 9e-06
 Identities = 30/70 (42%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN    A + +LER F  YG +  V +     GFAF+  +D RDAEDA+RGLD    
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 61

Query: 114 GRKGRRLRVE 123
              G R+RVE
Sbjct: 62  C--GSRVRVE 69

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 71  LERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK 126
           L  LF  YG+V+RV     +AF++ ++  DA  A+  ++  E    G  + V   K
Sbjct: 18  LRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELE--GSPIEVSLAK 71

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

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRAL 202
           KT  ++N+ P +    ++   F   G+I S ++ R+        + FV Y   EDA +A+
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 203 DATNMSKLTDRVISVEYA 220
           +  N  +L ++ I V YA
Sbjct: 61  NTLNGLRLQNKTIKVSYA 78

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

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
           T  ++N+ P      +L   FE  G I S +I R+        + FV Y  + DA +A++
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 204 ATNMSKLTDRVISVEYA 220
             N  ++ ++ + V YA
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

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

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

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 8/71 (11%)

Query: 168 LERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F+P+G ++SVR+ R+        + +V ++   DA RAL+  N  +L  + I + +
Sbjct: 17  LYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMW 76

Query: 220 AVRDDDDRRNG 230
           + RD   RR+G
Sbjct: 77  SQRDPSLRRSG 87

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

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           +FV N D   T   +L   FE YG ++S  + R FAFV    +  A RA++  N  +L  
Sbjct: 3   IFVGNVDE-DTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAADRAIEELNGRELHG 61

Query: 213 RVISVE 218
           R + VE
Sbjct: 62  RKLVVE 67

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

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

 Score = 46.1 bits (108), Expect = 2e-05
 Identities = 37/210 (17%), Positives = 63/210 (30%), Gaps = 10/210 (4%)

Query: 132 RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------- 184
                  S +    +   + TLFV N  PY     DL   F+ +G +  VR+        
Sbjct: 97  ELFRSSESPKSRQKSKEENNTLFVGNL-PYDVTEEDLRELFKKFGPVKRVRLVRDRETGK 155

Query: 185 -RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDR 243
            R FAFV++E +E A +A++  N  +L  R + V+ A      R    +           
Sbjct: 156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLS 215

Query: 244 GRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSR 303
             +             +    ++         S     VR+  P  +D   P        
Sbjct: 216 RGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGD-IVRASLPPSKDGKIPKSRSFVGN 274

Query: 304 SPYKKERAAIGHGRGPSRSPYRRDRGSPEN 333
              K    +   G           +   + 
Sbjct: 275 EASKDALESNSRGNKKKILGRGPRKAFSQP 304

Length = 306

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 9/77 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
           T++V N  P+     DL + F  YGK++ V I ++         AF+ +  +EDA + + 
Sbjct: 3   TVYVSNL-PFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

Query: 204 ATNMSKLTDRVISVEYA 220
           A N  +L  R +    A
Sbjct: 62  ALNNKELFGRTLKCSIA 78

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

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 10/63 (15%)

Query: 70  DLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR 121
           DL  +F RYG +++V    D K+    GF F+Y +   DA++A   L        GRR+R
Sbjct: 15  DLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL--NGMEIDGRRIR 72

Query: 122 VEW 124
           V++
Sbjct: 73  VDY 75

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

>gnl|CDD|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 = 41.8 bits (99), Expect = 2e-05
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALD 203
             L V N  P+    ++L   F P+G++ SVR+        R FAFV++  +++A  A++
Sbjct: 1   TKLIVRNV-PFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 204 ATNMSKLTDRVISVEYA 220
           A   + L  R + +EYA
Sbjct: 60  ALKSTHLYGRHLVLEYA 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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 19/68 (27%), Positives = 35/68 (51%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           +F+ N +    +  D+E  F  YGKI+   + + FAFVQY  + +A  A+   +   +  
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 63

Query: 213 RVISVEYA 220
           +V+ +  A
Sbjct: 64  QVLDINLA 71

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

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAFVQYEVQEDATRALDA 204
           K L V N  P+  R  DL + F  +G I+ V I  N      F FV +    DA RA + 
Sbjct: 1   KRLHVSNI-PFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREK 59

Query: 205 TNMSKLTDRVISVEYA 220
            + + +  R I V  A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

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

 Score = 46.1 bits (109), Expect = 2e-05
 Identities = 80/335 (23%), Positives = 117/335 (34%), Gaps = 34/335 (10%)

Query: 89  GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTR 148
           GFAF+  +  R A  A R L        G  + V+W + E                 +  
Sbjct: 183 GFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE------------EVDEDVM 230

Query: 149 PS-KTLFVINFDPYHTRTRDLERHFEPY--GKIISVRIRRNFAFVQYEVQEDATRALDAT 205
              K L+V N     T    +E+ F  +  GK+  V+  R++AFV +E +EDA +A+D  
Sbjct: 231 AKVKILYVRNL-MTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDEL 289

Query: 206 NMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSP----SPYRRERGSPDY 261
           N  +L    I V  A   D      ++          +  R+S      P  R     DY
Sbjct: 290 NGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDY 349

Query: 262 GRGSSRSPYRRERGSPDY----GRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIGHGR 317
                 +P       P      GR  +PS     RG P YG  +    Y          R
Sbjct: 350 YYHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPYGYEAYYGDYYGYHD----YR 405

Query: 318 GPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERER--PSPENGRGGSR 375
           G     Y       + G   +P    +GKP    GR     P  R+   P P  G+ G +
Sbjct: 406 GKYEDKYY----GYDPGMELTPMNPVRGKPGGRGGRPAIPPPRGRKNGAPPPAIGQDGRQ 461

Query: 376 SPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADS 410
               +        + P+P+ +  PR S    GA  
Sbjct: 462 LFLYKITIPAGYSQRPAPHPLGPPRGSAFVRGARG 496

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

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 11/74 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           IF GN +Y     +L+  F+  G ++R+ +          GFA+I   D+   E+A+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 109 DRTEFGRKGRRLRV 122
           + +EF  +GR+++V
Sbjct: 61  NESEF--RGRQIKV 72

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

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

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 13/76 (17%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           +F GN  ++  + +L   F R G++ RV M +        GFAF+  ++   A +A++G 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 109 DRTEFGRKGRRLRVEW 124
                   GR LRVE+
Sbjct: 61  HLN-----GRALRVEY 71

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 8/59 (13%)

Query: 167 DLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVISV 217
           DL   FEP+G+I  V+++R+        + F+Q+   EDA +AL+  N  +L  R I V
Sbjct: 14  DLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72

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

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 30/78 (38%), Positives = 44/78 (56%), Gaps = 9/78 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN   +  +++LER F  YG +  V +     GFAF+  +D RDA DA+R LD    
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELD---- 62

Query: 114 GRK--GRRLRVEWTKHER 129
           GR   G R+RVE +  E+
Sbjct: 63  GRTLCGCRVRVELSNGEK 80

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 168 LERHFEPYGKIISV--RIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           L R FE YG +  +     + + FV Y   EDA  A DA N  +L  
Sbjct: 20  LLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELEL 66

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

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN----F---AFVQYEVQEDATRALDA 204
           T++V  F    T   D++  FE +GK+ ++R+RR+    F    FV+++ +EDA + L+ 
Sbjct: 1   TVYVKGFPKDAT-LDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

Query: 205 TNMSKLTDRVISVE 218
               K  ++ ++V 
Sbjct: 60  -EKLKYKEKELTVM 72

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

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRA 201
           S  LFV N  P+     +L+  F+ +G ++ VRI          NF FV ++  E   + 
Sbjct: 3   SHQLFVGNL-PHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 202 LDATNMSKLTDRVISVE 218
           L    +    D  ++VE
Sbjct: 62  LANKPIYFRGDHRLNVE 78

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

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDA 204
           LF+ +     T   DL + F P+G +IS ++  +        F FV Y+  E A  A+ A
Sbjct: 1   LFIYHLPNEFTDQ-DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

Query: 205 TNMSKLTDRVISVE 218
            N  ++  + + V+
Sbjct: 60  MNGFQVGGKRLKVQ 73

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

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

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 24/58 (41%), Positives = 29/58 (50%), Gaps = 8/58 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRAL 202
           TL+V  F    TR RDL   FE YG+++   I        R FAFV+YE   DA  A 
Sbjct: 1   TLYVTGF-GAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAY 57

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

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

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQ---EDATRALDATNM 207
           + +F  NF+ Y  R  ++ER F  YG++  V ++  FAFV  E +   EDA R LD    
Sbjct: 1   RPVFCGNFE-YDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDAEDAIRGLDNFEF 59

Query: 208 SKLTDRVISVEYA 220
            +   R + VE+A
Sbjct: 60  GR-QRRRLRVEWA 71

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

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 10/73 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           IF G    D  + +L   F R+G V       DR  +  G+ F+  + + DAE  I  + 
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-ILAMG 63

Query: 110 RTEFGRKGRRLRV 122
              F  +G++L +
Sbjct: 64  NLNF--RGKKLNI 74

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

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 9/61 (14%)

Query: 71  LERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE 123
           L+++F RYGKV    +         GFAF+ M   ++AE A+   +  E    GR + V+
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEI--DGRPVAVD 75

Query: 124 W 124
           W
Sbjct: 76  W 76

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

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

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 9/73 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------GFAFIYMDDERDAEDAIRGLD 109
           IF  N  +     DL+ LFR  G V R D+K+       GF  +  +   DA+ AI   +
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 110 RTEFGRKGRRLRV 122
             +   +GR L V
Sbjct: 61  GYDL--EGRELEV 71

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

>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 44.9 bits (106), Expect = 6e-05
 Identities = 39/154 (25%), Positives = 61/154 (39%), Gaps = 18/154 (11%)

Query: 235 RNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGS 294
           R   R   RG+R   S  + +R   + GR SS+ P +++  S    + +S  P +  RG 
Sbjct: 445 RPVSRGRGRGQRGPRSQPQNQRRQQNRGRQSSQPPRQQQNRSNQNNQRQSQGPNQGPRGQ 504

Query: 295 PDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRG 354
             Y  N     Y+ +R   G GR  + +PYR+       G G S              + 
Sbjct: 505 GGY--NLRPRTYQPQRYGGGQGRRWNPNPYRQS------GQGRSQQ---------QQPQP 547

Query: 355 PSRSPYERERPSPENGRGGSRSPYRRERPSPDNG 388
            +R    R  P P  G+GG  +  R +R   +  
Sbjct: 548 EARGNQSR-TPGPGRGQGGRGNQNRNQRSGNNTV 580

Length = 582

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

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT 205
           + TL V N  P       L  HF  +G I+++++      A VQ+   E+A +A  + 
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRSP 58

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

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATN 206
           T+FV   DP      +L   F P+G+I+ V+I   +   FVQ+  +  A  A+    
Sbjct: 3   TVFVGGLDP-AVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQ 58

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 11/79 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMD-DERDAEDAIRG 107
           +F G       +SDLE  F R+G V  V++          GFA+I +   E   +     
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 108 LDRTEFGRKGRRLRVEWTK 126
           L+ T++  KG  L++E  K
Sbjct: 62  LNGTKW--KGSVLKIEEAK 78

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 13/79 (16%)

Query: 151 KTLFV--INFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           KTLFV  +N+D   T    L R FE YG I  +R+ R+        +AF+++E + D   
Sbjct: 2   KTLFVARLNYD---TTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKA 58

Query: 201 ALDATNMSKLTDRVISVEY 219
           A    +  K+  R + V+ 
Sbjct: 59  AYKYADGKKIDGRRVLVDV 77

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

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 10/81 (12%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN--------FAFVQYEVQEDATRALD 203
           LF+ N DP     + L   F  +G I+ + +I R+        FAF+ Y+  E +  A++
Sbjct: 4   LFIGNLDP-EVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 204 ATNMSKLTDRVISVEYAVRDD 224
           A N   L +R I+V YA + D
Sbjct: 63  AMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 57  IFCGNFE-YDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTE 112
           +F  NF+  + R  DLER F  YGK+  V ++  FAF+  + +   EDA + L+ T 
Sbjct: 2   LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQ---EDATKALESTN 55

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

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 27/75 (36%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALD 203
            LFV N  PY T   DL  HF+  G   SVR+         +  AFV+++  E  T+AL 
Sbjct: 2   ILFVGNL-PYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60

Query: 204 ATNMSKLTDRVISVE 218
             + + L  R I+VE
Sbjct: 61  -LHHTLLKGRKINVE 74

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

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

 Score = 40.1 bits (94), Expect = 9e-05
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           ++   F  D  +S +  +F  YG V  V M S FAF+  +    A  A   + 
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAIRAKDSVH 54

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

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 167 DLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
           +L   FE +G+++     +++AFV  E +E+A  A++A N  ++  R I+VE
Sbjct: 16  ELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVE 67

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 10/79 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDR---VDMKS-----GFAFIYMDDERDAEDAIRGL 108
           +F  N  YD     LE  F   G + R   V  K      GF ++    E DA+ A+   
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 109 DRTEFGRKGRRLRVEWTKH 127
            +T+F   GR++ VE+ K 
Sbjct: 62  KKTKF--GGRKIHVEFAKK 78

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

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 9/79 (11%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           P   LFV   +P  T   DLE  F  +GKI S  + R+        +AF+++E +ED   
Sbjct: 2   PENVLFVCKLNPV-TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 201 ALDATNMSKLTDRVISVEY 219
           A    +   + DR I V++
Sbjct: 61  AYFKMDNVLIDDRRIHVDF 79

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 11/78 (14%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIR 106
             IF G   Y      L + F ++G++       DR   KS G+ F+   D+  AE A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 107 GLDRTEFGRKGRRLRVEW 124
             +       GR+  V  
Sbjct: 61  DPNPI---IDGRKANVNL 75

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 153 LFVINFDPYHTRTRDLERHF-EPYGKIISVRIRRN-------FAFVQYEVQEDATRALDA 204
           L V N     T   +L+ HF +  G+I  V++ R         AF+ Y+ +E+A +A D 
Sbjct: 3   LIVKNLPASLT-EAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 205 TNMSKLTDRVISVEYA 220
            N + +    ISVE+A
Sbjct: 62  FNNTYINTSKISVEFA 77

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 46/205 (22%), Positives = 58/205 (28%), Gaps = 13/205 (6%)

Query: 228 RNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSP 287
               SP   R  SP      SP+P      + D G  SS S      G         P P
Sbjct: 199 PAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLP 258

Query: 288 YRRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKP 347
               R +P                +   G   S S  R    SP      S       + 
Sbjct: 259 ----RPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRA 314

Query: 348 SPNNGR-------GPSRSPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPR 400
           S ++           S S       +   G   SRSP    RP P      SP   P P 
Sbjct: 315 SSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSP-SPSRPPPPA-DPSSPRKRPRPS 372

Query: 401 DSPGYDGADSPINERYRSRSPPAED 425
            +P    A +    R R+R+  A  
Sbjct: 373 RAPSSPAASAGRPTRRRARAAVAGR 397

Length = 1352

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKL 210
           K LFV N     T    LE+ F  +GK+  V+  +++AFV +E ++ A RA+D  N  ++
Sbjct: 2   KVLFVRNLATTVTE-EILEKSFSEFGKLERVKKLKDYAFVHFEERDAAVRAMDEMNGKEI 60

Query: 211 TDRVISVEYA 220
               I +  A
Sbjct: 61  EGEEIEIVLA 70

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           LFV N  P  T  +++   FE YGK++   I +N+ FV  + +  A  A+   +  KL  
Sbjct: 3   LFVGNLPPEATE-QEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAADEAIRNLHHYKLHG 61

Query: 213 RVISVE 218
             I+VE
Sbjct: 62  VAINVE 67

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

>gnl|CDD|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 = 39.2 bits (92), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F  N  +   + +L  LF  +G++       D+   +S GFAF+       A  A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 109 DRTEFGRKGRRLRV 122
           D + F  +GR L V
Sbjct: 62  DGSIF--QGRLLHV 73

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

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 11/80 (13%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRV--------DMKSGFAFIYMDDERDAEDAIR 106
           R +F  N  +DA + +L+ LF ++G+V               G AF+    +  A+  + 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 107 GLDRTEFGR---KGRRLRVE 123
             D  E       GRRL V 
Sbjct: 61  AADNAEDSGLSLDGRRLIVT 80

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

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 6/48 (12%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-----FAFVQY 192
           ++TLF+ N +   T   DL   FE +G+II + I++      +AF+QY
Sbjct: 2   TRTLFIGNLEK-TTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQY 48

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

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

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 168 LERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           L++ F  YGK+    I R        FAFV  + +++A  AL+ TN  ++  R ++V++A
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77

Query: 221 VRDD 224
           V+ +
Sbjct: 78  VQKN 81

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDAT 205
           +FV N  P+    +DL+  F   G ++   ++       + F  V +E  EDA RA++  
Sbjct: 1   IFVRNL-PFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 206 NMSKLTDRVISV 217
           N   L  R + V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 17/86 (19%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERDAEDAIR 106
           + +F     YD  +S L R F  YG + R+ +       K  G+AFI  + ERD + A +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 107 GLDRTEFGRK--GRRLRVEWTKHERG 130
             D    G+K  GRR+ V+    ERG
Sbjct: 62  YAD----GKKIDGRRVLVDV---ERG 80

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|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 = 39.8 bits (93), Expect = 2e-04
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 161 YHTRTRDLERHFEPYGKI---ISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTD 212
           + T  + LE+ F  YG+I   + V+ R     R F FV +E  +DA  A+ A N   +  
Sbjct: 10  FDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69

Query: 213 RVISVEYA 220
           R I V+ A
Sbjct: 70  RQIRVDQA 77

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

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 10/76 (13%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAFVQYEVQEDATRALD 203
           SK L V N   Y      L+  FE   K  S+RI +N      +AFV++E  EDA  AL+
Sbjct: 1   SKVLVVNNLS-YSASEDSLQEVFE---KATSIRIPQNNGRPKGYAFVEFESAEDAKEALN 56

Query: 204 ATNMSKLTDRVISVEY 219
           + N +++  R I +E+
Sbjct: 57  SCNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDAT 205
           + V N   Y T  R L  HFE  G++  V++ R        F FV ++ +EDA +A+   
Sbjct: 3   IIVKNLPKYVTEDR-LREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 206 NMSKLTDRVISVEYA 220
           N + +    ISVE A
Sbjct: 62  NKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 168 LERHFEPYGKIISV--RIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR 222
           L++ F P+G II++     +N  FV +E  E A RA+   N + +    + V  A +
Sbjct: 19  LKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLARK 75

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

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L+  FE +G ++  R+         R F +V +E  EDA +A++A +  +L  R I+V++
Sbjct: 16  LKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDF 75

Query: 220 A 220
           +
Sbjct: 76  S 76

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 43.2 bits (102), Expect = 3e-04
 Identities = 33/159 (20%), Positives = 49/159 (30%), Gaps = 7/159 (4%)

Query: 243 RGRRRSPSPYRRERGSPDYGRGSS-RSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNS 301
                   P R    SP     ++ R P R  R  P        +  R+ R     G + 
Sbjct: 772 LALLEPAEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSE 831

Query: 302 SRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYE 361
           S  P +   AA         S   + + +   G     +  R+ +P       P   P  
Sbjct: 832 SSGPARPPGAA-ARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPE-----PRARPGA 885

Query: 362 RERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPR 400
              P        + +P  R RP+P     P P   P+PR
Sbjct: 886 AAPPKAAAAAPPAGAPAPRPRPAPRVKLGPMPPGGPDPR 924

Length = 1352

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMS 208
             + V N  P+ T   +L   FE +G +  + +   R  A V++    DA +A  +    
Sbjct: 1   TVILVKNL-PFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYK 59

Query: 209 KLTDRVISVEYA 220
           +     + +E+A
Sbjct: 60  RFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           +   N   D  +SDL  L   +GKV  V +      A + MD    A+  +         
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPAL 61

Query: 115 RKGRRLRVEWTKH 127
            +GRR+ ++++ H
Sbjct: 62  IRGRRVYIQYSNH 74

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV--DMKSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           +F GN   D  + ++ +LF +YGK   +      GF FI ++    AE A   LD     
Sbjct: 4   LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPL- 62

Query: 115 RKGRRLRVEW 124
            +G++LRV +
Sbjct: 63  -RGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNM 207
           S TL++ +     T   DL+  FE YG+I S+ +   R  A+V  E ++DA RAL     
Sbjct: 2   STTLWIGHLSKKVTE-EDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 208 SKLTDRVISVEYA 220
            KL  + I V +A
Sbjct: 61  VKLAGKKIKVAWA 73

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

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 12/76 (15%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-----------RRNFAFVQYEVQEDATRA 201
           L+V N +P  T    L + F  +G + SV+I            RN  FV +  + DA RA
Sbjct: 4   LYVGNLNPKVTE-EVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 202 LDATNMSKLTDRVISV 217
           LD  +   +    + +
Sbjct: 63  LDELDGKDVMGYELKL 78

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 10/63 (15%)

Query: 68  QSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
           Q +L  LF   G +       DR+  +S G+ F+   DE DA+ AI  L+  E   K  R
Sbjct: 14  QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNK--R 71

Query: 120 LRV 122
           L+V
Sbjct: 72  LKV 74

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

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMS 208
            T+ V NF PY T   +L   FEP+GK+  V +      A V++   + A  A  A    
Sbjct: 1   TTILVKNF-PYGTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYR 59

Query: 209 KLTDRVISVEYA 220
           +  D ++ +E  
Sbjct: 60  RFKDSILYLEKG 71

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI---------RRNFAFVQYEVQEDATRALDA 204
           P+    ++L   F  +G++ +VR+          R F FV +  ++DA RA  A
Sbjct: 9   PFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 10/71 (14%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKL- 210
           P     ++LE  F PYG+II+ RI         R   F++++ + +A RA+ A N +   
Sbjct: 9   PKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPP 68

Query: 211 -TDRVISVEYA 220
                I+V++A
Sbjct: 69  GATEPITVKFA 79

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

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS--GFAFIYMDDERDAEDAIRGL 108
           ++ GN  +   +  +  LF R G + R+ M      K+  GF F+      DAE+A++ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 109 DRTEFGRKGRRLRVEW 124
           + T+     R +RV+W
Sbjct: 61  NGTKLD--DRIIRVDW 74

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|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGL 108
           +F  N   D R  DL R F RYG +  V +          GFA++  +D RDAEDA+  L
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 109 DRTEFGRKGRRLRVEWTKHER 129
           DR      GR++ +++ + +R
Sbjct: 63  DRKWIC--GRQIEIQFAQGDR 81

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

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           L V N     T  ++L   FE YG +I   I +++AFV  E  EDA  A+   + ++   
Sbjct: 3   LHVGNISSSCT-NQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQG 61

Query: 213 RVISVE 218
           + + V+
Sbjct: 62  KRMHVQ 67

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

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

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTE 112
             ++ G+      + DL+ LF  YG++  +DM    G A++ M+  +DA  A++ L    
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLR--N 60

Query: 113 FGRKGRRLRVEW 124
               G++++V W
Sbjct: 61  VKLAGKKIKVAW 72

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

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

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 10/81 (12%)

Query: 149 PSKTLFVINFDPYHTRTRDLE----RHFEPYGKIISVRIRRN-----FAFVQYEVQEDAT 199
           PS  +FV +  P      +LE     HF  YG ++ V++ R+     +AFVQ+   +DA 
Sbjct: 1   PSACVFVASL-PASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAK 59

Query: 200 RALDATNMSKLTDRVISVEYA 220
            AL     + L  R I  E A
Sbjct: 60  NALAKGQGTILDGRHIRCERA 80

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

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

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 9/80 (11%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDA 204
           L+V +  P  T    L   F P G ++S+R+ R+        +A+V ++   DA RALD 
Sbjct: 2   LYVGDLHPDVTE-AMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 205 TNMSKLTDRVISVEYAVRDD 224
            N   +  + I + ++ RD 
Sbjct: 61  LNFDVIKGKPIRIMWSQRDP 80

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

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 172 FEPYGKIISVRIRRNF-----AFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           F  +G ++ +   +       AFV ++  E AT AL A       D+ + ++YA
Sbjct: 24  FSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQYA 77

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

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

 Score = 38.2 bits (89), Expect = 5e-04
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI----RRNFAFVQYEVQEDATRALDA 204
           P+K + V N  P      D+  H   +G I++V++     +  A V++  +E AT AL  
Sbjct: 6   PTKMIHVSNL-PSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALAC 64

Query: 205 TNMSKLTDRVISVEY 219
            + S L    I + +
Sbjct: 65  KHASSLNGSTIRLAF 79

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

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

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 18/57 (31%), Positives = 36/57 (63%)

Query: 164 RTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           R +D+ER F+ YG+I  + ++R F FV+++   DA  A+   +  +L +  +++E+A
Sbjct: 12  REKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCNERVTIEHA 68

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

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 9/67 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRN--FAFVQYEVQEDATRALD 203
           T+FV+       R RDL   F   GK+  VRI      RR+   A+V++  +E    AL 
Sbjct: 1   TVFVMQLSL-KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59

Query: 204 ATNMSKL 210
            T    L
Sbjct: 60  LTGQRLL 66

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

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDAT 205
           L+V N D      R L   F P+G I S ++  +       F FV +   E+AT+A+   
Sbjct: 4   LYVKNLDDSIDDER-LREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 206 NMSKLTDRVISVEYAVR 222
           N   +  + + V  A R
Sbjct: 63  NGRIIGGKPLYVALAQR 79

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

 Score = 37.9 bits (88), Expect = 6e-04
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDATNMSKLTD 212
           P+    +D+   F  YG++ SVR+        R FAFV++   ++A  A++A   + L  
Sbjct: 9   PFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLG 68

Query: 213 RVISVEYA 220
           R + ++YA
Sbjct: 69  RRLVLQYA 76

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

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

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 163 TRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRV 214
               DL   F P+G I  V + ++        FAFV +  +EDA RA++  N     + +
Sbjct: 11  ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLI 70

Query: 215 ISVEYA 220
           +SVE+A
Sbjct: 71  LSVEWA 76

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

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 9/58 (15%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRAL 202
           LFV N   + T   +L  HF   G+I  VR+         + FAFV +E  E AT AL
Sbjct: 1   LFVGNLS-FETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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|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 = 37.9 bits (88), Expect = 7e-04
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           +F G   +D  +  LE++F +YG++  V +          GF F+  ++  DA+DA+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 109 DRTEFGRKGRRLRVE 123
           +       GR++RV+
Sbjct: 63  NGKSV--DGRQIRVD 75

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|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 57  IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRG 107
           +F GN      +++D+E +F +YGK+    +  G+AF+    ER A  A+ G
Sbjct: 4   VFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFVQYISERHARAAVAG 55

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 27/92 (29%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------------RNF------ 187
           +T+FV N  P  T+ +DL++ F+ +G I SVR R                 + F      
Sbjct: 1   RTVFVGNL-PLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDN 59

Query: 188 --AFVQYEVQEDATRALDATNMSKLTDRVISV 217
             A+V ++ +E A +AL   N ++     I V
Sbjct: 60  VNAYVVFKEEESAEKALKL-NGTEFEGHHIRV 90

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

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

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 201
           SKT  ++N+ P      ++   F   G+I S ++ R+        + FV Y   EDA +A
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 202 LDATNMSKLTDRVISVEYA 220
           +++ N  +L ++ I V YA
Sbjct: 62  VNSLNGLRLQNKTIKVSYA 80

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

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 9/78 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDA 204
            +FV    P  T   +L   F  +G +  V+I        + + FV +E QEDA + L  
Sbjct: 4   RIFVGGIPPDTTEE-ELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 205 TNMSKLTDRVISVEYAVR 222
            N++    + +++  A+R
Sbjct: 63  GNLN-FRGKKLNIGPAIR 79

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

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 12/79 (15%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKI-----ISVRI---RRNFAFVQYEVQEDATRAL 202
             +FV    PYHT    L ++F  +G+I     I+ R     R + FV ++ +E A RA 
Sbjct: 1   TKIFVGGL-PYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59

Query: 203 DATNMSKLTD-RVISVEYA 220
              + + + D R  +V  A
Sbjct: 60  K--DPNPIIDGRKANVNLA 76

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 35/175 (20%), Positives = 45/175 (25%), Gaps = 10/175 (5%)

Query: 240 SPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGR 299
           +P     R          S   G  SS S  R    SP      S       R S     
Sbjct: 261 APITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSS 320

Query: 300 N-------SSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNG 352
           +       +S S      AA+  G  PSRSP    R  P     S     R  +   +  
Sbjct: 321 SRESSSSSTSSSSESSRGAAVSPGPSPSRSP-SPSRPPPPADPSSPRKRPRPSRAPSSPA 379

Query: 353 RGPSRSPYERERPSPENGRGGSRSPYRRE--RPSPDNGRVPSPNSMPEPRDSPGY 405
               R    R R +         +  R    RP P      + +     R     
Sbjct: 380 ASAGRPTRRRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASGAFYARYPLLT 434

Length = 1352

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN 206
           +F+ N +    +  D+E  F  YGKI+   + + +AFVQY  +  A  A+   N
Sbjct: 4   VFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFVQYISERHARAAVAGEN 57

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 8/62 (12%)

Query: 167 DLERHFEPYGKIISVRI---RRN-----FAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
           D+   F  +G+I ++ +   RR      +A ++YE +++A  A++  N  +L  + ISV+
Sbjct: 22  DVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVD 81

Query: 219 YA 220
           +A
Sbjct: 82  WA 83

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

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 8/47 (17%)

Query: 71  LERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLD 109
           L+ +F  YG V  VD+          G+A++  +   DAE AI+ +D
Sbjct: 15  LKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMD 61

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

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 8/64 (12%)

Query: 163 TRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRV 214
           TR  DL+  F  YGK++  ++  N        + FV     E+AT+ ++  + ++L  R+
Sbjct: 13  TRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRM 72

Query: 215 ISVE 218
           ISVE
Sbjct: 73  ISVE 76

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

>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 52/232 (22%), Positives = 74/232 (31%), Gaps = 14/232 (6%)

Query: 193 EVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPD--RGRRRSPS 250
           EV E     + +  +S+   R I +   V           P   R   P+  R  RR   
Sbjct: 60  EVLEGRLAPIISETLSRELGRPIRIAITVDPSAGEPAPPPPHARRTSEPELPRPGRRPYE 119

Query: 251 PYRRERGSPDYGRGSSRSPYRRER--GSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKK 308
            Y   R   D   G  R           P Y +   P  +   R + DYG    R  +  
Sbjct: 120 GYGGPRAD-DRPPGLPRQDQLPTARPAYPAYQQRPEPGAW--PRAADDYGWQQQRLGFP- 175

Query: 309 ERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPE 368
            RA        +     RDR   + G        R       +   P R   +R  P P 
Sbjct: 176 PRAPYASPASYAPEQ-ERDREPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPEPPPG 234

Query: 369 NG---RGGSRSPYRRERPSPDNGRVPSPNSMP-EPRDSPGYDGADSPINERY 416
            G   RGG   P R + P     R  +P  +  +P  +PG     + +N +Y
Sbjct: 235 AGHVHRGGPGPPERDDAPVV-PIRPSAPGPLAAQPAPAPGPGEPTARLNPKY 285

Length = 617

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

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           IF G  ++   ++DL + F +YG V       DR  +  G+ F+  + + DA+  ++  +
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 110 RTEFGRK 116
           R  F  K
Sbjct: 65  RLCFRDK 71

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

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

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 201
           SKT  ++N+ P +    +L+  F   G+I S ++ R+        + FV Y   +DA +A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 202 LDATNMSKLTDRVISVEYA 220
           ++  N  +L  + I V YA
Sbjct: 63  INTLNGLRLQTKTIKVSYA 81

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

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 11/74 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++ GN +Y +   +LE  F   G ++RV +          G+A+I     RD+ +A   L
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVAL 60

Query: 109 DRTEFGRKGRRLRV 122
           D + F  +GR ++V
Sbjct: 61  DESSF--RGRVIKV 72

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

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
           ++FV N  P+     +L +HFE  G + +VRI R+        F +V ++ ++    AL 
Sbjct: 1   SVFVGNL-PFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL- 58

Query: 204 ATNMSKLTDRVISVE 218
             N  KL  R I V+
Sbjct: 59  KLNGIKLKGRKIRVK 73

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATNMS 208
           TL V N DP  +   DL + F  YG+I  +R    +R+  F+++     A  AL A N S
Sbjct: 3   TLVVFNLDPSVS-NDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRS 61

Query: 209 KLTDRVISVE 218
           ++  + I +E
Sbjct: 62  EIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
            +FV N  P       L + F P+G + +V++ R+        + FV     E+A  A+ 
Sbjct: 3   CIFVYNLPP-DADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 204 ATNMSKLTDRVISVEY 219
           + N  +L  RV+ V +
Sbjct: 62  SLNGYRLGGRVLQVSF 77

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

>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++ G  +  A Q DL  LF  +G+++ ++M    G A++ M   +DA  A++ L    + 
Sbjct: 5   LWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSGSYK 64

Query: 115 RKGRRLRVEW 124
              + +++ W
Sbjct: 65  IGSKVIKIAW 74

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 11/61 (18%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF----AFVQYEVQEDATRALDAT 205
           S  L+ +  D  H       + F PYG +  + I        A VQ++  E A  A  A 
Sbjct: 7   SNLLYPVTVDVLH-------QVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKAL 59

Query: 206 N 206
           N
Sbjct: 60  N 60

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

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 57  IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRG 107
           +F GN      ++SD+E +F +YG+V    +  G+AF+   +ER A  A+ G
Sbjct: 4   VFIGNLNTAVVKKSDVETIFSKYGRVVGCSVHKGYAFVQYSNERHARGAVIG 55

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 161 YHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           Y  R RD+ER F+ YGKI+ V ++  + FV+++   DA  A+   N   L    + VE+
Sbjct: 9   YQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEH 67

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 13/79 (16%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM-----------KSGFAFIYMDDERDAEDAI 105
           ++ GN +    +  L +LF +YGK+ + D              G+ F+  + + +AE A+
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 106 RGLDRTEFGRKGRRLRVEW 124
           + L+       G++L V W
Sbjct: 62  KSLNGKTAL--GKKLVVRW 78

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

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG-------FAFIYMDDERDAEDAIRGLD 109
           ++   F  + R  DL   F RYG++ R D+          FAF+  +  RDAEDA   + 
Sbjct: 2   LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61

Query: 110 RTEFGRKGRRLRVEWTK 126
              F   G  L V+W K
Sbjct: 62  GRRFPDTGDTLHVQWAK 78

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 32/169 (18%), Positives = 47/169 (27%), Gaps = 11/169 (6%)

Query: 239 RSPDRGRRRSPS-PYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDY 297
            SP R R R+ +        S      +  +         +  R    SP  R   +   
Sbjct: 739 YSPRRARARASAWDITDALFSNPSLVPAKLAEALALLEPAEPQRGAGSSPPVRAEAA--- 795

Query: 298 GRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSR 357
                R P +  R+          +  R+ R    +G   S  P R   P     R P  
Sbjct: 796 ----FRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPAR---PPGAAARPPPA 848

Query: 358 SPYERERPSPENGRGGSRSPYRRERPSPDNGRVPSPNSMPEPRDSPGYD 406
              E  +  P    G +R    R RP P   R     + P    +    
Sbjct: 849 RSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPP 897

Length = 1352

>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 = 36.4 bits (85), Expect = 0.002
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 61  NFEYDARQSDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRTEFGRKGR 118
           N  +   + +L  LF ++G + R+ +      A +   +  DA  A + L    F  K  
Sbjct: 7   NLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKRF--KHV 64

Query: 119 RLRVEW 124
            L +EW
Sbjct: 65  PLYLEW 70

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 8/55 (14%)

Query: 172 FEPYGKIISVR--------IRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
           F  YG +  V         + R +A+V++E  EDA +A+   +  ++  + ++VE
Sbjct: 19  FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73

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

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 5/55 (9%)

Query: 156 INFDPYHTRTRDLERHFEPYGKIISVRI----RRNFAFVQYEVQEDATRALDATN 206
              D   T   D+  +F  +G ++ VRI    +R F FV +E  E   R L   N
Sbjct: 5   FPADSRFTE-EDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVKRILSKGN 58

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

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++ GN      Q+DL  LF+ +G +     +   GFAF+ +D    A  AI  L      
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPV- 61

Query: 115 RKGRRLRVEWTK 126
             GR LR  W K
Sbjct: 62  -HGRPLRCGWGK 72

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

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 8/77 (10%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALD 203
           T  +IN+ P      +    F   G + + +I R+        F FV Y+  EDA RA+ 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 204 ATNMSKLTDRVISVEYA 220
             N  +L ++ I V YA
Sbjct: 61  TLNGLQLQNKRIKVAYA 77

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

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 3/71 (4%)

Query: 151 KTLFVINFDPYHTRTRD-LERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSK 209
           K LFV N    +T T + LE+ F  +GK+  V+  +++AF+ ++ ++ A +A++  N  +
Sbjct: 2   KVLFVRNLA--NTVTEEILEKAFGQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKE 59

Query: 210 LTDRVISVEYA 220
           L    I + +A
Sbjct: 60  LEGENIEIVFA 70

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 7/46 (15%)

Query: 55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFI 93
          R +F GN E    + +L R F RYG V+ VD+K       + +AF+
Sbjct: 3  RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFV 48

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

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

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDAT 205
           L+V N DP  T    L++ F+  G + +V+I         N+ FV+Y    DA  AL   
Sbjct: 1   LYVGNLDPRVTEDI-LKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 206 NMSKLTDRVISVEYA 220
           N  ++ +  I V +A
Sbjct: 60  NGRQIENNEIRVNWA 74

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

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

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 201
           SKT  ++N+ P +    + +  F   G+I S ++ R+        + FV Y    DA +A
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 202 LDATNMSKLTDRVISVEYA 220
           ++  N  KL  + I V YA
Sbjct: 62  INTLNGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 10/63 (15%)

Query: 69  SDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL 120
            DL +LF  +G V       D+   +S  F F+  D+   A+ AI+ ++  + G K  RL
Sbjct: 13  QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK--RL 70

Query: 121 RVE 123
           +V+
Sbjct: 71  KVQ 73

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

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 37/157 (23%), Positives = 49/157 (31%), Gaps = 12/157 (7%)

Query: 237 RDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPD 296
               P R       P R  R  P     S  +  R+ R     G   S  P R    +  
Sbjct: 785 GSSPPVRAEAAFRRPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAAR 844

Query: 297 YGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPS 356
               +  S   K + A   GR   ++  RR R         + +P     P       P+
Sbjct: 845 -PPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAP-----PKAAAAAPPA 898

Query: 357 RSPYERERPSPENGRGGSRSPYRRERPSPDNG--RVP 391
            +P  R RP+P    G    P     P P  G  RVP
Sbjct: 899 GAPAPRPRPAPRVKLG----PMPPGGPDPRGGFRRVP 931

Length = 1352

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           ++ +F  N      +  LE+ F  +GK++RV     +AF++  +ERDA  A+R +D
Sbjct: 1   VKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHF-EERDA--AVRAMD 53

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDAT 205
           +FV   D + T   DL + F  YG +  V+I        + + FV +E QEDA + L   
Sbjct: 5   IFVGGID-FKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63

Query: 206 NMSKLTDRVISVEYAVR 222
           N     D+ +++  A+R
Sbjct: 64  NRLCFRDKKLNIGQAIR 80

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 5/57 (8%)

Query: 70  DLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE 123
           DL ++F  YG++  +     K    FI   D R AE A++ L+R+E    G+R+++E
Sbjct: 17  DLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSEIA--GKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 3/53 (5%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRAL 202
           T++V N  PY T+  DL   F+ +G I+  R +  R FAFV+ +  E A  A+
Sbjct: 2   TVYVGNIPPYTTQA-DLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAI 53

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

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 8/59 (13%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR-------NFAFVQYEVQEDATRA 201
           ++TLFV N +   T   +L R FE YG +  V I+R        +AFV++   + A RA
Sbjct: 2   TRTLFVGNLEITITE-EELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59

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

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 167 DLERHFE----PYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV 221
           DL + FE    P   ++  +    +AFV    Q  A +A++  N   L  +VI VE++V
Sbjct: 14  DLRQLFEEHKIPVSSVLVKK--GGYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSV 70

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 150 SKTLFV--INFDPYHTRTRD-LERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDA 204
           ++TL+V  I       +  + L RHF  +G I  +R+   +  AFV+Y+ +  A  A +A
Sbjct: 1   NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEA 60

Query: 205 -TNMSKLTDRVISVEYA 220
             + S     V++V +A
Sbjct: 61  MADQSLDGGEVLNVRWA 77

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

>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++ G  +    Q D+  L   +G ++ ++M    G A+I M   +DA  A++ L R    
Sbjct: 7   LWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKLSRGNVK 66

Query: 115 RKGRRLRVEW 124
              + +++ W
Sbjct: 67  VNQKSIKIAW 76

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 8/59 (13%)

Query: 165 TRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVI 215
           T  L   F P+G+I   R+ ++        + FV +  +EDA  A+ + N   L  R I
Sbjct: 13  TETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the matrin 3 family of nuclear proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 55  RPIFCGNF-EYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRT 111
           R +   N  E    +++L +L   +GKVD          AFI M+   DA+  +      
Sbjct: 1   RVVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQALVSFYKTY 60

Query: 112 EFGRKGRRLRV 122
                G+ ++V
Sbjct: 61  PLTIGGKSIKV 71

This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region. . Length = 76

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 33/199 (16%), Positives = 51/199 (25%), Gaps = 6/199 (3%)

Query: 195 QEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRR 254
           +  A  A  A    +      + +             + +        + R R       
Sbjct: 78  RRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAA 137

Query: 255 ERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIG 314
            RG+          P    R              RR RG  +  +  +    +  R   G
Sbjct: 138 RRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERG 197

Query: 315 HGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSP----ENG 370
                     RR++G      G      R+G+    + R         +R         G
Sbjct: 198 RDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEG 257

Query: 371 RGGSRSPYRRERPSPDNGR 389
           RGG R   RR R     GR
Sbjct: 258 RGGRRG--RRFRDRDRRGR 274

Length = 672

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           +F GN  + A Q DLE  F+  G+V       D      GF  +    E  A+ A+    
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KS 60

Query: 110 RTEFGRKGRRLRVE 123
             E    GR +RV+
Sbjct: 61  GEELL--GREIRVD 72

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

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 70  DLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK 126
           DL R+F  YG++ ++ +K+ + F+  D      +AI          +GR+L +E +K
Sbjct: 16  DLFRIFSTYGELAQIVLKNAYGFVQFDSPESCANAINCEQGKMI--RGRKLHLEVSK 70

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

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

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRAL 202
           +T  ++N+ P +    +L   F   G++ S ++ R+        + FV Y   +DA RA+
Sbjct: 1   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 203 DATNMSKLTDRVISVEYA 220
           +  N  +L  + I V YA
Sbjct: 61  NTLNGLRLQSKTIKVSYA 78

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

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 8/55 (14%)

Query: 160 PYHTRTRDLERHFEPYGKIISVR--IRRN------FAFVQYEVQEDATRALDATN 206
           P +T   DLE+  +P+GKIIS +  + +       + FV ++  E A +A++  N
Sbjct: 9   PPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLN 63

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 8/57 (14%)

Query: 172 FEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           F  YG+I+ + + R+        FAF+ YE Q     A+D  N  KL  R I V++ 
Sbjct: 30  FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRVDHV 86

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	425
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.93
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.91
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.91
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.91
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.89
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.89
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.88
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.88
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.86
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.82
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.82
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.82
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.8
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.8
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.8
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.8
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.79
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.79
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.77
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.73
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.72
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.71
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.71
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.7
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.65
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.63
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.63
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.58
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.57
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.57
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.56
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.55
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.52
PLN03120	260	nucleic acid binding protein; Provisional	99.51
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.51
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.49
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.48
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.47
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.46
PLN03121	243	nucleic acid binding protein; Provisional	99.43
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.43
KOG0122	270	consensus Translation initiation factor 3, subunit	99.42
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.41
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.4
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.4
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.39
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.34
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.33
smart00362	72	RRM_2 RNA recognition motif.	99.33
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.32
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.31
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.31
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.3
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.29
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.28
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.27
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.27
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.26
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.25
PLN03120	260	nucleic acid binding protein; Provisional	99.22
smart00360	71	RRM RNA recognition motif.	99.22
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.22
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.18
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.16
PLN03213	759	repressor of silencing 3; Provisional	99.15
KOG0122	270	consensus Translation initiation factor 3, subunit	99.15
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.12
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.12
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.1
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.1
PLN03121	243	nucleic acid binding protein; Provisional	99.09
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.08
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.03
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.02
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.98
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.98
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.96
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.95
smart00361	70	RRM_1 RNA recognition motif.	98.94
smart00360	71	RRM RNA recognition motif.	98.93
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.91
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.89
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.85
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.84
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.83
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.76
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.75
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.75
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.73
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.73
smart00361	70	RRM_1 RNA recognition motif.	98.72
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.72
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.7
KOG4210	285	consensus Nuclear localization sequence binding pr	98.68
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.67
KOG0151	877	consensus Predicted splicing regulator, contains R	98.64
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.62
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.6
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.59
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.55
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.52
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.47
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.41
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.39
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.31
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.3
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.25
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.25
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.21
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.18
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.14
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.13
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.12
KOG0226	290	consensus RNA-binding proteins [General function p	98.06
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.04
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.01
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.95
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.93
KOG0151	877	consensus Predicted splicing regulator, contains R	97.92
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.91
KOG0226	290	consensus RNA-binding proteins [General function p	97.87
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.86
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.77
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.77
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.74
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.7
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.7
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.57
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.53
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.48
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.45
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.44
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.43
KOG3152	278	consensus TBP-binding protein, activator of basal	97.32
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.28
KOG2314	698	consensus Translation initiation factor 3, subunit	97.27
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.24
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.22
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.14
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.12
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.07
KOG4210	285	consensus Nuclear localization sequence binding pr	97.03
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.93
KOG2314	698	consensus Translation initiation factor 3, subunit	96.88
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.86
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.86
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.68
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.66
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.64
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.6
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.56
KOG3152	278	consensus TBP-binding protein, activator of basal	96.39
KOG2135	526	consensus Proteins containing the RNA recognition	96.31
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	96.3
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.27
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.88
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.65
KOG2135	526	consensus Proteins containing the RNA recognition	95.61
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.51
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.24
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.16
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.02
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.85
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.7
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.7
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.61
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.56
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.26
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	93.92
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.81
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.72
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.37
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.23
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.06
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	92.53
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.5
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.46
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.3
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.3
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.16
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.13
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.72
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	91.08
KOG2318	650	consensus Uncharacterized conserved protein [Funct	90.6
KOG2318	650	consensus Uncharacterized conserved protein [Funct	89.6
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	88.02
KOG2891	445	consensus Surface glycoprotein [General function p	86.9
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	86.59
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	85.66
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	83.62
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	80.76

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=3e-29  Score=243.60  Aligned_cols=157  Identities=24%  Similarity=0.431  Sum_probs=139.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+++|+++|+++|..||+|+.|+|.        +|||||+|.++++|+.||+.|||..|  .++.|+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l--~gr~i~  180 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITV--RNKRLK  180 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCcc--CCceee
Confidence            44567899999999999999999999999999999883        59999999999999999999999999  899999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEc
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYE  193 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~  193 (425)
                      |.|+.....                ....++|||+|| +..+++++|+++|++||.|+.|.|.        ++||||+|.
T Consensus       181 V~~a~p~~~----------------~~~~~~lfV~nL-p~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~  243 (346)
T TIGR01659       181 VSYARPGGE----------------SIKDTNLYVTNL-PRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN  243 (346)
T ss_pred             eeccccccc----------------ccccceeEEeCC-CCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEEC
Confidence            999865321                123468999999 8899999999999999999999885        479999999


Q ss_pred             CHHHHHHHHHHcCCCccCC--eEEEEEEeeeCCC
Q 014384          194 VQEDATRALDATNMSKLTD--RVISVEYAVRDDD  225 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g--~~i~v~~a~~~~~  225 (425)
                      +.++|++||+.||+..|.|  ..|.|.++.....
T Consensus       244 ~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       244 KREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             CHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            9999999999999998876  6899999887543

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=99.96  E-value=8.7e-28  Score=237.23  Aligned_cols=214  Identities=19%  Similarity=0.250  Sum_probs=156.1

Q ss_pred             eeeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---   86 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---   86 (425)
                      ..||||.|.....+..+...-....+....................+|||+|||..+++++|.++|..||.|..+.+   
T Consensus        45 ~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~  124 (352)
T TIGR01661        45 LGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSD  124 (352)
T ss_pred             ceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEec
Confidence            35999999987776665532111211111111100011112334678999999999999999999999999998887   


Q ss_pred             -----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCC------------CC-C--CC-------
Q 014384           87 -----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRP------------GG-G--SS-------  139 (425)
Q Consensus        87 -----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~------------~~-~--~~-------  139 (425)
                           .+|||||+|.+.++|+.|+..|||..+...+..|.|.|+.........            .. .  ..       
T Consensus       125 ~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (352)
T TIGR01661       125 NVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAG  204 (352)
T ss_pred             CCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccC
Confidence                 278999999999999999999999988434478899988643310000            00 0  00       


Q ss_pred             ---------------------------------------CCC---------------CCCCCCCCcEEEEEcCCCCCCCH
Q 014384          140 ---------------------------------------ARR---------------PSTNTRPSKTLFVINFDPYHTRT  165 (425)
Q Consensus       140 ---------------------------------------~~~---------------~~~~~~~~~~l~V~nl~p~~~~~  165 (425)
                                                             ...               .........+|||+|| |..+++
T Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL-~~~~~e  283 (352)
T TIGR01661       205 IGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNL-SPDTDE  283 (352)
T ss_pred             CCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCC-CCCCCH
Confidence                                                   000               0000122347999999 788999


Q ss_pred             HHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          166 RDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       166 ~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ++|.++|++||.|..|.|.        +|||||+|.+.++|..|+..|||..|+|+.|.|.|+..+.
T Consensus       284 ~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       284 TVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            9999999999999999985        7899999999999999999999999999999999987753

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

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

Probab=99.96  E-value=2.6e-27  Score=241.26  Aligned_cols=198  Identities=24%  Similarity=0.321  Sum_probs=153.6

Q ss_pred             eeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEE---
Q 014384           11 HYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGK-VDRVDM---   86 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~-V~~v~i---   86 (425)
                      .||||.|.+...+..+...-....+..-..     .........++|||+|||.++|+++|.++|.+++. |+++.+   
T Consensus       100 GfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~-----l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~  174 (578)
T TIGR01648       100 GYAFVTFCGKEEAKEAVKLLNNYEIRPGRL-----LGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHS  174 (578)
T ss_pred             ceEEEEeCCHHHHHHHHHHcCCCeecCCcc-----ccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEecc
Confidence            489999998776555543221111110000     00112345789999999999999999999999864 444443   


Q ss_pred             ------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCC
Q 014384           87 ------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDP  160 (425)
Q Consensus        87 ------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p  160 (425)
                            ++|||||+|.++++|..|+..|+...+.+.|+.|.|+|+......           .........+|||+|| +
T Consensus       175 ~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~-----------d~~~~~~~k~LfVgNL-~  242 (578)
T TIGR01648       175 AADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEV-----------DEDVMAKVKILYVRNL-M  242 (578)
T ss_pred             ccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccc-----------cccccccccEEEEeCC-C
Confidence                  279999999999999999988865332227999999999865421           1122344579999999 7


Q ss_pred             CCCCHHHHHhhhccC--CcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          161 YHTRTRDLERHFEPY--GKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~--G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      ..+++++|+++|++|  |.|+.|.+.++||||+|.+.++|.+|++.||+.+|+|+.|.|.|++....
T Consensus       243 ~~~tee~L~~~F~~f~~G~I~rV~~~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       243 TTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             CCCCHHHHHHHHHhcCCCceEEEEeecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence            899999999999999  99999999999999999999999999999999999999999999987643

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.

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

Probab=99.95  E-value=1.3e-27  Score=226.35  Aligned_cols=198  Identities=22%  Similarity=0.317  Sum_probs=162.9

Q ss_pred             eeeEEEEeCCCCcccccc--cCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEE
Q 014384           10 CHYLLIVYSHSVWPVQKK--YLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGK-VDRVDM   86 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~-V~~v~i   86 (425)
                      -.|+||.|.+...+..+.  +..-.|....++..+       ....++.|||||||.+.++++|.+.|++.++ |++|.|
T Consensus       125 RGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc-------~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdViv  197 (506)
T KOG0117|consen  125 RGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC-------VSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIV  197 (506)
T ss_pred             cceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE-------EeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEE
Confidence            359999998876554444  222233333332222       4467899999999999999999999999986 677777


Q ss_pred             ---------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEc
Q 014384           87 ---------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVIN  157 (425)
Q Consensus        87 ---------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n  157 (425)
                               ++|||||+|++...|..|...|-.-.|.+.|..|.|+||.+..           ..........+.|||.|
T Consensus       198 y~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~-----------e~ded~ms~VKvLYVRN  266 (506)
T KOG0117|consen  198 YPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEE-----------EPDEDTMSKVKVLYVRN  266 (506)
T ss_pred             ecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCccc-----------CCChhhhhheeeeeeec
Confidence                     3899999999999999999876554444489999999999876           33334556678999999


Q ss_pred             CCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCCC
Q 014384          158 FDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDD  226 (425)
Q Consensus       158 l~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~~  226 (425)
                      | +..+|++.|+++|.+||.|..|..++.||||.|.+.++|.+|++.|||++|+|..|.|.+|++....
T Consensus       267 L-~~~tTeE~lk~~F~~~G~veRVkk~rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  267 L-MESTTEETLKKLFNEFGKVERVKKPRDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             c-chhhhHHHHHHHHHhccceEEeecccceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            9 8999999999999999999999999999999999999999999999999999999999999987543

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

Probab=99.95  E-value=5.2e-27  Score=239.32  Aligned_cols=165  Identities=18%  Similarity=0.415  Sum_probs=140.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+||++.+|+++|+++|.+||.|..|.|        ++|||||+|.+.++|..|+..|||..|  .|+.|.|.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i--~GR~IkV~  182 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQML--GGRNIKVG  182 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEE--ecceeeec
Confidence            45689999999999999999999999999999998        489999999999999999999999999  89999998


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQ  195 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~  195 (425)
                      +...........     ...........+|||+|| +..+++++|+++|+.||.|..|.|.        +|||||+|.+.
T Consensus       183 rp~~~p~a~~~~-----~~~~~~~~~~~rLfVgnL-p~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~  256 (612)
T TIGR01645       183 RPSNMPQAQPII-----DMVQEEAKKFNRIYVASV-HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL  256 (612)
T ss_pred             cccccccccccc-----ccccccccccceEEeecC-CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCH
Confidence            654332110000     001112234579999999 7889999999999999999999985        57999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          196 EDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ++|.+|++.||+..|+|+.|.|.++..+.
T Consensus       257 e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       257 QSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             HHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            99999999999999999999999988653

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.

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

Probab=99.95  E-value=3.3e-27  Score=210.43  Aligned_cols=168  Identities=20%  Similarity=0.426  Sum_probs=136.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .|||+.|.+.++.++|++.|.+||+|.+++|        +|||+||.|...++|+.||..|||.-|  .++.|+..||.-
T Consensus        64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl--G~R~IRTNWATR  141 (321)
T KOG0148|consen   64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL--GRRTIRTNWATR  141 (321)
T ss_pred             eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee--ccceeecccccc
Confidence            4667777777777777777777777666665        389999999999999999999999999  599999999987


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc
Q 014384          128 ERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT  205 (425)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l  205 (425)
                      +....+...-.....-....+.+++|||+|+ +..+++++|++.|..||.|.+|++.  +||+||.|.+.|.|..||..|
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I-~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~m  220 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNI-ASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQM  220 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCc-CccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHh
Confidence            6632222111111122455677899999999 6678899999999999999999996  789999999999999999999


Q ss_pred             CCCccCCeEEEEEEeeeCCCC
Q 014384          206 NMSKLTDRVISVEYAVRDDDD  226 (425)
Q Consensus       206 ~g~~~~g~~i~v~~a~~~~~~  226 (425)
                      |+++|.|..+++.|.++....
T Consensus       221 Nntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  221 NNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             cCceeCceEEEEeccccCCCC
Confidence            999999999999998886543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=1.3e-27  Score=215.01  Aligned_cols=149  Identities=30%  Similarity=0.539  Sum_probs=141.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCC
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRR  133 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~  133 (425)
                      +-+|||||||..+++.+|+.||++||+|.+|.|-|.||||..++...|+.||..|||..|  +|..|+|+-++.+.    
T Consensus         2 ~~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdktaaedairNLhgYtL--hg~nInVeaSksKs----   75 (346)
T KOG0109|consen    2 PVKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTAAEDAIRNLHGYTL--HGVNINVEASKSKS----   75 (346)
T ss_pred             ccchhccCCCcccchHHHHHHHHhhCceEeeeeecccceEEeecccccHHHHhhccccee--cceEEEEEeccccC----
Confidence            357999999999999999999999999999999999999999999999999999999999  99999999887653    


Q ss_pred             CCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCe
Q 014384          134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDR  213 (425)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  213 (425)
                                    .+.++|+|+|| ...++.++|+..|++||+|.+|.|.++|+||.|.-.++|..|+..|++++|.|+
T Consensus        76 --------------k~stkl~vgNi-s~tctn~ElRa~fe~ygpviecdivkdy~fvh~d~~eda~~air~l~~~~~~gk  140 (346)
T KOG0109|consen   76 --------------KASTKLHVGNI-SPTCTNQELRAKFEKYGPVIECDIVKDYAFVHFDRAEDAVEAIRGLDNTEFQGK  140 (346)
T ss_pred             --------------CCccccccCCC-CccccCHHHhhhhcccCCceeeeeecceeEEEEeeccchHHHHhcccccccccc
Confidence                          45689999999 788889999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEeeeC
Q 014384          214 VISVEYAVRD  223 (425)
Q Consensus       214 ~i~v~~a~~~  223 (425)
                      .++|..+...
T Consensus       141 ~m~vq~stsr  150 (346)
T KOG0109|consen  141 RMHVQLSTSR  150 (346)
T ss_pred             eeeeeeeccc
Confidence            9999998764

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=1.7e-26  Score=228.11  Aligned_cols=152  Identities=21%  Similarity=0.469  Sum_probs=136.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++|||+|||+.+|+++|+++|..||+|..|.|.        +|||||+|.+.++|++||..|||..|  .|+.|.|.|
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~~   79 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL--QNKTIKVSY   79 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEE--CCeeEEEEe
Confidence            36799999999999999999999999999999983        68999999999999999999999999  899999999


Q ss_pred             eccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHH
Q 014384          125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQE  196 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~  196 (425)
                      +.....                .....+|||+|| |..+++++|+.+|..||.|..+.+.        +|||||+|.+.+
T Consensus        80 a~~~~~----------------~~~~~~l~v~~l-~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~  142 (352)
T TIGR01661        80 ARPSSD----------------SIKGANLYVSGL-PKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRD  142 (352)
T ss_pred             eccccc----------------ccccceEEECCc-cccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHH
Confidence            875431                123468999999 8899999999999999999988884        579999999999


Q ss_pred             HHHHHHHHcCCCccCC--eEEEEEEeeeC
Q 014384          197 DATRALDATNMSKLTD--RVISVEYAVRD  223 (425)
Q Consensus       197 ~A~~A~~~l~g~~~~g--~~i~v~~a~~~  223 (425)
                      +|..|++.|||..+.|  ..|.|.++...
T Consensus       143 ~A~~ai~~l~g~~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       143 EADRAIKTLNGTTPSGCTEPITVKFANNP  171 (352)
T ss_pred             HHHHHHHHhCCCccCCCceeEEEEECCCC
Confidence            9999999999999987  56888887654

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

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

Probab=99.95  E-value=1.7e-26  Score=235.92  Aligned_cols=165  Identities=27%  Similarity=0.433  Sum_probs=141.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|+++|++||.|..|.|.        +|||||+|.+.++|.+|| .|+|..|  .|+.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~--~g~~i~  161 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQML--LGRPII  161 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEE--CCeeeE
Confidence            34567899999999999999999999999999999983        799999999999999999 6999999  799999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEc
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYE  193 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~  193 (425)
                      |.++...........    .......+...+|||+|| +..+++++|+++|++||.|..|.|.        +|||||+|.
T Consensus       162 v~~~~~~~~~~~~~~----~~~~~~~p~~~~l~v~nl-~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~  236 (457)
T TIGR01622       162 VQSSQAEKNRAAKAA----THQPGDIPNFLKLYVGNL-HFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH  236 (457)
T ss_pred             Eeecchhhhhhhhcc----cccCCCCCCCCEEEEcCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEEC
Confidence            998765432211100    111112234789999999 8899999999999999999999886        579999999


Q ss_pred             CHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          194 VQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      +.++|..|++.|||..|.|+.|.|.|+..
T Consensus       237 ~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       237 DAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            99999999999999999999999999874

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.

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

Probab=99.94  E-value=6.4e-26  Score=234.81  Aligned_cols=169  Identities=20%  Similarity=0.339  Sum_probs=136.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|..||.|..|.|        ++|||||+|.+.++|..||..|||+.|  .|+.|.|.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~--~~~~l~v~  370 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDT--GDNKLHVQ  370 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEE
Confidence            34579999999999999999999999999999887        379999999999999999999999999  79999999


Q ss_pred             EeccccCCCCCCCCC------------CCCCCCCCCCCCcEEEEEcCCCCC----------CCHHHHHhhhccCCcEEEE
Q 014384          124 WTKHERGIRRPGGGS------------SARRPSTNTRPSKTLFVINFDPYH----------TRTRDLERHFEPYGKIISV  181 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~------------~~~~~~~~~~~~~~l~V~nl~p~~----------~~~~~L~~~f~~~G~v~~v  181 (425)
                      ++.............            ..........+..+|+|.|| ...          ...++|+++|.+||.|+.|
T Consensus       371 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~-~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v  449 (509)
T TIGR01642       371 RACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNL-VTGDDLMDDEEYEEIYEDVKTEFSKYGPLINI  449 (509)
T ss_pred             ECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccC-CchhHhcCcchHHHHHHHHHHHHHhcCCeeEE
Confidence            986543221110000            00011122346788999998 321          0136789999999999999


Q ss_pred             EEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          182 RIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       182 ~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .|+           .|+|||+|.+.++|.+|+..|||..|+|+.|.|.|....
T Consensus       450 ~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       450 VIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGED  502 (509)
T ss_pred             EeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHH
Confidence            986           278999999999999999999999999999999997653

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

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

Probab=99.93  E-value=2.1e-25  Score=233.33  Aligned_cols=209  Identities=20%  Similarity=0.341  Sum_probs=160.6

Q ss_pred             eeEEEEeCCCCccccccc-------CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE
Q 014384           11 HYLLIVYSHSVWPVQKKY-------LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR   83 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~   83 (425)
                      .|+||.|.....+..+..       ....+.+..+.......  .......++|||+||+.++|+++|.++|..||+|..
T Consensus       130 g~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~--~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~  207 (562)
T TIGR01628       130 GYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE--AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITS  207 (562)
T ss_pred             cEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc--cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEE
Confidence            599999988765444331       12333333333222111  123455688999999999999999999999999999


Q ss_pred             EEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCC----CcEEEEEEeccccCCCCCCCC--CCCCCCCCCCCCC
Q 014384           84 VDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRK----GRRLRVEWTKHERGIRRPGGG--SSARRPSTNTRPS  150 (425)
Q Consensus        84 v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~----gr~l~V~~a~~~~~~~~~~~~--~~~~~~~~~~~~~  150 (425)
                      |.+.       +|||||+|.+.++|.+|++.|||..|  .    |+.|.|.++............  .............
T Consensus       208 ~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i--~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~  285 (562)
T TIGR01628       208 AAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKI--GLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQG  285 (562)
T ss_pred             EEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEe--cccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCC
Confidence            9883       78999999999999999999999999  7    999999987654321000000  0000111223456


Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .+|||+|| +..+++++|+++|+.||.|+.|.+.       +|||||+|.+.++|.+|+..|||..|+|+.|.|.+|..+
T Consensus       286 ~~l~V~nl-~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       286 VNLYVKNL-DDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             CEEEEeCC-CCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            78999999 7889999999999999999999985       589999999999999999999999999999999999875


Q ss_pred             C
Q 014384          224 D  224 (425)
Q Consensus       224 ~  224 (425)
                      .
T Consensus       365 ~  365 (562)
T TIGR01628       365 E  365 (562)
T ss_pred             H
Confidence            3

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=99.93  E-value=7.2e-25  Score=224.24  Aligned_cols=164  Identities=21%  Similarity=0.233  Sum_probs=135.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhc--CCCeecCCCcEEEEEEeccc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGL--DRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~l--ng~~ig~~gr~l~V~~a~~~  128 (425)
                      +.++|||+|||+.+|+++|.++|..||+|..|.|.  ++||||+|++.++|++|+..|  |+..|  .|+.|.|+|+...
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l--~g~~l~v~~s~~~   78 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYI--RGQPAFFNYSTSQ   78 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceE--cCeEEEEEecCCc
Confidence            36899999999999999999999999999999884  799999999999999999864  67788  8999999999754


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHH
Q 014384          129 RGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDA  204 (425)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~  204 (425)
                      ........    ...........+|+|.|| +..+++++|+++|+.||.|..|.+.    .++|||+|.+.++|.+|++.
T Consensus        79 ~~~~~~~~----~~~~~~~~~~~~v~v~nl-~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A~~~  153 (481)
T TIGR01649        79 EIKRDGNS----DFDSAGPNKVLRVIVENP-MYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAA  153 (481)
T ss_pred             ccccCCCC----cccCCCCCceEEEEEcCC-CCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHHHHH
Confidence            31111100    000111123357899999 7889999999999999999999885    24899999999999999999


Q ss_pred             cCCCccCC--eEEEEEEeeeC
Q 014384          205 TNMSKLTD--RVISVEYAVRD  223 (425)
Q Consensus       205 l~g~~~~g--~~i~v~~a~~~  223 (425)
                      |||..|.|  ..|.|+|++..
T Consensus       154 Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       154 LNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             hcCCcccCCceEEEEEEecCC
Confidence            99999965  58999998763

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

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

Probab=99.93  E-value=9.6e-25  Score=223.33  Aligned_cols=168  Identities=25%  Similarity=0.332  Sum_probs=139.0

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           52 AMMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        52 ~~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .+.++|||+||++ .+|+++|.+||+.||.|..|+|.   +|||||+|.+.++|..||..|||..|  .|+.|.|.+++.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l--~g~~l~v~~s~~  350 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKL--FGKPLRVCPSKQ  350 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEE--CCceEEEEEccc
Confidence            3568999999998 69999999999999999999984   79999999999999999999999999  899999999876


Q ss_pred             ccCCCCCC----CCC------CC-----CC------CCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc--EEEEEEe
Q 014384          128 ERGIRRPG----GGS------SA-----RR------PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK--IISVRIR  184 (425)
Q Consensus       128 ~~~~~~~~----~~~------~~-----~~------~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~--v~~v~~~  184 (425)
                      ........    .+.      ..     ..      .....++..+|||.|| |..+++++|+++|+.||.  |+.|.+.
T Consensus       351 ~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NL-p~~~tee~L~~lF~~~G~~~i~~ik~~  429 (481)
T TIGR01649       351 QNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNI-PLSVSEEDLKELFAENGVHKVKKFKFF  429 (481)
T ss_pred             ccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecC-CCCCCHHHHHHHHHhcCCccceEEEEe
Confidence            43211000    000      00     00      0012356789999999 789999999999999998  8888774


Q ss_pred             ------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE------EEEEEeee
Q 014384          185 ------RNFAFVQYEVQEDATRALDATNMSKLTDRV------ISVEYAVR  222 (425)
Q Consensus       185 ------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~------i~v~~a~~  222 (425)
                            +++|||+|.+.++|.+||..||+..|.|..      |+|.|++.
T Consensus       430 ~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       430 PKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             cCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence                  489999999999999999999999999985      99998865

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

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

Probab=99.93  E-value=8.6e-25  Score=226.38  Aligned_cols=170  Identities=16%  Similarity=0.270  Sum_probs=136.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhc------------CCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRY------------GKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~------------G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~  115 (425)
                      .....++|||||||+.+|+++|.+||..|            +.|..|.+.  +|||||+|.+.++|..|| .|||+.|  
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~~--  247 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAM-ALDSIIY--  247 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhh-cCCCeEe--
Confidence            45567899999999999999999999975            356666663  899999999999999999 7999999  


Q ss_pred             CCcEEEEEEeccccCCCCCC-----CCC--C------CCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEE
Q 014384          116 KGRRLRVEWTKHERGIRRPG-----GGS--S------ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVR  182 (425)
Q Consensus       116 ~gr~l~V~~a~~~~~~~~~~-----~~~--~------~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~  182 (425)
                      .|..|.|.............     ...  .      ............+|||+|| |..+++++|+++|+.||.|..+.
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-p~~~~~~~l~~~f~~~G~i~~~~  326 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNL-PLYLGEDQIKELLESFGDLKAFN  326 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEE
Confidence            89999997654332110000     000  0      0011112345679999999 89999999999999999999988


Q ss_pred             Ee--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          183 IR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       183 ~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      |.        +|||||+|.+.++|..|++.|||..|+|..|.|.++...
T Consensus       327 ~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            74        589999999999999999999999999999999998653

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

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

Probab=99.93  E-value=1.6e-24  Score=226.80  Aligned_cols=199  Identities=20%  Similarity=0.296  Sum_probs=155.2

Q ss_pred             eeEEEEeCCCCccccccc-CCcc-eeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--
Q 014384           11 HYLLIVYSHSVWPVQKKY-LPRR-LYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--   86 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--   86 (425)
                      .||||.|.+...+..+.. +... +........+.............+|||+||+.++|+++|.++|++||.|..|.|  
T Consensus        43 G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~  122 (562)
T TIGR01628        43 GYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT  122 (562)
T ss_pred             eEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeee
Confidence            499999998776555542 2222 111111111111111122334568999999999999999999999999999988  


Q ss_pred             -----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCC
Q 014384           87 -----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPY  161 (425)
Q Consensus        87 -----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~  161 (425)
                           ++|||||+|.+.++|..|+..|||..+  .|+.|.|..........           .......++|||.|| +.
T Consensus       123 ~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~--~~~~i~v~~~~~~~~~~-----------~~~~~~~~~l~V~nl-~~  188 (562)
T TIGR01628       123 DENGKSRGYGFVHFEKEESAKAAIQKVNGMLL--NDKEVYVGRFIKKHERE-----------AAPLKKFTNLYVKNL-DP  188 (562)
T ss_pred             cCCCCcccEEEEEECCHHHHHHHHHHhcccEe--cCceEEEeccccccccc-----------cccccCCCeEEEeCC-CC
Confidence                 379999999999999999999999999  89999998655433111           112344578999999 78


Q ss_pred             CCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccC----CeEEEEEEeeeC
Q 014384          162 HTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLT----DRVISVEYAVRD  223 (425)
Q Consensus       162 ~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~----g~~i~v~~a~~~  223 (425)
                      .+++++|+++|..||.|..+.+.       +|||||+|.+.++|.+|++.|+|..|.    |..|.|.++..+
T Consensus       189 ~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k  261 (562)
T TIGR01628       189 SVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKR  261 (562)
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccCh
Confidence            89999999999999999999885       569999999999999999999999999    999999887654

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

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

Probab=99.92  E-value=5.4e-24  Score=217.51  Aligned_cols=212  Identities=16%  Similarity=0.324  Sum_probs=152.8

Q ss_pred             eeeEEEEeCCCCcccccccCCcceeecccc-----cccchhh------hhhhcCCCceEEEcCCCCCCCHHHHHHHHhhc
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLYVLGFR-----RSHSQLS------IAAFEAMMRPIFCGNFEYDARQSDLERLFRRY   78 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~------~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~   78 (425)
                      ..||||+|.+...+..+..+........-+     .......      ........++|||+|||..+|+++|.++|+.|
T Consensus       131 kg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~  210 (457)
T TIGR01622       131 KGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPF  210 (457)
T ss_pred             ceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhc
Confidence            359999999877766655444333211110     0000000      00011235899999999999999999999999


Q ss_pred             CCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCC-------------CC-
Q 014384           79 GKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRP-------------GG-  136 (425)
Q Consensus        79 G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~-------------~~-  136 (425)
                      |.|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+.........             +. 
T Consensus       211 G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i--~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~  288 (457)
T TIGR01622       211 GDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFEL--AGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKN  288 (457)
T ss_pred             CCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEE--CCEEEEEEEccCCCccccchhhhccccccccCCcC
Confidence            999999883        68999999999999999999999999  8999999996532110000             00 


Q ss_pred             ----------------C---C-----C-------------------CC-------------C----CCCCCCCCcEEEEE
Q 014384          137 ----------------G---S-----S-------------------AR-------------R----PSTNTRPSKTLFVI  156 (425)
Q Consensus       137 ----------------~---~-----~-------------------~~-------------~----~~~~~~~~~~l~V~  156 (425)
                                      .   .     .                   ..             .    ......+..+|+|.
T Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~  368 (457)
T TIGR01622       289 LNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLS  368 (457)
T ss_pred             CCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEe
Confidence                            0   0     0                   00             0    00022456789999


Q ss_pred             cCCCCCCC---------HHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          157 NFDPYHTR---------TRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       157 nl~p~~~~---------~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ||......         .++|++.|.+||.|+.|.+.    .|++||+|.+.++|..|++.|||..|+|+.|.|.|....
T Consensus       369 n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       369 NMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             cCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            99322211         26799999999999999885    689999999999999999999999999999999998654

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.

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

Probab=99.91  E-value=1.1e-23  Score=186.82  Aligned_cols=212  Identities=18%  Similarity=0.267  Sum_probs=161.3

Q ss_pred             eeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----
Q 014384           11 HYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----   86 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----   86 (425)
                      .|.||.|-....+..+.+.-..+....-..+..-.....+......|||.+||..+|..+|+++|.+||.|..-.|    
T Consensus        84 GYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dq  163 (360)
T KOG0145|consen   84 GYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQ  163 (360)
T ss_pred             ccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhc
Confidence            5999999888877766654444433322222222222245566789999999999999999999999998865444    


Q ss_pred             ----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCC----------CC--------------
Q 014384           87 ----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGG----------GS--------------  138 (425)
Q Consensus        87 ----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~----------~~--------------  138 (425)
                          ++|.+||.|....+|+.||..|||..-...-.+|.|.|++..........          +.              
T Consensus       164 vtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~  243 (360)
T KOG0145|consen  164 VTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLD  243 (360)
T ss_pred             ccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccc
Confidence                69999999999999999999999975533677999999976542211100          00              


Q ss_pred             -----------------------CCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccE
Q 014384          139 -----------------------SARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNF  187 (425)
Q Consensus       139 -----------------------~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~  187 (425)
                                             .+...+.......||||.|| ...+++..|.++|..||.|..|++.        +||
T Consensus       244 ~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL-spd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGf  322 (360)
T KOG0145|consen  244 NLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL-SPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGF  322 (360)
T ss_pred             cccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEec-CCCchHhHHHHHhCcccceeeEEEEecCCcccccce
Confidence                                   00001222334689999999 5677799999999999999999985        789


Q ss_pred             EEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       188 afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +||.+.+-++|..|+..|||..++++.|.|.|...+
T Consensus       323 gFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  323 GFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             eEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            999999999999999999999999999999997653

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.91  E-value=3.8e-24  Score=180.67  Aligned_cols=159  Identities=28%  Similarity=0.465  Sum_probs=138.1

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      -....|||||||+..++++.|.+||-++|+|..|.|+        +|||||+|.++++|+.|+..||...|  -|++|+|
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkL--YgrpIrv   83 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKL--YGRPIRV   83 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHh--cCceeEE
Confidence            3556899999999999999999999999999999993        89999999999999999999998888  6999999


Q ss_pred             EEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEE-EE--------eccEEEEEEc
Q 014384          123 EWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV-RI--------RRNFAFVQYE  193 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v-~~--------~~g~afV~f~  193 (425)
                      ..+..-.               ....-+..|||+||++ .+++..|.+.|+.||.+... .+        +++||||.|.
T Consensus        84 ~kas~~~---------------~nl~vganlfvgNLd~-~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~  147 (203)
T KOG0131|consen   84 NKASAHQ---------------KNLDVGANLFVGNLDP-EVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYA  147 (203)
T ss_pred             Eeccccc---------------ccccccccccccccCc-chhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEech
Confidence            9876221               1123347899999976 88899999999999987663 22        2679999999


Q ss_pred             CHHHHHHHHHHcCCCccCCeEEEEEEeeeCCCCC
Q 014384          194 VQEDATRALDATNMSKLTDRVISVEYAVRDDDDR  227 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~~~  227 (425)
                      +.+.+.+|+..|||..+++++|.|.++..+....
T Consensus       148 sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  148 SFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             hHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            9999999999999999999999999999875443

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=3.6e-24  Score=190.09  Aligned_cols=161  Identities=42%  Similarity=0.683  Sum_probs=139.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCC
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRR  133 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~  133 (425)
                      +..||||+|++.+.+.+|+.||..||.|.+|.|+.||+||+|+++.+|..|++.|||++|  .|..|.|+|+........
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rda~Dav~~l~~~~l--~~e~~vve~~r~~~~~~g   78 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKEL--CGERLVVEHARGKRRGRG   78 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCcee--cceeeeeecccccccccC
Confidence            357999999999999999999999999999999999999999999999999999999999  677799999987554331


Q ss_pred             CCCCC----CCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCc
Q 014384          134 PGGGS----SARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSK  209 (425)
Q Consensus       134 ~~~~~----~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~  209 (425)
                      ...+.    .......+....+.|+|.++ +..+.|++|.++|.++|++....+..+++||+|.+.++|..|+..|++..
T Consensus        79 ~~~~g~r~~~~~~~~~p~~s~~r~~~~~~-~~r~~~qdl~d~~~~~g~~~~~~~~~~~~~v~Fs~~~da~ra~~~l~~~~  157 (216)
T KOG0106|consen   79 RPRGGDRRSDSRRYRPPSRTHFRLIVRNL-SLRVSWQDLKDHFRPAGEVTYVDARRNFAFVEFSEQEDAKRALEKLDGKK  157 (216)
T ss_pred             CCCCCCccchhhccCCcccccceeeeccc-hhhhhHHHHhhhhcccCCCchhhhhccccceeehhhhhhhhcchhccchh
Confidence            11111    01222344556678889999 78888999999999999998888889999999999999999999999999


Q ss_pred             cCCeEEEE
Q 014384          210 LTDRVISV  217 (425)
Q Consensus       210 ~~g~~i~v  217 (425)
                      +.|+.|++
T Consensus       158 ~~~~~l~~  165 (216)
T KOG0106|consen  158 LNGRRISV  165 (216)
T ss_pred             hcCceeee
Confidence            99999999

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

Probab=99.91  E-value=5.2e-24  Score=201.07  Aligned_cols=162  Identities=23%  Similarity=0.417  Sum_probs=140.8

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCC-eecCCCcE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRT-EFGRKGRR  119 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~-~ig~~gr~  119 (425)
                      +.+...-+||||-||..++|.||++||++||.|.+|.|        ++|||||.|.+.++|.+|+.+|++. .|.....+
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~p  108 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHP  108 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcc
Confidence            34566789999999999999999999999999999998        3899999999999999999999885 44347789


Q ss_pred             EEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEE
Q 014384          120 LRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQY  192 (425)
Q Consensus       120 l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f  192 (425)
                      |.|.+|..+...               .....+|||+-| +..+++.+|+.+|.+||.|++|.|.       +|||||+|
T Consensus       109 vqvk~Ad~E~er---------------~~~e~KLFvg~l-sK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~f  172 (510)
T KOG0144|consen  109 VQVKYADGERER---------------IVEERKLFVGML-SKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKF  172 (510)
T ss_pred             eeecccchhhhc---------------cccchhhhhhhc-cccccHHHHHHHHHhhCccchhhheecccccccceeEEEE
Confidence            999999876522               134578999999 7899999999999999999999995       68999999


Q ss_pred             cCHHHHHHHHHHcCCCc-cCC--eEEEEEEeeeCCCC
Q 014384          193 EVQEDATRALDATNMSK-LTD--RVISVEYAVRDDDD  226 (425)
Q Consensus       193 ~~~~~A~~A~~~l~g~~-~~g--~~i~v~~a~~~~~~  226 (425)
                      .+.+.|..|++.|||.. +.|  .+|.|.||..+++.
T Consensus       173 stke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  173 STKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             ehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            99999999999999954 444  68999999887544

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

Probab=99.90  E-value=2.5e-22  Score=169.70  Aligned_cols=158  Identities=31%  Similarity=0.540  Sum_probs=132.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ...++|||+|||.++.+.+|++||-+||.|.+|.|+     ..||||+|+++.+|+.||..-+|..+  +|..|.|+|+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdy--dg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDY--DGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhccccccc--CcceEEEEecc
Confidence            456899999999999999999999999999999995     67999999999999999999999999  89999999998


Q ss_pred             cccCCCCCCC----------CCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-ccEEEEEEcCH
Q 014384          127 HERGIRRPGG----------GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-RNFAFVQYEVQ  195 (425)
Q Consensus       127 ~~~~~~~~~~----------~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-~g~afV~f~~~  195 (425)
                      .........+          +.......+.-.....|+|.+| |...+|++|++++.+.|.|....+. -+++.|+|...
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGL-p~SgSWQDLKDHmReaGdvCfadv~rDg~GvV~~~r~  160 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGL-PPSGSWQDLKDHMREAGDVCFADVQRDGVGVVEYLRK  160 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecC-CCCCchHHHHHHHHhhCCeeeeeeecccceeeeeeeh
Confidence            7642211111          0111122233344568999999 7888899999999999999999987 46999999999


Q ss_pred             HHHHHHHHHcCCCccCC
Q 014384          196 EDATRALDATNMSKLTD  212 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g  212 (425)
                      ++++-|+..|+...+.-
T Consensus       161 eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  161 EDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             hhHHHHHHhhccccccC
Confidence            99999999999887763

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

Probab=99.90  E-value=2.5e-23  Score=201.47  Aligned_cols=168  Identities=27%  Similarity=0.538  Sum_probs=143.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .||||++||+.+|.++|.++|+.+|+|..+.+        ++||+||.|.-.++++.|+..+++..|  .|+.|.|.++.
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf--~Gr~l~v~~A~   83 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKF--EGRILNVDPAK   83 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcc--cceeccccccc
Confidence            79999999999999999999999999998887        489999999999999999999999999  89999999987


Q ss_pred             cccCCC--CCCCCCCCCCC--------CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEE
Q 014384          127 HERGIR--RPGGGSSARRP--------STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAF  189 (425)
Q Consensus       127 ~~~~~~--~~~~~~~~~~~--------~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~af  189 (425)
                      ...-..  ..+.+......        .....+...|.|.|| |+.+...+|+.+|+.||.|..|.||       .||||
T Consensus        84 ~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNL-Pf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaF  162 (678)
T KOG0127|consen   84 KRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNL-PFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAF  162 (678)
T ss_pred             ccccchhcccccchhhhcccccCCcchhhccCccceEEeecC-CcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEE
Confidence            544221  11111100000        112344789999999 9999999999999999999999997       47999


Q ss_pred             EEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       190 V~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      |+|....+|..|++.+|+.+|+|++|.|.||..+..
T Consensus       163 V~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  163 VQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             EEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            999999999999999999999999999999998753

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

Probab=99.89  E-value=1.5e-22  Score=206.63  Aligned_cols=149  Identities=26%  Similarity=0.418  Sum_probs=127.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      +...++|||+|||.++|+++|.++|++||.|.+|+|       ++|||||+|.+.++|++||+.||+..|. .|+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~-~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIR-PGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeec-CCcccccc
Confidence            345689999999999999999999999999999988       3899999999999999999999999883 47887776


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc-EEEEEE---------eccEEEEEEc
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK-IISVRI---------RRNFAFVQYE  193 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~-v~~v~~---------~~g~afV~f~  193 (425)
                      ++.                      ..++|||+|| |..+++++|.++|.+++. ++.+.+         .+|||||+|.
T Consensus       134 ~S~----------------------~~~rLFVgNL-P~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~  190 (578)
T TIGR01648       134 ISV----------------------DNCRLFVGGI-PKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYE  190 (578)
T ss_pred             ccc----------------------cCceeEeecC-CcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcC
Confidence            542                      2478999999 888899999999999863 444333         2689999999


Q ss_pred             CHHHHHHHHHHcCC--CccCCeEEEEEEeeeC
Q 014384          194 VQEDATRALDATNM--SKLTDRVISVEYAVRD  223 (425)
Q Consensus       194 ~~~~A~~A~~~l~g--~~~~g~~i~v~~a~~~  223 (425)
                      ++++|..|+..|+.  ..+.|+.|.|.|+..+
T Consensus       191 s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~  222 (578)
T TIGR01648       191 SHRAAAMARRKLMPGRIQLWGHVIAVDWAEPE  222 (578)
T ss_pred             CHHHHHHHHHHhhccceEecCceEEEEeeccc
Confidence            99999999998864  4578999999998765

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

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

Probab=99.89  E-value=1.1e-22  Score=180.40  Aligned_cols=154  Identities=23%  Similarity=0.485  Sum_probs=138.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....+.|.|.-||.++|+++|+.||+..|+|+.|+|        +.||+||.|-++++|++|+..|||..|  ..++|+|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrL--Q~KTIKV  115 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRL--QNKTIKV  115 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceee--ccceEEE
Confidence            445578999999999999999999999999999999        379999999999999999999999999  8999999


Q ss_pred             EEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--------eccEEEEEEcC
Q 014384          123 EWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEV  194 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--------~~g~afV~f~~  194 (425)
                      .||.+...                ......|||.+| |..+++.+|+++|.+||.|..-+|        .+|.+||.|..
T Consensus       116 SyARPSs~----------------~Ik~aNLYvSGl-PktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDK  178 (360)
T KOG0145|consen  116 SYARPSSD----------------SIKDANLYVSGL-PKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDK  178 (360)
T ss_pred             EeccCChh----------------hhcccceEEecC-CccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecc
Confidence            99987652                333467999999 899999999999999999876665        38999999999


Q ss_pred             HHHHHHHHHHcCCCccCC--eEEEEEEeeeC
Q 014384          195 QEDATRALDATNMSKLTD--RVISVEYAVRD  223 (425)
Q Consensus       195 ~~~A~~A~~~l~g~~~~g--~~i~v~~a~~~  223 (425)
                      ..+|+.||+.|||..--|  .+|.|.||..+
T Consensus       179 r~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  179 RIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             hhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            999999999999998877  57999999875

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

Probab=99.88  E-value=8.3e-22  Score=190.98  Aligned_cols=167  Identities=26%  Similarity=0.519  Sum_probs=137.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      --.|.|.|||+.+.+.+|..+|+.||.|.+|.|+       .|||||+|....+|..||..|||..|  +|++|.|.||.
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i--~gR~VAVDWAV  194 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKI--DGRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCcee--cCceeEEeeec
Confidence            5689999999999999999999999999999994       69999999999999999999999999  89999999986


Q ss_pred             cccCCCCCCC-----------------------------------------C----------CC---------C------
Q 014384          127 HERGIRRPGG-----------------------------------------G----------SS---------A------  140 (425)
Q Consensus       127 ~~~~~~~~~~-----------------------------------------~----------~~---------~------  140 (425)
                      .+......+.                                         .          ..         .      
T Consensus       195 ~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~  274 (678)
T KOG0127|consen  195 DKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKK  274 (678)
T ss_pred             ccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccC
Confidence            5542211100                                         0          00         0      


Q ss_pred             --------CCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHH
Q 014384          141 --------RRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDA  204 (425)
Q Consensus       141 --------~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~  204 (425)
                              ...........+|||.|| |+.+++++|.++|.+||.|.++.|.        +|.|||.|.++.+|.+||..
T Consensus       275 ~~~k~~q~k~~~en~~~~~tVFvRNL-~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~  353 (678)
T KOG0127|consen  275 ESDKKAQNKTTRENITEGKTVFVRNL-PFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEA  353 (678)
T ss_pred             cccchhccccccccccccceEEEecC-CccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHh
Confidence                    000111223379999999 9999999999999999999999884        78999999999999999987


Q ss_pred             c-----CC-CccCCeEEEEEEeeeC
Q 014384          205 T-----NM-SKLTDRVISVEYAVRD  223 (425)
Q Consensus       205 l-----~g-~~~~g~~i~v~~a~~~  223 (425)
                      .     .| ..|+|+.|.|..|...
T Consensus       354 Aspa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  354 ASPASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             cCccCCCceEEEeccEEeeeeccch
Confidence            6     23 6788999999998664

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

Probab=99.88  E-value=1e-21  Score=186.51  Aligned_cols=149  Identities=26%  Similarity=0.422  Sum_probs=132.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...+.||||.||.++.|++|.-||++.|+|-++.|+        +|||||.|.+.++|+.|+..||+.+|- .|+.|.|.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir-~GK~igvc  159 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR-PGKLLGVC  159 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcccc-CCCEeEEE
Confidence            445899999999999999999999999999999983        899999999999999999999999996 79999999


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc-EEEEEEe---------ccEEEEEEc
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK-IISVRIR---------RNFAFVQYE  193 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~-v~~v~~~---------~g~afV~f~  193 (425)
                      .+..                      ++.|||+|| |...+.++|.+.|.+.++ |++|.+.         +|||||+|.
T Consensus       160 ~Sva----------------------n~RLFiG~I-PK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe  216 (506)
T KOG0117|consen  160 VSVA----------------------NCRLFIGNI-PKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYE  216 (506)
T ss_pred             Eeee----------------------cceeEeccC-CccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEee
Confidence            7654                      589999999 888889999999999985 6666663         689999999


Q ss_pred             CHHHHHHHHHHcCC--CccCCeEEEEEEeeeCC
Q 014384          194 VQEDATRALDATNM--SKLTDRVISVEYAVRDD  224 (425)
Q Consensus       194 ~~~~A~~A~~~l~g--~~~~g~~i~v~~a~~~~  224 (425)
                      ++..|..|-..|-.  .++-|..|.|.||....
T Consensus       217 ~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~  249 (506)
T KOG0117|consen  217 SHRAAAMARRKLMPGKIKLWGNAITVDWAEPEE  249 (506)
T ss_pred             cchhHHHHHhhccCCceeecCCcceeeccCccc
Confidence            99999999887754  45669999999998864

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.86  E-value=1.3e-21  Score=195.47  Aligned_cols=159  Identities=26%  Similarity=0.540  Sum_probs=139.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ++|||.||++.+|.++|..+|.+.|.|..|.|.           .|||||+|.++++|+.|++.|||+.|  +|+.|.|.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvl--dGH~l~lk  593 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVL--DGHKLELK  593 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCcee--cCceEEEE
Confidence            449999999999999999999999999999872           49999999999999999999999999  99999999


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQ  195 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~  195 (425)
                      ++......  ..     ..........+.|+|.|| |+.++-.+|+++|..||.|..|.|+        +|||||+|-++
T Consensus       594 ~S~~k~~~--~~-----gK~~~~kk~~tKIlVRNi-pFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~  665 (725)
T KOG0110|consen  594 ISENKPAS--TV-----GKKKSKKKKGTKILVRNI-PFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTP  665 (725)
T ss_pred             eccCcccc--cc-----ccccccccccceeeeecc-chHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCc
Confidence            99822210  00     112222333689999999 9999999999999999999999997        57999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          196 EDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .+|..|+++|..+.+.|+.|.++||...
T Consensus       666 ~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  666 REAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             HHHHHHHHhhcccceechhhheehhccc
Confidence            9999999999999999999999999875

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.82  E-value=1.3e-20  Score=174.48  Aligned_cols=165  Identities=19%  Similarity=0.440  Sum_probs=138.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .-++.||||.|.+.+.|+.|+..|..||+|+.|.|+        +|||||+|+-+|.|..|++.|||..+  .|+.|+|.
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~ml--GGRNiKVg  188 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQML--GGRNIKVG  188 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccc--cCcccccc
Confidence            346899999999999999999999999999999993        99999999999999999999999999  59999998


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQ  195 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~  195 (425)
                      ........+ +    ...........-+.|||..+ ..+.+++||+..|+-||+|+.|.+.        +||+||+|.+.
T Consensus       189 rPsNmpQAQ-p----iID~vqeeAk~fnRiYVaSv-HpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~  262 (544)
T KOG0124|consen  189 RPSNMPQAQ-P----IIDMVQEEAKKFNRIYVASV-HPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL  262 (544)
T ss_pred             CCCCCcccc-h----HHHHHHHHHHhhheEEeeec-CCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccc
Confidence            543322000 0    00001122344579999999 5677799999999999999999995        78999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          196 EDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ....+|+..||-..++|.-|.|..+....
T Consensus       263 qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  263 QSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             cchHHHhhhcchhhcccceEecccccCCC
Confidence            99999999999999999999998876653

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

Probab=99.82  E-value=7.3e-20  Score=173.18  Aligned_cols=212  Identities=19%  Similarity=0.314  Sum_probs=154.7

Q ss_pred             eeEEEEeCCCCcccccccCCcceeecccccccchhhhh----hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE
Q 014384           11 HYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIA----AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM   86 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i   86 (425)
                      .+|||.|.+...+..+.+.--.....+-.....++...    +.....++|||+.|+..+||.+|+++|.+||.|++|.|
T Consensus        77 gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~i  156 (510)
T KOG0144|consen   77 GCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYI  156 (510)
T ss_pred             ceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhh
Confidence            48999998876544333221111111111111111110    11134689999999999999999999999999999998


Q ss_pred             -------eCCEEEEEEcCHHHHHHHHHhcCCC-eecCCCcEEEEEEeccccCCCCC-------------------CC---
Q 014384           87 -------KSGFAFIYMDDERDAEDAIRGLDRT-EFGRKGRRLRVEWTKHERGIRRP-------------------GG---  136 (425)
Q Consensus        87 -------~kg~aFV~F~~~~~A~~A~~~lng~-~ig~~gr~l~V~~a~~~~~~~~~-------------------~~---  136 (425)
                             ++|||||.|.+.+.|..||++|||. .+.....+|.|.||..++.....                   ..   
T Consensus       157 lrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~  236 (510)
T KOG0144|consen  157 LRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLAS  236 (510)
T ss_pred             eecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhh
Confidence                   4899999999999999999999996 33237789999999766521000                   00   


Q ss_pred             -----------------------------------------------------------C-----------CCC------
Q 014384          137 -----------------------------------------------------------G-----------SSA------  140 (425)
Q Consensus       137 -----------------------------------------------------------~-----------~~~------  140 (425)
                                                                                 +           ...      
T Consensus       237 ~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~  316 (510)
T KOG0144|consen  237 LGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSAS  316 (510)
T ss_pred             hhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCcccc
Confidence                                                                       0           000      


Q ss_pred             --------------------------------------------------------------------------------
Q 014384          141 --------------------------------------------------------------------------------  140 (425)
Q Consensus       141 --------------------------------------------------------------------------------  140 (425)
                                                                                                      
T Consensus       317 ~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~  396 (510)
T KOG0144|consen  317 APSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANL  396 (510)
T ss_pred             CccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhh
Confidence                                                                                            


Q ss_pred             ------------------CCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcC
Q 014384          141 ------------------RRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEV  194 (425)
Q Consensus       141 ------------------~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~  194 (425)
                                        .......+.+..|||.+| |...-+.+|...|..||.|+..++.        +.|+||.|++
T Consensus       397 a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhl-Pqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen  475 (510)
T KOG0144|consen  397 AAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHL-PQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYEN  475 (510)
T ss_pred             cccchhhhhHhhhhhhcccCccccCCCccceeeeeC-chhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccc
Confidence                              000223344578999999 8888899999999999999877763        5699999999


Q ss_pred             HHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          195 QEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       195 ~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..+|.+||..|||..|+.+.++|......
T Consensus       476 ~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  476 AQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             hhhhHHHHHHhcchhhccccceEEeeecc
Confidence            99999999999999999999999887664

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

Probab=99.82  E-value=2e-19  Score=175.83  Aligned_cols=143  Identities=24%  Similarity=0.486  Sum_probs=131.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..||||   ++||+..|.++|+.+|+|..|.+.     .|||||.|.++++|+.||..||...|  +|++|.|.|+....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~--~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVL--KGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCccc--CCcEEEeehhccCC
Confidence            479999   999999999999999999999984     69999999999999999999999999  89999999987543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHH
Q 014384          130 GIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALD  203 (425)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~  203 (425)
                                           ..|||.|| +..++..+|.++|+.||+|+.|.+.      +|| ||+|+++++|.+|++
T Consensus        77 ---------------------~~~~i~nl-~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~  133 (369)
T KOG0123|consen   77 ---------------------SLVFIKNL-DESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIE  133 (369)
T ss_pred             ---------------------ceeeecCC-CcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHH
Confidence                                 11999999 5777899999999999999999995      679 999999999999999


Q ss_pred             HcCCCccCCeEEEEEEeeeCCC
Q 014384          204 ATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       204 ~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      .|||..+.|+.|.|.....+..
T Consensus       134 ~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen  134 KLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             HhcCcccCCCeeEEeeccchhh
Confidence            9999999999999998877543

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

Probab=99.81  E-value=1.3e-18  Score=149.96  Aligned_cols=79  Identities=37%  Similarity=0.516  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .......+|.|.|| .+.|+.++|..+|++||.|.+|.|+        +|||||.|.+..+|++|+++|+|..|+|+.|.
T Consensus         8 Pdv~gm~SLkVdNL-TyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNL-TYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCcccceeEEecce-eccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            34555689999999 8999999999999999999999996        68999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |++|.-..
T Consensus        87 Vq~arygr   94 (256)
T KOG4207|consen   87 VQMARYGR   94 (256)
T ss_pred             ehhhhcCC
Confidence            99987643

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

Probab=99.80  E-value=3.3e-19  Score=174.36  Aligned_cols=196  Identities=20%  Similarity=0.310  Sum_probs=155.5

Q ss_pred             eeeeEEEEeCCCCcccccc--cCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE
Q 014384            9 QCHYLLIVYSHSVWPVQKK--YLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM   86 (425)
Q Consensus         9 ~~~y~~i~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i   86 (425)
                      .+.|+++.|.....+-.+.  +....+...++...+       .+.+...|||.||++.+|...|.++|+.||+|..|++
T Consensus        36 slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~-------s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv  108 (369)
T KOG0123|consen   36 SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMW-------SQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKV  108 (369)
T ss_pred             ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeeh-------hccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEE
Confidence            4679999997755433222  112222222233333       2233334999999999999999999999999999999


Q ss_pred             ------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCC
Q 014384           87 ------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDP  160 (425)
Q Consensus        87 ------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p  160 (425)
                            ++|| ||+|+++++|.+|+..|||..+  .|+.|.|...........+.       .. .......++|.|+ +
T Consensus       109 ~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll--~~kki~vg~~~~~~er~~~~-------~~-~~~~~t~v~vk~~-~  176 (369)
T KOG0123|consen  109 ATDENGSKGY-FVQFESEESAKKAIEKLNGMLL--NGKKIYVGLFERKEEREAPL-------GE-YKKRFTNVYVKNL-E  176 (369)
T ss_pred             EEcCCCceee-EEEeCCHHHHHHHHHHhcCccc--CCCeeEEeeccchhhhcccc-------cc-hhhhhhhhheecc-c
Confidence                  4899 9999999999999999999999  89999998877654222111       11 3455678899999 7


Q ss_pred             CCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          161 YHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..++++.|.++|..||.|..+.++       ++|+||.|.++++|..|++.|++..+++..+.|.-+..+
T Consensus       177 ~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk  246 (369)
T KOG0123|consen  177 EDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQKK  246 (369)
T ss_pred             cccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCCccceeecccccc
Confidence            889999999999999999999985       679999999999999999999999999999999887763

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.80  E-value=1.4e-18  Score=152.94  Aligned_cols=167  Identities=22%  Similarity=0.418  Sum_probs=137.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEE-----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLER----LFRRYGKVDRVDM-----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~----lF~~~G~V~~v~i-----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .++.||||.||+..+..++|..    ||++||+|.+|..     .+|.|||.|.+.+.|-.|+..|+|..|  -|+++.|
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpF--ygK~mri   84 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPF--YGKPMRI   84 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcc--cCchhhe
Confidence            4455999999999999999888    9999999999988     389999999999999999999999999  6999999


Q ss_pred             EEeccccCCCCCCC------------------------CCC------CCC----CCCCCCCCcEEEEEcCCCCCCCHHHH
Q 014384          123 EWTKHERGIRRPGG------------------------GSS------ARR----PSTNTRPSKTLFVINFDPYHTRTRDL  168 (425)
Q Consensus       123 ~~a~~~~~~~~~~~------------------------~~~------~~~----~~~~~~~~~~l~V~nl~p~~~~~~~L  168 (425)
                      +||+..........                        ...      ...    .....+++.+||+.|| |..++.+.|
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~ni-P~es~~e~l  163 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNI-PSESESEML  163 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecC-CcchhHHHH
Confidence            99976542211100                        000      000    0234678889999999 888989999


Q ss_pred             HhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccC-CeEEEEEEee
Q 014384          169 ERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLT-DRVISVEYAV  221 (425)
Q Consensus       169 ~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a~  221 (425)
                      ..+|.+|.....|.+.   .+.|||+|.+...|..|...|++..|. ...+.|.++.
T Consensus       164 ~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  164 SDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999988888775   679999999999999999999998887 7888887764

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

Probab=99.80  E-value=2.8e-18  Score=144.41  Aligned_cols=76  Identities=38%  Similarity=0.631  Sum_probs=71.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..+++||||||+..+|+.||+.+|.+||+|..|+|   +.|||||||+++.+|++|+..|||+.|  +|..|.|+++...
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~--cG~r~rVE~S~G~   85 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDI--CGSRIRVELSTGR   85 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccc--cCceEEEEeecCC
Confidence            34789999999999999999999999999999999   589999999999999999999999999  9999999999876


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        86 ~   86 (195)
T KOG0107|consen   86 P   86 (195)
T ss_pred             c
Confidence            5

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

Probab=99.80  E-value=4.2e-18  Score=174.31  Aligned_cols=116  Identities=14%  Similarity=0.243  Sum_probs=86.0

Q ss_pred             eeeEEEEeCCCCccccccc-CCcceeecc-----cccccc--h---hhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhc
Q 014384           10 CHYLLIVYSHSVWPVQKKY-LPRRLYVLG-----FRRSHS--Q---LSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRY   78 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~-~~~~~~~~~-----~~~~~~--~---~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~   78 (425)
                      ..||||.|.+...+..+.. ++..+....     ......  .   ..........++|||+||++++++++|+++|+.|
T Consensus       149 kGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~F  228 (612)
T TIGR01645       149 KGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF  228 (612)
T ss_pred             CCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhc
Confidence            5699999998776555542 222221111     100000  0   0001122345799999999999999999999999


Q ss_pred             CCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           79 GKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        79 G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      |+|..|.|        ++|||||+|.+.++|.+||..|||..|  .|+.|.|.++..
T Consensus       229 G~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~el--gGr~LrV~kAi~  283 (612)
T TIGR01645       229 GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDL--GGQYLRVGKCVT  283 (612)
T ss_pred             CCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCee--CCeEEEEEecCC
Confidence            99999988        379999999999999999999999999  799999998764

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.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.79  E-value=8.7e-20  Score=178.03  Aligned_cols=170  Identities=29%  Similarity=0.444  Sum_probs=142.5

Q ss_pred             hhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           48 AAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        48 ~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ..++...+|||+--|...+++.+|++||+.+|+|.+|.|        ++|+|||+|.|.+.+..|| .|.|..+  .|.+
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrl--lg~p  249 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRL--LGVP  249 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcc--cCce
Confidence            345567799999999999999999999999999999988        4899999999999999999 9999999  7999


Q ss_pred             EEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEE
Q 014384          120 LRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQ  191 (425)
Q Consensus       120 l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~  191 (425)
                      |.|+.....+......  ..+........|...|||+|| ...+++++|..+|+.||.|..|.++        +||+||+
T Consensus       250 v~vq~sEaeknr~a~~--s~a~~~k~~~~p~~rl~vgnL-HfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~  326 (549)
T KOG0147|consen  250 VIVQLSEAEKNRAANA--SPALQGKGFTGPMRRLYVGNL-HFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFIT  326 (549)
T ss_pred             eEecccHHHHHHHHhc--cccccccccccchhhhhhccc-ccCchHHHHhhhccCcccceeeeeccccccccccCcceEE
Confidence            9999876655331111  111111222333344999999 7889999999999999999999885        6899999


Q ss_pred             EcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          192 YEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       192 f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      |.+.++|.+|+++|||.+|.|+.|+|......
T Consensus       327 f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  327 FVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             EecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            99999999999999999999999999886654

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

Probab=99.79  E-value=5.3e-18  Score=142.75  Aligned_cols=77  Identities=29%  Similarity=0.427  Sum_probs=71.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ...++|||+|| +..+++.+|+.+|..||+|..|+|.   .|||||||+++.||.+|+..|+|..|+|..|.|++.....
T Consensus         8 ~~~~kVYVGnL-~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen    8 NGNTKVYVGNL-GSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CCCceEEeccC-CCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            34689999999 7899999999999999999999994   7899999999999999999999999999999999998764


Q ss_pred             C
Q 014384          225 D  225 (425)
Q Consensus       225 ~  225 (425)
                      .
T Consensus        87 r   87 (195)
T KOG0107|consen   87 R   87 (195)
T ss_pred             c
Confidence            4

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.77  E-value=3.1e-18  Score=167.29  Aligned_cols=169  Identities=24%  Similarity=0.466  Sum_probs=130.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .++..||||||-.++|+++|..+|+.||.|+.|.+        ++||+||+|.+.++|.+|+..|||.+|  -|+.|+|.
T Consensus       276 ~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfel--AGr~ikV~  353 (549)
T KOG0147|consen  276 GPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFEL--AGRLIKVS  353 (549)
T ss_pred             cchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcccee--cCceEEEE
Confidence            34555999999999999999999999999999988        389999999999999999999999888  89999997


Q ss_pred             EeccccCCCCC-------------C-----CC-----------CC----------------------CC-----CCCCCC
Q 014384          124 WTKHERGIRRP-------------G-----GG-----------SS----------------------AR-----RPSTNT  147 (425)
Q Consensus       124 ~a~~~~~~~~~-------------~-----~~-----------~~----------------------~~-----~~~~~~  147 (425)
                      ...........             +     ++           ..                      ..     ....+.
T Consensus       354 ~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~  433 (549)
T KOG0147|consen  354 VVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPA  433 (549)
T ss_pred             EeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcc
Confidence            54322111100             0     00           00                      00     001112


Q ss_pred             -------CCCcEEEEEcC-CCCCCCH--------HHHHhhhccCCcEEEEEEec---cEEEEEEcCHHHHHHHHHHcCCC
Q 014384          148 -------RPSKTLFVINF-DPYHTRT--------RDLERHFEPYGKIISVRIRR---NFAFVQYEVQEDATRALDATNMS  208 (425)
Q Consensus       148 -------~~~~~l~V~nl-~p~~~~~--------~~L~~~f~~~G~v~~v~~~~---g~afV~f~~~~~A~~A~~~l~g~  208 (425)
                             .+..|+.+.|+ +|...|+        ++|.+.+.+||+|..|.+-+   |+.||.|.+.++|..|+.+|||.
T Consensus       434 ~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgr  513 (549)
T KOG0147|consen  434 DASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGR  513 (549)
T ss_pred             ccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhh
Confidence                   55677778776 4433332        66778889999999999953   79999999999999999999999


Q ss_pred             ccCCeEEEEEEeee
Q 014384          209 KLTDRVISVEYAVR  222 (425)
Q Consensus       209 ~~~g~~i~v~~a~~  222 (425)
                      +|.|+.|++.|-..
T Consensus       514 WF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  514 WFAGRMITAKYLPL  527 (549)
T ss_pred             hhccceeEEEEeeh
Confidence            99999999998654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.73  E-value=2.7e-18  Score=160.65  Aligned_cols=154  Identities=16%  Similarity=0.148  Sum_probs=111.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ...|.|.||.+.+|.++|..||+.+|+|.++.|.           ...|||.|.|...+..|.+..|.++|   ++.|.|
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfv---draliv   83 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFV---DRALIV   83 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceee---eeeEEE
Confidence            4489999999999999999999999999998882           57999999999999999987787777   555555


Q ss_pred             E-EeccccCCC----------------CCCCCCC---------CCCC----CCCC----------CCCcEEEEEcCCCCC
Q 014384          123 E-WTKHERGIR----------------RPGGGSS---------ARRP----STNT----------RPSKTLFVINFDPYH  162 (425)
Q Consensus       123 ~-~a~~~~~~~----------------~~~~~~~---------~~~~----~~~~----------~~~~~l~V~nl~p~~  162 (425)
                      - +........                .+++-..         ..+.    .+..          ....+|+|++| +..
T Consensus        84 ~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl-~~~  162 (479)
T KOG4676|consen   84 RPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSL-ISA  162 (479)
T ss_pred             EecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcc-hhh
Confidence            4 433322111                0000000         0000    0000          11156888888 666


Q ss_pred             CCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 014384          163 TRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTD  212 (425)
Q Consensus       163 ~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g  212 (425)
                      +...++..+|+.+|.|.+..+.    .-+|.|+|........|+. ++|.++.-
T Consensus       163 ~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k~  215 (479)
T KOG4676|consen  163 AILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERKR  215 (479)
T ss_pred             hcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhhh
Confidence            6688999999999999988885    3488899999999999997 56666653

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.72  E-value=1.7e-17  Score=156.96  Aligned_cols=158  Identities=19%  Similarity=0.429  Sum_probs=133.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++|||++|++.+|++.|.+.|.+||+|.+|.++        +||+||+|++++.+..+|. .....|  +|+.|.+.-
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~--dgr~ve~k~   81 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKL--DGRSVEPKR   81 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-cccccc--CCcccccee
Confidence            67899999999999999999999999999999885        5999999999999999984 334445  789888887


Q ss_pred             eccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHH
Q 014384          125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQE  196 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~  196 (425)
                      |..........          .......|||++| +..+++++|++.|++||.|..+.++        ++|+||.|.+++
T Consensus        82 av~r~~~~~~~----------~~~~tkkiFvGG~-~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~  150 (311)
T KOG4205|consen   82 AVSREDQTKVG----------RHLRTKKIFVGGL-PPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSED  150 (311)
T ss_pred             ccCcccccccc----------cccceeEEEecCc-CCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecccc
Confidence            76544222221          1225779999999 8899999999999999998888875        789999999999


Q ss_pred             HHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          197 DATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       197 ~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      .+.+++. +..+.|+|+.+.|..|.++..
T Consensus       151 sVdkv~~-~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  151 SVDKVTL-QKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             ccceecc-cceeeecCceeeEeeccchhh
Confidence            9999986 678899999999999988653

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

Probab=99.71  E-value=8.3e-16  Score=132.68  Aligned_cols=78  Identities=37%  Similarity=0.647  Sum_probs=72.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ....+++|.|-||.+.+|.++|..+|++||.|-+|.|+        +|||||-|.+..+|++||++|+|..|  +|+.|.
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l--dgRelr   86 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL--DGRELR   86 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceee--ccceee
Confidence            34678999999999999999999999999999999993        89999999999999999999999999  999999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |++|....
T Consensus        87 Vq~arygr   94 (256)
T KOG4207|consen   87 VQMARYGR   94 (256)
T ss_pred             ehhhhcCC
Confidence            99987643

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=1.8e-17  Score=147.98  Aligned_cols=173  Identities=22%  Similarity=0.432  Sum_probs=139.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCee-cCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEF-GRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~i-g~~gr~l~V  122 (425)
                      ....++||||.|...-.|+|+..||..||.|++|.+       +||+|||.|.+..+|..||..|+|..- ..-...|.|
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV   95 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEE
Confidence            346789999999999999999999999999999998       499999999999999999999999643 225668999


Q ss_pred             EEeccccCCC--------------CC----CC------------------------------------------------
Q 014384          123 EWTKHERGIR--------------RP----GG------------------------------------------------  136 (425)
Q Consensus       123 ~~a~~~~~~~--------------~~----~~------------------------------------------------  136 (425)
                      +|+...++..              .+    .+                                                
T Consensus        96 K~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~  175 (371)
T KOG0146|consen   96 KFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLA  175 (371)
T ss_pred             EeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccc
Confidence            9986654110              00    00                                                


Q ss_pred             --------C--------------------CC----------CC-------------------------------------
Q 014384          137 --------G--------------------SS----------AR-------------------------------------  141 (425)
Q Consensus       137 --------~--------------------~~----------~~-------------------------------------  141 (425)
                              +                    .+          ..                                     
T Consensus       176 A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~A  255 (371)
T KOG0146|consen  176 AAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAA  255 (371)
T ss_pred             cCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhh
Confidence                    0                    00          00                                     


Q ss_pred             ---------------------CCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEE
Q 014384          142 ---------------------RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQY  192 (425)
Q Consensus       142 ---------------------~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f  192 (425)
                                           ......+.++.|||..| |....+.+|.+.|-.||.|+..++.        +.|+||.|
T Consensus       256 aypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHL-PQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSf  334 (371)
T KOG0146|consen  256 AYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHL-PQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSF  334 (371)
T ss_pred             hcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeC-chhhccHHHHHHhccccceeeeeeeehhccccccceeeEec
Confidence                                 00123455699999999 8888899999999999999888773        77999999


Q ss_pred             cCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          193 EVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       193 ~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      .++..|+.||..|||..|+=+.|+|....+++
T Consensus       335 DNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  335 DNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             CCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            99999999999999999999999998876653

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.70  E-value=2.7e-16  Score=137.19  Aligned_cols=162  Identities=23%  Similarity=0.376  Sum_probs=123.2

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecC-CCc
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGR-KGR  118 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~-~gr  118 (425)
                      .+....+||||.+||.++...+|..||..|--.+.+.|+         +-+|||.|.+..+|.+|+.+|||+.|-. .+.
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCc
Confidence            455668999999999999999999999998666666662         4699999999999999999999998843 588


Q ss_pred             EEEEEEeccccCCCCCCCCC-----------------------------------------CCCCC--------------
Q 014384          119 RLRVEWTKHERGIRRPGGGS-----------------------------------------SARRP--------------  143 (425)
Q Consensus       119 ~l~V~~a~~~~~~~~~~~~~-----------------------------------------~~~~~--------------  143 (425)
                      .|+|++|+...+.++.....                                         .+...              
T Consensus       109 tLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~  188 (284)
T KOG1457|consen  109 TLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDS  188 (284)
T ss_pred             eeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhh
Confidence            99999987654322111100                                         00000              


Q ss_pred             ---------------CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--cc--EEEEEEcCHHHHHHHHHH
Q 014384          144 ---------------STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RN--FAFVQYEVQEDATRALDA  204 (425)
Q Consensus       144 ---------------~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g--~afV~f~~~~~A~~A~~~  204 (425)
                                     ........||||.|| ...+++++|+++|..|-....++|.  .|  .||++|++.+.|..|+..
T Consensus       189 ~~P~a~a~l~ks~q~~~~~~acstlfianl-~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~  267 (284)
T KOG1457|consen  189 KAPSANAHLEKSSQGGSGARACSTLFIANL-GPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNH  267 (284)
T ss_pred             cCCcccchhhhhhcccccchhhhhHhhhcc-CCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHH
Confidence                           000111258999999 5678899999999999877777774  33  899999999999999999


Q ss_pred             cCCCccC
Q 014384          205 TNMSKLT  211 (425)
Q Consensus       205 l~g~~~~  211 (425)
                      |+|..|.
T Consensus       268 lqg~~~s  274 (284)
T KOG1457|consen  268 LQGNLLS  274 (284)
T ss_pred             hhcceec
Confidence            9987653

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=5.1e-16  Score=153.83  Aligned_cols=171  Identities=20%  Similarity=0.326  Sum_probs=132.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ......|||+|||..+++.++.+++..||.+....+        ++||||.+|.++.-...|+..|||+.+  .++.|.|
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~l--gd~~lvv  363 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQL--GDKKLVV  363 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhh--cCceeEe
Confidence            344578999999999999999999999999887666        489999999999999999999999999  5899999


Q ss_pred             EEeccccCCCCCCCC--------CCCCCCCCCCCCCcEEEEEcC-CCCCC-CH-------HHHHhhhccCCcEEEEEEe-
Q 014384          123 EWTKHERGIRRPGGG--------SSARRPSTNTRPSKTLFVINF-DPYHT-RT-------RDLERHFEPYGKIISVRIR-  184 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~--------~~~~~~~~~~~~~~~l~V~nl-~p~~~-~~-------~~L~~~f~~~G~v~~v~~~-  184 (425)
                      +.|............        ...........+...|.+.|+ ++... .+       ++|+..+.+||.|..|.++ 
T Consensus       364 q~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr  443 (500)
T KOG0120|consen  364 QRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPR  443 (500)
T ss_pred             ehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCC
Confidence            988765433322221        001112344555666666554 11111 11       3456677899999999996 


Q ss_pred             ----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          185 ----------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       185 ----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                                .|..||+|.+.++|+.|..+|+|.+|.|++|...|...+
T Consensus       444 ~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  444 PYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             CCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence                      368999999999999999999999999999999987653

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

Probab=99.65  E-value=8.9e-16  Score=131.12  Aligned_cols=77  Identities=27%  Similarity=0.531  Sum_probs=71.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+||++.+|+++|+++|.+||+|..|.|.        +|||||+|.+.++|++||..||+..|  +|+.|+|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i--~Gr~l~V  108 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKEL--NGRHIRV  108 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEE
Confidence            3557899999999999999999999999999999883        79999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      +|+....
T Consensus       109 ~~a~~~~  115 (144)
T PLN03134        109 NPANDRP  115 (144)
T ss_pred             EeCCcCC
Confidence            9997654

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.63  E-value=1.6e-15  Score=152.34  Aligned_cols=168  Identities=25%  Similarity=0.391  Sum_probs=135.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-CC-EEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-SG-FAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-kg-~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ....+.|+|+|||..+..++|..+|..||.|..|.|+ -| .|+|+|-++.+|.+|+..|+...+  ...+|.++|+...
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~--k~~plyle~aP~d  459 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRF--KSAPLYLEWAPED  459 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecCcccceeeeeecCccchHHHHHHhchhhh--ccCccccccChhh
Confidence            3445899999999999999999999999999999885 33 599999999999999999999998  8999999987543


Q ss_pred             cCCCCC------CC---C-----------CCCCCC-------------CCCCCCC-cEEEEEcCCCCCCCHHHHHhhhcc
Q 014384          129 RGIRRP------GG---G-----------SSARRP-------------STNTRPS-KTLFVINFDPYHTRTRDLERHFEP  174 (425)
Q Consensus       129 ~~~~~~------~~---~-----------~~~~~~-------------~~~~~~~-~~l~V~nl~p~~~~~~~L~~~f~~  174 (425)
                      .....+      +.   .           ......             ....... +.|||.|| .+.++.++|..+|..
T Consensus       460 vf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNl-nf~Tt~e~l~~~F~k  538 (725)
T KOG0110|consen  460 VFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNL-NFDTTLEDLEDLFSK  538 (725)
T ss_pred             hccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcC-CcccchhHHHHHHHh
Confidence            321000      00   0           000000             0011122 33999999 799999999999999


Q ss_pred             CCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          175 YGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       175 ~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .|.|..+.|.           .|||||+|.+.++|..|+..|+|+.|+|+.|.|.++.
T Consensus       539 ~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  539 QGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             cCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999884           2899999999999999999999999999999999998

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.63  E-value=1.1e-14  Score=135.08  Aligned_cols=172  Identities=19%  Similarity=0.312  Sum_probs=132.3

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--------VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--------v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      ..+..++.|||.|||.++|.+++.++|++||.|..        |+|       .+|-|.|.|-..+++..|+..|++..|
T Consensus       129 ~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  129 PEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             cccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            34556788999999999999999999999998753        444       289999999999999999999999999


Q ss_pred             cCCCcEEEEEEeccccCCCCCCCCC----------------------CCCCCCCCCCCCcEEEEEcCC-C--CCCC----
Q 014384          114 GRKGRRLRVEWTKHERGIRRPGGGS----------------------SARRPSTNTRPSKTLFVINFD-P--YHTR----  164 (425)
Q Consensus       114 g~~gr~l~V~~a~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~l~V~nl~-p--~~~~----  164 (425)
                        .|+.|+|+.|+-...........                      ............++|.|.|+- |  ...+    
T Consensus       209 --rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~  286 (382)
T KOG1548|consen  209 --RGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLL  286 (382)
T ss_pred             --cCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHH
Confidence              79999999886543211110000                      001112233445788888871 1  1122    


Q ss_pred             ---HHHHHhhhccCCcEEEEEE----eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          165 ---TRDLERHFEPYGKIISVRI----RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       165 ---~~~L~~~f~~~G~v~~v~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                         +++|.+-+.+||.|..|.+    +.|.+.|.|.+.++|..||+.|+|..|+|+.|...+-..
T Consensus       287 ~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  287 NDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence               3566777899999999988    478999999999999999999999999999999887544

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=7.2e-16  Score=123.18  Aligned_cols=84  Identities=24%  Similarity=0.446  Sum_probs=75.9

Q ss_pred             hhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCC
Q 014384           45 LSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRK  116 (425)
Q Consensus        45 ~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~  116 (425)
                      .+...+....+||||+||+..+||++|.+||++||+|..|.|        +.|||||+|...++|+.||..+||..+  +
T Consensus        27 ~e~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrL--d  104 (153)
T KOG0121|consen   27 EEQLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRL--D  104 (153)
T ss_pred             HHHHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcc--c
Confidence            344556778899999999999999999999999999999999        379999999999999999999999999  9


Q ss_pred             CcEEEEEEeccccC
Q 014384          117 GRRLRVEWTKHERG  130 (425)
Q Consensus       117 gr~l~V~~a~~~~~  130 (425)
                      .++|.|.|.-.-..
T Consensus       105 dr~ir~D~D~GF~e  118 (153)
T KOG0121|consen  105 DRPIRIDWDAGFVE  118 (153)
T ss_pred             ccceeeeccccchh
Confidence            99999999766543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=2.6e-15  Score=146.26  Aligned_cols=118  Identities=15%  Similarity=0.220  Sum_probs=84.7

Q ss_pred             eeEEEEeCCCCccccccc-CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--
Q 014384           11 HYLLIVYSHSVWPVQKKY-LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--   87 (425)
                      .||||+|.+...+..+.. +....+ ...................++|||+|||..+|+++|+++|++||+|+.|.|.  
T Consensus       150 GyaFVeF~~~e~A~~Ai~~LnG~~l-~gr~i~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d  228 (346)
T TIGR01659       150 GYAFVDFGSEADSQRAIKNLNGITV-RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD  228 (346)
T ss_pred             cEEEEEEccHHHHHHHHHHcCCCcc-CCceeeeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeec
Confidence            589999988776655552 121111 1110000000011123346789999999999999999999999999998883  


Q ss_pred             ------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           88 ------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        88 ------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                            +|||||+|.+.++|++||+.||++.|...++.|.|.|+....
T Consensus       229 ~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       229 KLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence                  589999999999999999999999883234789999987643

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).

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.58  E-value=5.1e-14  Score=132.96  Aligned_cols=166  Identities=27%  Similarity=0.333  Sum_probs=135.1

Q ss_pred             CceEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           54 MRPIFCGNFE-YDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        54 ~~~l~V~nL~-~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      +.+|.|.||. ..+|.+-|..||+-||.|..|+|   ++..|.|+|.|...|..|++.|+|..|  .|+.|+|.+++...
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l--~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKL--YGKKLRVTLSKHTN  374 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhccee--cCceEEEeeccCcc
Confidence            6889999996 57899999999999999999999   478999999999999999999999999  79999999998655


Q ss_pred             CCCCCCCCCC-------------------CCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE-e---cc
Q 014384          130 GIRRPGGGSS-------------------ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-R---RN  186 (425)
Q Consensus       130 ~~~~~~~~~~-------------------~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~-~---~g  186 (425)
                      ......+...                   .+.-....+|..+|++.|+ |..+++++|+.+|..-|....... .   +.
T Consensus       375 vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsni-p~svsee~lk~~f~~~g~~vkafkff~kd~k  453 (492)
T KOG1190|consen  375 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNI-PPSVSEEDLKNLFQEPGGQVKAFKFFQKDRK  453 (492)
T ss_pred             ccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccC-CcccchhHHHHhhhcCCceEEeeeecCCCcc
Confidence            3221111000                   0111223477789999999 888999999999999886654443 2   46


Q ss_pred             EEEEEEcCHHHHHHHHHHcCCCccCCe-EEEEEEeee
Q 014384          187 FAFVQYEVQEDATRALDATNMSKLTDR-VISVEYAVR  222 (425)
Q Consensus       187 ~afV~f~~~~~A~~A~~~l~g~~~~g~-~i~v~~a~~  222 (425)
                      +|++.+.+.++|..|+..+++..+++. .|.|.|++.
T Consensus       454 mal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  454 MALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             eeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            999999999999999999999998854 899999864

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.57  E-value=4e-14  Score=133.65  Aligned_cols=171  Identities=20%  Similarity=0.240  Sum_probs=136.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-eC--C-EEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-KS--G-FAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-~k--g-~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..-.++|+|+-+-||-+.|.++|++||.|..|.- .|  + .|.|+|.+++.|..|..+|+|..|....+.|+|.|++-.
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt  228 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLT  228 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcc
Confidence            4457889999999999999999999999987655 32  3 578999999999999999999999866788999887543


Q ss_pred             cCCCCCCC-------------C-----------------------CCCCC--------C-CCCCCC--CcEEEEEcCCCC
Q 014384          129 RGIRRPGG-------------G-----------------------SSARR--------P-STNTRP--SKTLFVINFDPY  161 (425)
Q Consensus       129 ~~~~~~~~-------------~-----------------------~~~~~--------~-~~~~~~--~~~l~V~nl~p~  161 (425)
                      ....+...             +                       ..+.+        . .....+  +..|.|.||.++
T Consensus       229 ~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~  308 (492)
T KOG1190|consen  229 DLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEE  308 (492)
T ss_pred             cceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchh
Confidence            31110000             0                       00000        0 111111  578899999999


Q ss_pred             CCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          162 HTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       162 ~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .+|.+.|..+|.-||.|..|.|.   +..|+|+|.+...|+-|+..|+|..+.|+.|+|.+++-.
T Consensus       309 ~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  309 AVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             ccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            99999999999999999999995   569999999999999999999999999999999998764

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.57  E-value=1.9e-13  Score=127.75  Aligned_cols=173  Identities=18%  Similarity=0.186  Sum_probs=139.2

Q ss_pred             cCCCceEEEcCC--CCCCCHHHHHHHHhhcCCeeEEEEe--CC-EEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNF--EYDARQSDLERLFRRYGKVDRVDMK--SG-FAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL--~~~~t~~~L~~lF~~~G~V~~v~i~--kg-~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ...++.|.++=|  -+.+|.+.|.++...+|+|..|.|.  .| .|.|||++.+.|++|.+.|||..|.-...+|+|+||
T Consensus       117 ~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyA  196 (494)
T KOG1456|consen  117 ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYA  196 (494)
T ss_pred             CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEEec
Confidence            344555555544  4678999999999999999998884  23 799999999999999999999999767889999999


Q ss_pred             ccccCCC-----CC--------------CCC------C-----------------------------------------C
Q 014384          126 KHERGIR-----RP--------------GGG------S-----------------------------------------S  139 (425)
Q Consensus       126 ~~~~~~~-----~~--------------~~~------~-----------------------------------------~  139 (425)
                      ++....-     ..              +.+      .                                         .
T Consensus       197 kP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~  276 (494)
T KOG1456|consen  197 KPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGR  276 (494)
T ss_pred             CcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCC
Confidence            8765110     00              000      0                                         0


Q ss_pred             CCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       140 ~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .........+.+.++|.+|+...++-+.|..+|..||.|..|.++   .|.|+|++.+..+.+.|+..||+..+.|.+|.
T Consensus       277 g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  277 GYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            000113345668899999998999999999999999999999987   57999999999999999999999999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.+++..
T Consensus       357 v~~SkQ~  363 (494)
T KOG1456|consen  357 VCVSKQN  363 (494)
T ss_pred             Eeecccc
Confidence            9998775

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.56  E-value=8.9e-14  Score=132.19  Aligned_cols=166  Identities=29%  Similarity=0.470  Sum_probs=131.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFR-RYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~-~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...+.|||+|||+++..++|++||. +.|+|+.|.|       .+|+|.|||+++|.+++|++.||...+  .|++|+|.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~--~GR~l~vK  119 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEV--NGRELVVK  119 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccc--cCceEEEe
Confidence            3456799999999999999999998 5799999998       489999999999999999999999999  89999997


Q ss_pred             EeccccCCC--------------------------CCCC-C-----C--------------CC-----------------
Q 014384          124 WTKHERGIR--------------------------RPGG-G-----S--------------SA-----------------  140 (425)
Q Consensus       124 ~a~~~~~~~--------------------------~~~~-~-----~--------------~~-----------------  140 (425)
                      -.......+                          .... +     .              ..                 
T Consensus       120 Ed~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl  199 (608)
T KOG4212|consen  120 EDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGL  199 (608)
T ss_pred             ccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccc
Confidence            543321000                          0000 0     0              00                 


Q ss_pred             ------CCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCC
Q 014384          141 ------RRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       141 ------~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                            ..-....+...++||.|| .+.+....|++.|.-.|.|..|.+.       +|++.|+|.++-+|.+||..|++
T Consensus       200 ~~~Flr~~h~f~pPl~~k~fvanl-~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  200 SASFLRSLHIFSPPLHNKVFVANL-DYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhhccCCCCCccceeeeecc-ccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhcc
Confidence                  000113344578999999 6889899999999999999888773       68999999999999999999998


Q ss_pred             CccCCeEEEEEEe
Q 014384          208 SKLTDRVISVEYA  220 (425)
Q Consensus       208 ~~~~g~~i~v~~a  220 (425)
                      .-+..++..+...
T Consensus       279 ~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  279 QGLFDRRMTVRLD  291 (608)
T ss_pred             CCCccccceeecc
Confidence            7777777777664

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

Probab=99.55  E-value=1.1e-13  Score=118.13  Aligned_cols=79  Identities=24%  Similarity=0.393  Sum_probs=72.0

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ......++|||+|| +..+++++|+++|++||.|..|.|+        ++||||+|.+.++|+.||+.||+..|+|+.|.
T Consensus        29 ~~~~~~~~lfVgnL-~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~  107 (144)
T PLN03134         29 SLRLMSTKLFIGGL-SWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR  107 (144)
T ss_pred             cccCCCCEEEEeCC-CCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            33456789999999 8899999999999999999999985        68999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |+++....
T Consensus       108 V~~a~~~~  115 (144)
T PLN03134        108 VNPANDRP  115 (144)
T ss_pred             EEeCCcCC
Confidence            99997653

>PF00076 RRM_1: RNA recognition motif

Probab=99.55  E-value=1.9e-14  Score=107.23  Aligned_cols=63  Identities=30%  Similarity=0.745  Sum_probs=59.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      |||+|||+++|+++|.++|++||.|..+.+.       +++|||+|.+.++|++|+..|||..|  .|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKI--NGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEE--CccCcC
Confidence            7999999999999999999999999998883       78999999999999999999999999  788875

(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 ....

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.52  E-value=2.1e-13  Score=132.09  Aligned_cols=160  Identities=19%  Similarity=0.255  Sum_probs=122.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      +......|.+.+||+++|++||.+||+-|+ |+.+.+.      .|-|||+|.+.+++++|| +++...+  ..+-|.|.
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Al-kkdR~~m--g~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKAL-KKDRESM--GHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHH-HhhHHHh--CCceEEEE
Confidence            445567889999999999999999999997 7777773      689999999999999999 7888888  58888887


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE-EEE-------eccEEEEEEcCH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS-VRI-------RRNFAFVQYEVQ  195 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~-v~~-------~~g~afV~f~~~  195 (425)
                      -+........-.     ............|-+.+| |+.|+++||.++|+..-.|.. |.+       +.|-|||+|+++
T Consensus        82 ~~~~~e~d~~~~-----~~g~~s~~~d~vVRLRGL-Pfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sq  155 (510)
T KOG4211|consen   82 TAGGAEADWVMR-----PGGPNSSANDGVVRLRGL-PFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQ  155 (510)
T ss_pred             ccCCcccccccc-----CCCCCCCCCCceEEecCC-CccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCH
Confidence            765443211000     001111245678999999 999999999999998765555 323       257999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          196 EDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      +.|++|+.. |...|+-+-|.|-.+
T Consensus       156 e~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  156 ESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             HHHHHHHHH-HHHhhccceEEeehh
Confidence            999999974 566677777777654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.51  E-value=5.9e-14  Score=128.34  Aligned_cols=74  Identities=20%  Similarity=0.370  Sum_probs=68.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      ..++|||+||++.+|+++|+++|+.||+|+.|.|     .+|||||+|.++++|+.|| .|||..|  .|+.|.|.++..
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~Al-lLnG~~l--~gr~V~Vt~a~~   79 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETAL-LLSGATI--VDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHH-HhcCCee--CCceEEEEeccC
Confidence            3579999999999999999999999999999999     3799999999999999999 6999999  899999999875


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        80 ~~   81 (260)
T PLN03120         80 YQ   81 (260)
T ss_pred             CC
Confidence            43

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

Probab=99.51  E-value=2.8e-12  Score=116.88  Aligned_cols=78  Identities=33%  Similarity=0.543  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      +...|-+||||+-| ++.+++..|+..|+.||+|+.|.|.        +|||||+|.++.++..|.+..+|.+|+|+.|.
T Consensus        96 a~gDPy~TLFv~RL-nydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~  174 (335)
T KOG0113|consen   96 AIGDPYKTLFVARL-NYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRIL  174 (335)
T ss_pred             ccCCccceeeeeec-cccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEE
Confidence            44578899999999 8999999999999999999999995        78999999999999999999999999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.+....
T Consensus       175 VDvERgR  181 (335)
T KOG0113|consen  175 VDVERGR  181 (335)
T ss_pred             EEecccc
Confidence            9986653

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.49  E-value=8.2e-14  Score=107.33  Aligned_cols=79  Identities=23%  Similarity=0.388  Sum_probs=72.5

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ..+..++.|||.|||.++|.+++.+||++||+|..|.|     .+|.|||.|++..+|++|+..|+|..+  +++.|.|-
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~--~~ryl~vl   90 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNV--DNRYLVVL   90 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhccccc--CCceEEEE
Confidence            45677899999999999999999999999999999999     389999999999999999999999999  89999998


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      +.....
T Consensus        91 yyq~~~   96 (124)
T KOG0114|consen   91 YYQPED   96 (124)
T ss_pred             ecCHHH
Confidence            866543

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

Probab=99.48  E-value=2.4e-12  Score=117.38  Aligned_cols=75  Identities=31%  Similarity=0.636  Sum_probs=70.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ..+.+||||+-|+++++|..|+..|++||+|+.|.|        ++|||||+|+++.+..+|.+..+|..|  +|+.|.|
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~I--dgrri~V  175 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKI--DGRRILV  175 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCcee--cCcEEEE
Confidence            356799999999999999999999999999999998        489999999999999999999999999  9999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .+-..
T Consensus       176 DvERg  180 (335)
T KOG0113|consen  176 DVERG  180 (335)
T ss_pred             Eeccc
Confidence            97654

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.47  E-value=9.8e-13  Score=125.19  Aligned_cols=72  Identities=28%  Similarity=0.405  Sum_probs=65.8

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ...++|||.|| |..+||+.|++.|..||.|.++.|+   +..+.|.|.++++|+.|+..|+|..++|+.|.|.|.
T Consensus       534 rKa~qIiirNl-P~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNL-PFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecC-CccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            34489999999 9999999999999999999999995   346689999999999999999999999999999873

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

Probab=99.46  E-value=7.5e-13  Score=124.96  Aligned_cols=128  Identities=32%  Similarity=0.565  Sum_probs=102.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ..+|||+||+..+|+++|.++|.+||.|..|.|        .+|||||+|.+.++|..|+..|+|..|  .|+.|.|.++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~--~~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL--EGRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeE--CCceeEeecc
Confidence            699999999999999999999999999988887        379999999999999999999999999  8999999996


Q ss_pred             cc--c-cCCCCC--C---CCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe
Q 014384          126 KH--E-RGIRRP--G---GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR  184 (425)
Q Consensus       126 ~~--~-~~~~~~--~---~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~  184 (425)
                      ..  . ......  .   .................+++.++ +..++..++..+|..+|.+..+.+.
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  258 (306)
T COG0724         193 QPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNL-PLKTAEEELADLFKSRGDIVRASLP  258 (306)
T ss_pred             ccccccccccccccchhhhccccccccccccccceeecccc-ccccchhHHHHhccccccceeeecc
Confidence            53  1 111110  0   00011222344556678999999 7888899999999999999777664

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=6.2e-13  Score=119.69  Aligned_cols=73  Identities=16%  Similarity=0.197  Sum_probs=67.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      ...+|||+||++.+|+++|++||+.||+|..|.|.     .+||||+|.++++|+.|+ .|||..|  .++.|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l--~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATI--VDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCee--CCceEEEEeCcc
Confidence            35799999999999999999999999999999994     589999999999999999 8999999  799999987664


Q ss_pred             c
Q 014384          128 E  128 (425)
Q Consensus       128 ~  128 (425)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            3

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=4e-12  Score=118.52  Aligned_cols=76  Identities=18%  Similarity=0.422  Sum_probs=68.8

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ++......|||..+.++++++||+..|+.||+|..|.|        ++||+||+|.+..+-..|+..||=..|  .|..|
T Consensus       205 eeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDL--GGQyL  282 (544)
T KOG0124|consen  205 EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDL--GGQYL  282 (544)
T ss_pred             HHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhc--ccceE
Confidence            34556789999999999999999999999999999999        489999999999999999999999899  59999


Q ss_pred             EEEEec
Q 014384          121 RVEWTK  126 (425)
Q Consensus       121 ~V~~a~  126 (425)
                      .|.-+.
T Consensus       283 RVGk~v  288 (544)
T KOG0124|consen  283 RVGKCV  288 (544)
T ss_pred             eccccc
Confidence            996553

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

Probab=99.42  E-value=5e-13  Score=118.64  Aligned_cols=74  Identities=36%  Similarity=0.617  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ++.+|-|.||+.++++++|++||..||.|..|.|        ++|||||.|.+.++|.+||..|||.-+  +.-.|.|+|
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gy--d~LILrvEw  265 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGY--DNLILRVEW  265 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCccc--ceEEEEEEe
Confidence            5678999999999999999999999999999988        489999999999999999999999988  899999999


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      +++.
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9864

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=3.9e-13  Score=108.54  Aligned_cols=74  Identities=23%  Similarity=0.503  Sum_probs=69.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .-.|||+++...+|+++|.+.|..||+|+.|.|+        +|||+|+|++.++|++|+..|||..|  .|+.|.|.|+
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~l--l~q~v~VDw~  149 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAEL--LGQNVSVDWC  149 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhh--hCCceeEEEE
Confidence            3579999999999999999999999999999994        89999999999999999999999999  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      -...
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            7654

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

Probab=99.40  E-value=5.8e-13  Score=122.75  Aligned_cols=77  Identities=27%  Similarity=0.519  Sum_probs=71.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ....+.|+|.|||....+.||..+|++||+|.+|.|      +|||+||+|+++++|+.|-++|||..|  .|++|.|..
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~V--EGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVV--EGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhccee--eceEEEEec
Confidence            344589999999999999999999999999999988      599999999999999999999999999  899999998


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus       171 ATarV  175 (376)
T KOG0125|consen  171 ATARV  175 (376)
T ss_pred             cchhh
Confidence            86543

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

Probab=99.40  E-value=1.1e-12  Score=117.87  Aligned_cols=79  Identities=22%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      +....+++||||||+..+|+++|++.|+.||.|.+|.+  .+|||||.|++.|.|..||..+|+.+|  .|..++|.|-+
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaAahAIv~mNntei--~G~~VkCsWGK  236 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAAAHAIVQMNNTEI--GGQLVRCSWGK  236 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhHHHHHHHhcCcee--CceEEEEeccc
Confidence            45667899999999999999999999999999999999  489999999999999999999999999  79999999987


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus       237 e~~  239 (321)
T KOG0148|consen  237 EGD  239 (321)
T ss_pred             cCC
Confidence            654

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.40  E-value=9.9e-13  Score=98.17  Aligned_cols=63  Identities=35%  Similarity=0.694  Sum_probs=57.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      |||+|||+.+|+++|.++|..||.|..|.+.       +++|||+|.++++|..|+..++|..|  +|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~--~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEI--DGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEE--CCEEcC
Confidence            7999999999999999999999999999983       58999999999999999999999999  898874

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 ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.40  E-value=8.7e-13  Score=127.28  Aligned_cols=77  Identities=23%  Similarity=0.353  Sum_probs=70.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCH--HHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDE--RDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~--~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ......+||||||++.||+++|..+|..||.|..|.|.    +|||||+|.+.  .++.+||..|||..|  +|+.|+|+
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEW--KGR~LKVN   83 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVW--KGGRLRLE   83 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCee--cCceeEEe
Confidence            34456899999999999999999999999999999995    89999999987  789999999999999  99999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      .|+..
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            88653

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.39  E-value=6.8e-13  Score=120.42  Aligned_cols=76  Identities=33%  Similarity=0.605  Sum_probs=72.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ....++|+|+||.+.+|.++|++.|.+||+|.+|+|-++|+||.|.-.++|..|+..||+.+|  +|+.|+|+++...
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy~fvh~d~~eda~~air~l~~~~~--~gk~m~vq~stsr  150 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDYAFVHFDRAEDAVEAIRGLDNTEF--QGKRMHVQLSTSR  150 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecceeEEEEeeccchHHHHhccccccc--ccceeeeeeeccc
Confidence            456789999999999999999999999999999999999999999999999999999999999  9999999998653

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.34  E-value=1.4e-11  Score=120.44  Aligned_cols=163  Identities=17%  Similarity=0.299  Sum_probs=115.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----------eCC---EEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----------KSG---FAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----------~kg---~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      .-.++||||+||++++|++|...|..||.|..=+-          ++|   |+|+.|+++..+..-|.++.-.     ..
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~-----~~  331 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEG-----EG  331 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhc-----cc
Confidence            34589999999999999999999999998753222          367   9999999999998877654321     22


Q ss_pred             EEEEEEeccccCCC-------CCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhc-cCCcEEEEEE-------
Q 014384          119 RLRVEWTKHERGIR-------RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE-PYGKIISVRI-------  183 (425)
Q Consensus       119 ~l~V~~a~~~~~~~-------~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~-~~G~v~~v~~-------  183 (425)
                      .+.+.++......+       .......-........+..||||++| |..++.++|..+|+ .||.|..+-|       
T Consensus       332 ~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgv-prpl~A~eLA~imd~lyGgV~yaGIDtD~k~K  410 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGL-PRPLTAEELAMIMEDLFGGVLYVGIDTDPKLK  410 (520)
T ss_pred             ceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCC-CCcchHHHHHHHHHHhcCceEEEEeccCcccC
Confidence            22233222222111       00111111224566788999999999 89999999999999 7999998887       


Q ss_pred             -eccEEEEEEcCHHHHHHHHHH----cCCCccCCeEEEEEEee
Q 014384          184 -RRNFAFVQYEVQEDATRALDA----TNMSKLTDRVISVEYAV  221 (425)
Q Consensus       184 -~~g~afV~f~~~~~A~~A~~~----l~g~~~~g~~i~v~~a~  221 (425)
                       ++|.|=|+|.+..+-.+||.+    |+...|. +.|.|.-..
T Consensus       411 YPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~-KRVEIkPYv  452 (520)
T KOG0129|consen  411 YPKGAGRVTFSNQQAYIKAISARFVQLDHTDID-KRVEIKPYV  452 (520)
T ss_pred             CCCCcceeeecccHHHHHHHhhheEEEeccccc-eeeeeccee
Confidence             489999999999999999874    3444443 355554433

>PF00076 RRM_1: RNA recognition motif

Probab=99.33  E-value=4.9e-12  Score=94.04  Aligned_cols=63  Identities=37%  Similarity=0.662  Sum_probs=59.2

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      |||+|| |..+++++|+++|.+||.|..+.+.       +++|||+|.+.++|..|++.|+|..++|+.|+
T Consensus         1 l~v~nl-p~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNL-PPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESE-TTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCC-CCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999 8999999999999999999999885       46999999999999999999999999999885

(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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.33  E-value=8.6e-12  Score=92.39  Aligned_cols=65  Identities=42%  Similarity=0.793  Sum_probs=60.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +|||+|||..++.++|.++|..||.|..+.+.      +++|||+|.+.++|+.|+..|+|..|  .|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~--~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKL--GGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEE--CCEEEee
Confidence            58999999999999999999999999998884      39999999999999999999999999  7988877

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.32  E-value=2.9e-11  Score=113.20  Aligned_cols=165  Identities=18%  Similarity=0.257  Sum_probs=130.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....-.|+|.+|-..+++.+|.+.++.||+|..|.+  .+..|.|+|++.+.|+.++..-....|.+.|+...+.++..
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NySts  106 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTS  106 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccchh
Confidence            3456678999999999999999999999999988887  48899999999999999985433334433677777777644


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCC-CCCCHHHHHhhhccCCcEEEEEEecc---EEEEEEcCHHHHHHHHH
Q 014384          128 ERGIRRPGGGSSARRPSTNTRPSKTLFVINFDP-YHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYEVQEDATRALD  203 (425)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p-~~~~~~~L~~~f~~~G~v~~v~~~~g---~afV~f~~~~~A~~A~~  203 (425)
                      +...         .+......+++.|++.=|+| +.+|.+.|..+....|+|..|.|.+.   .|+|||++.+.|++|..
T Consensus       107 q~i~---------R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~  177 (494)
T KOG1456|consen  107 QCIE---------RPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKA  177 (494)
T ss_pred             hhhc---------cCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHh
Confidence            3311         11223455666666655533 57788999999999999999998743   89999999999999999


Q ss_pred             HcCCCccC-C-eEEEEEEeeeC
Q 014384          204 ATNMSKLT-D-RVISVEYAVRD  223 (425)
Q Consensus       204 ~l~g~~~~-g-~~i~v~~a~~~  223 (425)
                      .|||..|. | ++|+|+||++.
T Consensus       178 alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  178 ALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             hcccccccccceeEEEEecCcc
Confidence            99998876 4 68999999875

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

Probab=99.31  E-value=2.4e-12  Score=112.30  Aligned_cols=79  Identities=24%  Similarity=0.528  Sum_probs=73.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++||||+|...||+.-|...|-.||.|.+|.|+        +|||||+|+..|+|.+||..||+.+|  .|++|.
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL--~Grtir   83 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESEL--FGRTIR   83 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhh--cceeEE
Confidence            34567899999999999999999999999999999993        89999999999999999999999999  799999


Q ss_pred             EEEeccccC
Q 014384          122 VEWTKHERG  130 (425)
Q Consensus       122 V~~a~~~~~  130 (425)
                      |.+|++.+.
T Consensus        84 VN~AkP~ki   92 (298)
T KOG0111|consen   84 VNLAKPEKI   92 (298)
T ss_pred             EeecCCccc
Confidence            999998763

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

Probab=99.31  E-value=8.7e-12  Score=106.13  Aligned_cols=74  Identities=27%  Similarity=0.478  Sum_probs=68.9

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..++|||+|| |..+.+.+|+++|-+||.|..|.|.     ..||||+|+++.+|..||..-+|..++|..|.|+|+...
T Consensus         5 ~~~~iyvGNL-P~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNL-PGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCC-CcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            4579999999 8889999999999999999999995     469999999999999999999999999999999998764

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

Probab=99.30  E-value=5.4e-12  Score=116.42  Aligned_cols=75  Identities=35%  Similarity=0.516  Sum_probs=70.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ....+.|+|.|| |+...+.||+.+|++||+|.+|+|.      |||+||+|++.+||++|-++|||..|.|++|.|..|
T Consensus        93 ~~~pkRLhVSNI-PFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   93 KDTPKRLHVSNI-PFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCceeEeecC-CccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            344589999999 9999999999999999999999995      899999999999999999999999999999999998


Q ss_pred             ee
Q 014384          221 VR  222 (425)
Q Consensus       221 ~~  222 (425)
                      ..
T Consensus       172 Ta  173 (376)
T KOG0125|consen  172 TA  173 (376)
T ss_pred             ch
Confidence            65

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=1.5e-11  Score=99.35  Aligned_cols=80  Identities=24%  Similarity=0.458  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      +........|||.++ ...+++++|.+.|..||+|++|.+.        +|||+|+|++.++|++|+..|||..|.|..|
T Consensus        66 PqrSVEGwIi~Vtgv-HeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGV-HEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             CccceeeEEEEEecc-CcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            344555789999999 6788899999999999999999984        8999999999999999999999999999999


Q ss_pred             EEEEeeeCC
Q 014384          216 SVEYAVRDD  224 (425)
Q Consensus       216 ~v~~a~~~~  224 (425)
                      .|.|+--+.
T Consensus       145 ~VDw~Fv~g  153 (170)
T KOG0130|consen  145 SVDWCFVKG  153 (170)
T ss_pred             eEEEEEecC
Confidence            999998753

>PF13893 RRM_5: RNA recognition motif

Probab=99.29  E-value=1.8e-11  Score=87.14  Aligned_cols=53  Identities=36%  Similarity=0.746  Sum_probs=49.0

Q ss_pred             HHHHHhhcCCeeEEEEe--C-CEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           71 LERLFRRYGKVDRVDMK--S-GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        71 L~~lF~~~G~V~~v~i~--k-g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      |.++|++||+|..|.+.  + ++|||+|.+.++|..|+..|||..|  .|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~--~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQF--NGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEE--TTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEC
Confidence            68999999999999995  3 9999999999999999999999999  8999999986

(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 ....

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=4.4e-13  Score=113.75  Aligned_cols=79  Identities=24%  Similarity=0.497  Sum_probs=72.2

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ..-....-|||||||+.+||.+|..+|++||+|.+|.|        ++||||+.|++..+...|+..|||..|  .|+.|
T Consensus        30 ~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki--~gRti  107 (219)
T KOG0126|consen   30 QEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI--LGRTI  107 (219)
T ss_pred             hhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCcee--cceeE
Confidence            45567789999999999999999999999999999999        489999999999999999999999999  79999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      +|.......
T Consensus       108 rVDHv~~Yk  116 (219)
T KOG0126|consen  108 RVDHVSNYK  116 (219)
T ss_pred             Eeeeccccc
Confidence            999765544

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=2.6e-12  Score=132.29  Aligned_cols=155  Identities=24%  Similarity=0.359  Sum_probs=133.4

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....+.|||+|||+..+++.+|+..|..+|.|.+|.|.       ..||||.|.+...+-.|...|.+..|+ .| .+.
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~-~g-~~r  444 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIG-NG-THR  444 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccc-cC-ccc
Confidence            456678999999999999999999999999999999994       459999999999999999999999885 22 233


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEecc--EEEEEEcCHHHHH
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDAT  199 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g--~afV~f~~~~~A~  199 (425)
                      +.+...                  ...+.+.|||++| ..|+....|...|..||.|..|.+..|  ||+|.|++...|+
T Consensus       445 ~glG~~------------------kst~ttr~~sggl-g~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq  505 (975)
T KOG0112|consen  445 IGLGQP------------------KSTPTTRLQSGGL-GPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQ  505 (975)
T ss_pred             cccccc------------------ccccceeeccCCC-CCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccch
Confidence            322211                  3566789999999 788889999999999999999999876  9999999999999


Q ss_pred             HHHHHcCCCccCC--eEEEEEEeeeCC
Q 014384          200 RALDATNMSKLTD--RVISVEYAVRDD  224 (425)
Q Consensus       200 ~A~~~l~g~~~~g--~~i~v~~a~~~~  224 (425)
                      .|+..|-|..|+|  +.|.|.|+....
T Consensus       506 ~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  506 AATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             hhHHHHhcCcCCCCCcccccccccCCC
Confidence            9999999999986  679999987753

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=1e-11  Score=99.58  Aligned_cols=76  Identities=28%  Similarity=0.422  Sum_probs=69.5

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...++||||+|| ...+++++|.++|.++|.|..|.|        +-|||||+|...++|..|+..++|+.++.++|.+.
T Consensus        33 ~r~S~tvyVgNl-SfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   33 LRKSCTVYVGNL-SFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HhhcceEEEeee-eeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            345789999999 789999999999999999999988        35899999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      |...=
T Consensus       112 ~D~GF  116 (153)
T KOG0121|consen  112 WDAGF  116 (153)
T ss_pred             ccccc
Confidence            87553

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

Probab=99.26  E-value=9.2e-12  Score=110.31  Aligned_cols=74  Identities=19%  Similarity=0.484  Sum_probs=64.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +...++||||||++.++.+.|..+|++||+|++..+        +|||+||.|.|.++|..|++.-| -.|  +|++..|
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piI--dGR~aNc   85 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PII--DGRKANC   85 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccc--ccccccc
Confidence            445689999999999999999999999999988766        49999999999999999995443 345  8999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .+|..
T Consensus        86 nlA~l   90 (247)
T KOG0149|consen   86 NLASL   90 (247)
T ss_pred             chhhh
Confidence            98865

>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=99.25  E-value=4.6e-11  Score=88.93  Aligned_cols=67  Identities=45%  Similarity=0.827  Sum_probs=62.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      +|+|+|||+.+++++|.++|..||.|..+.+.       .++|||+|.+.++|..|+..+++..+  .|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~--~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKEL--GGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEeC
Confidence            58999999999999999999999999998883       58999999999999999999999998  899998864

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.22  E-value=4.7e-11  Score=109.40  Aligned_cols=71  Identities=23%  Similarity=0.334  Sum_probs=66.3

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ..+|||+|| +..+++++|+++|+.||.|..|.|+     +|||||+|.+.++|..||. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNL-s~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNV-SLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            579999999 7889999999999999999999995     6899999999999999995 999999999999999764

>smart00360 RRM RNA recognition motif

Probab=99.22  E-value=4.2e-11  Score=88.27  Aligned_cols=63  Identities=38%  Similarity=0.760  Sum_probs=58.1

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           59 CGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        59 V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      |+|||..+++++|.++|..||.|..|.+.        +|+|||+|.+.++|..|+..|++..|  .|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~--~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKEL--DGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCee--CCcEEEeC
Confidence            68999999999999999999999999883        57999999999999999999999999  79988873

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=2.5e-11  Score=120.69  Aligned_cols=171  Identities=19%  Similarity=0.347  Sum_probs=134.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhc-----------C-CeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRY-----------G-KVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~-----------G-~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~  115 (425)
                      .......++|++|++.++++.+..+|..-           | .|..|.|.  +.||||+|.+.++|..|+ .+++..+  
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~-~~~~~~f--  247 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAM-ALDGIIF--  247 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhh-cccchhh--
Confidence            33456789999999999999999999864           3 36777774  899999999999999999 8999888  


Q ss_pred             CCcEEEEEEeccccCCCCCCC-------CCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----
Q 014384          116 KGRRLRVEWTKHERGIRRPGG-------GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----  184 (425)
Q Consensus       116 ~gr~l~V~~a~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----  184 (425)
                      .|..+++.-.........-..       -.............+.+||++| |...++.++.+++..||.+....+.    
T Consensus       248 ~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~l-p~~l~~~q~~Ell~~fg~lk~f~lv~d~~  326 (500)
T KOG0120|consen  248 EGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGL-PLYLTEDQVKELLDSFGPLKAFRLVKDSA  326 (500)
T ss_pred             CCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccC-cCccCHHHHHHHHHhcccchhheeecccc
Confidence            899888864333221111000       0111222333445678999999 8999999999999999998877763    


Q ss_pred             ----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          185 ----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       185 ----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                          +||||.+|.+...+..|+..|||+.+++..|.|..|....
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence                7899999999999999999999999999999999987753

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=2e-10  Score=88.78  Aligned_cols=76  Identities=29%  Similarity=0.472  Sum_probs=69.9

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..-+..|||.|| |+.+|.+++.++|.+||.|.+|.|-     +|.|||.|++..+|.+|++.|.|..+.++.+.|-+-.
T Consensus        15 pevnriLyirNL-p~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   15 PEVNRILYIRNL-PFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hhhheeEEEecC-CccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            344678999999 9999999999999999999999994     7999999999999999999999999999999998865


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        94 ~~   95 (124)
T KOG0114|consen   94 PE   95 (124)
T ss_pred             HH
Confidence            54

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.16  E-value=1.6e-10  Score=86.10  Aligned_cols=63  Identities=35%  Similarity=0.643  Sum_probs=56.9

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      |||+|| |..+++++|.++|..||.|..+.+.       +++|||+|.++++|..|++.+++..|+|+.|.
T Consensus         1 v~i~nl-p~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNL-PPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESS-TTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999 7889999999999999999999885       47999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>PLN03213 repressor of silencing 3; Provisional

Probab=99.15  E-value=1.1e-10  Score=112.83  Aligned_cols=75  Identities=20%  Similarity=0.276  Sum_probs=69.4

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCH--HHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQ--EDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~--~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .....|||+|| .+.+++++|..+|..||.|..|.|+    +|||||+|.+.  .++.+||..|||..+.|+.|+|+.|+
T Consensus         8 ~~gMRIYVGNL-SydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          8 GGGVRLHVGGL-GESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CcceEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            44579999999 8999999999999999999999997    68999999987  78999999999999999999999987


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            64

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

Probab=99.15  E-value=1.3e-10  Score=103.43  Aligned_cols=75  Identities=32%  Similarity=0.524  Sum_probs=70.1

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ...++|-|.|| +..+++.+|+++|..||.|..|.|.        +|||||.|.+.++|++||..|||.-++.-.|.|+|
T Consensus       187 ~D~~tvRvtNL-sed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  187 DDEATVRVTNL-SEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CccceeEEecC-ccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            35678999999 8999999999999999999999984        78999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      +++.
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9874

>PF13893 RRM_5: RNA recognition motif

Probab=99.12  E-value=3.1e-10  Score=80.70  Aligned_cols=53  Identities=32%  Similarity=0.630  Sum_probs=49.3

Q ss_pred             HHhhhccCCcEEEEEEec---cEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          168 LERHFEPYGKIISVRIRR---NFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       168 L~~~f~~~G~v~~v~~~~---g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      |.++|++||+|..+.+..   ++|||+|.+.++|..|+..|||..++|+.|.|.||
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            678999999999999974   89999999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.12  E-value=1.6e-10  Score=117.40  Aligned_cols=77  Identities=23%  Similarity=0.534  Sum_probs=71.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ....+|||||+|+.++++.+|..+|+.||.|..|+|  .+++|||.+..-.+|.+||.+|+...|  .++.|+|.|+..+
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv--~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKV--ADKTIKIAWAVGK  495 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccc--cceeeEEeeeccC
Confidence            344699999999999999999999999999999999  599999999999999999999999988  8999999999765


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      -
T Consensus       496 G  496 (894)
T KOG0132|consen  496 G  496 (894)
T ss_pred             C
Confidence            3

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.10  E-value=1.7e-10  Score=114.23  Aligned_cols=73  Identities=36%  Similarity=0.679  Sum_probs=69.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ..|||||||+++++++|.++|+..|.|..+++        .+|||||+|.+.++|..|+..|||.++  .|++|+|.|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~--~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEF--NGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCccc--CCceEEeeccc
Confidence            89999999999999999999999999999999        389999999999999999999999999  79999999987


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        97 ~~~   99 (435)
T KOG0108|consen   97 NRK   99 (435)
T ss_pred             ccc
Confidence            654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.10  E-value=1e-10  Score=108.87  Aligned_cols=76  Identities=22%  Similarity=0.433  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .+..+|||..|++-+|.++|+-+|+.||+|..|.+        +..||||+|++.+++++|...|+++.|  +++.|+|.
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLI--DDrRIHVD  314 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLI--DDRRIHVD  314 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceee--ccceEEee
Confidence            34589999999999999999999999999999988        367999999999999999999999999  99999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus       315 FSQSVs  320 (479)
T KOG0415|consen  315 FSQSVS  320 (479)
T ss_pred             hhhhhh
Confidence            987544

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.09  E-value=4.7e-10  Score=101.25  Aligned_cols=72  Identities=18%  Similarity=0.171  Sum_probs=65.7

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ...+|||+|| +..+++++|+++|+.||.|..|.|.     .+||||+|.++++|..|+ .|+|..|.|..|.|.....
T Consensus         4 ~g~TV~V~NL-S~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNL-SPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecC-CCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            4579999999 7889999999999999999999997     469999999999999999 5999999999999987654

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

Probab=99.09  E-value=7.6e-11  Score=103.06  Aligned_cols=77  Identities=34%  Similarity=0.541  Sum_probs=71.9

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+|||++| ...+++..|...|-.||.|+.|.++        +|||||+|...+||.+|+..||+.++.|+.|.|.
T Consensus         7 a~~KrtlYVGGl-adeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    7 ANQKRTLYVGGL-ADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             cccceeEEeccc-hHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            445689999999 7899999999999999999999997        7899999999999999999999999999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      +|++.+
T Consensus        86 ~AkP~k   91 (298)
T KOG0111|consen   86 LAKPEK   91 (298)
T ss_pred             ecCCcc
Confidence            998864

>smart00362 RRM_2 RNA recognition motif

Probab=99.08  E-value=5.3e-10  Score=82.59  Aligned_cols=65  Identities=45%  Similarity=0.693  Sum_probs=60.3

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      +|+|.|| |..+++++|+++|.+||.|..+.+.      .++|||+|.+.++|..|+..+++..+.|..|.|
T Consensus         1 ~v~i~~l-~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNL-PPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCC-CCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            5899999 7888899999999999999999885      389999999999999999999999999999886

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.03  E-value=5.4e-11  Score=104.02  Aligned_cols=140  Identities=21%  Similarity=0.261  Sum_probs=114.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .++..+||||+||...|+++-|.+||-+-|+|..|.|.      ..||||+|+++-.+..|+..|||..+  .+..|.|.
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l--~~~e~q~~   82 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDL--EEDEEQRT   82 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchh--ccchhhcc
Confidence            34567899999999999999999999999999999994      33999999999999999999999999  79999998


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQE  196 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~  196 (425)
                      +-......                         -| -..++++.+...|...|.+..+.+.       .+++|+.+.-..
T Consensus        83 ~r~G~sha-------------------------pl-d~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~  136 (267)
T KOG4454|consen   83 LRCGNSHA-------------------------PL-DERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLC  136 (267)
T ss_pred             cccCCCcc-------------------------hh-hhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhh
Confidence            76543210                         04 3456688888889999998888885       458999998888


Q ss_pred             HHHHHHHHcCCCccCCeEEEE
Q 014384          197 DATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       197 ~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ..-.|+...++..+.-+++.+
T Consensus       137 ~~P~~~~~y~~l~~~~~~~~~  157 (267)
T KOG4454|consen  137 AVPFALDLYQGLELFQKKVTI  157 (267)
T ss_pred             cCcHHhhhhcccCcCCCCccc
Confidence            888888877776655554444

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.02  E-value=5.2e-10  Score=95.40  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=68.5

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+|||+|| +..++++.|.++|-+.|+|+.+.|+        +|||||+|.++++|+-|++.||...+.|++|.|.
T Consensus         6 rnqd~tiyvgnl-d~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    6 RNQDATLYVGNL-DEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             cCCCceEEEecC-CHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            344679999999 6788899999999999999999997        6899999999999999999999999999999999


Q ss_pred             Eee
Q 014384          219 YAV  221 (425)
Q Consensus       219 ~a~  221 (425)
                      .+.
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            987

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.98  E-value=1.3e-10  Score=98.89  Aligned_cols=73  Identities=29%  Similarity=0.489  Sum_probs=68.0

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .+.-|||+|| |+..|+.+|.-+|++||+|++|.+.        +||||+.|+++....-|+..|||..|.|+.|.|.+.
T Consensus        34 dsA~Iyiggl-~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   34 DSAYIYIGGL-PYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             cceEEEECCC-cccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            3568999999 8999999999999999999999996        689999999999999999999999999999999985


Q ss_pred             ee
Q 014384          221 VR  222 (425)
Q Consensus       221 ~~  222 (425)
                      ..
T Consensus       113 ~~  114 (219)
T KOG0126|consen  113 SN  114 (219)
T ss_pred             cc
Confidence            43

>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=98.98  E-value=2.8e-09  Score=79.14  Aligned_cols=67  Identities=46%  Similarity=0.711  Sum_probs=61.8

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      +|+|.|| |..+++++|.++|..||.|..+.+.       .++|||+|.+.++|..|++.+++..+.|..|.|.+
T Consensus         1 ~i~i~~l-~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNL-PPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCC-CCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999 7889999999999999999999885       47999999999999999999999999999998864

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).

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.96  E-value=1.9e-09  Score=100.55  Aligned_cols=77  Identities=19%  Similarity=0.463  Sum_probs=67.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCC-CeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDR-TEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng-~~ig~~gr~l~V~~a~  126 (425)
                      +....++|||++|...+++.+|.++|.+||+|..|.+.  +++|||+|.+.++|+.|...+-. ..|  +|..|.|.|..
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI--~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVI--NGFRLKIKWGR  301 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeee--cceEEEEEeCC
Confidence            44556899999999999999999999999999999884  88999999999999998876544 455  99999999998


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus       302 ~~  303 (377)
T KOG0153|consen  302 PK  303 (377)
T ss_pred             Cc
Confidence            83

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.95  E-value=5.5e-10  Score=110.26  Aligned_cols=167  Identities=19%  Similarity=0.268  Sum_probs=109.1

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ......+|+|.|||..|++++|..+|+.||+|.+|.+   ..|.+||+|.|..+|+.|+++||+..|  .|+.|+.....
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~--~~~~~k~~~~~  148 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREI--AGKRIKRPGGA  148 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHh--hhhhhcCCCcc
Confidence            4566789999999999999999999999999999888   489999999999999999999999999  78888832111


Q ss_pred             cccCCCCCCC-------CCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--eccEEEEEEcCHHH
Q 014384          127 HERGIRRPGG-------GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQED  197 (425)
Q Consensus       127 ~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--~~g~afV~f~~~~~  197 (425)
                      ... .....+       ...........-+..++|+- |.| ..+..-++.+|.-+|.+..-..  ....-|++|.+..+
T Consensus       149 ~~~-~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P-~~s~~~~~~~~~~~~~~~~~~~~~~~hq~~~~~~~~~s  225 (549)
T KOG4660|consen  149 RRA-MGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSP-TRSSILLEHISSVDGSSPGRETPLLNHQRFVEFADNRS  225 (549)
T ss_pred             ccc-chhcccchhhhhccchhhcCCCCCCcCCcceee-ecc-chhhhhhhcchhccCccccccccchhhhhhhhhccccc
Confidence            100 000000       00000001111112233333 744 4445566677777887666222  24577889998888


Q ss_pred             HHHHHHHcCCCccCCeEEEEEEeee
Q 014384          198 ATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       198 A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      +..++..+ |..+.+....+.+...
T Consensus       226 ~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  226 YAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             hhhcccCC-ceecCCCCceEEecCC
Confidence            86666533 5666666655555433

>smart00361 RRM_1 RNA recognition motif

Probab=98.94  E-value=3e-09  Score=79.31  Aligned_cols=53  Identities=32%  Similarity=0.632  Sum_probs=47.5

Q ss_pred             HHHHHHHHh----hcCCeeEEE-E----------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           68 QSDLERLFR----RYGKVDRVD-M----------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        68 ~~~L~~lF~----~~G~V~~v~-i----------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +++|.++|.    +||+|..|. |          ++|||||+|.+.++|.+|+..|||..|  .|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~--~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYF--DGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEe
Confidence            578899998    999999884 2          279999999999999999999999999  8999876

>smart00360 RRM RNA recognition motif

Probab=98.93  E-value=3e-09  Score=78.17  Aligned_cols=63  Identities=41%  Similarity=0.650  Sum_probs=57.0

Q ss_pred             EEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          155 VINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       155 V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      |+|| |..+++++|+++|.+||.|..+.+.        +++|||+|.+.++|..|+..|++..+.|..|.|.
T Consensus         1 i~~l-~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNL-PPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCC-CcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            4678 7888999999999999999999885        3699999999999999999999999999998873

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

Probab=98.93  E-value=1.7e-09  Score=96.11  Aligned_cols=73  Identities=25%  Similarity=0.416  Sum_probs=64.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..-++|||+|| ++.+..+.|++.|++||+|++..+.        +||+||+|.+.+.|..|++.. +-.|+|++..|.+
T Consensus        10 T~~TKifVggL-~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnl   87 (247)
T KOG0149|consen   10 TTFTKIFVGGL-AWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNL   87 (247)
T ss_pred             ceEEEEEEcCc-ccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccch
Confidence            34578999999 8899999999999999999988884        799999999999999999854 4568999998888


Q ss_pred             eee
Q 014384          220 AVR  222 (425)
Q Consensus       220 a~~  222 (425)
                      |.-
T Consensus        88 A~l   90 (247)
T KOG0149|consen   88 ASL   90 (247)
T ss_pred             hhh
Confidence            765

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.91  E-value=2.3e-10  Score=108.89  Aligned_cols=148  Identities=24%  Similarity=0.389  Sum_probs=123.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCC-eecCCCcEEEEEEeccccCC
Q 014384           55 RPIFCGNFEYDARQSDLERLFRR--YGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRT-EFGRKGRRLRVEWTKHERGI  131 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~--~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~-~ig~~gr~l~V~~a~~~~~~  131 (425)
                      ..||++||.+.+|..+|+.+|+.  .|--..+.|..|||||.+.+...|.+|++.|+|+ ++  .|+.+.|+.+..+.  
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~el--qGkr~e~~~sv~kk--   77 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVEL--QGKRQEVEHSVPKK--   77 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhh--cCceeeccchhhHH--
Confidence            57999999999999999999985  4445667788999999999999999999999996 55  89999999877654  


Q ss_pred             CCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec-----cEEEEEEcCHHHHHHHHHHcC
Q 014384          132 RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR-----NFAFVQYEVQEDATRALDATN  206 (425)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~-----g~afV~f~~~~~A~~A~~~l~  206 (425)
                                      .....+-|.|+ |....|+.|..++.+||.|..|....     ...-|+|...+.+..|+..|+
T Consensus        78 ----------------qrsrk~Qirni-ppql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~  140 (584)
T KOG2193|consen   78 ----------------QRSRKIQIRNI-PPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLN  140 (584)
T ss_pred             ----------------HHhhhhhHhcC-CHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhc
Confidence                            12345778899 56666999999999999999887642     234477888899999999999


Q ss_pred             CCccCCeEEEEEEeeeC
Q 014384          207 MSKLTDRVISVEYAVRD  223 (425)
Q Consensus       207 g~~~~g~~i~v~~a~~~  223 (425)
                      |..+.+..+.|.|-..+
T Consensus       141 g~Q~en~~~k~~YiPde  157 (584)
T KOG2193|consen  141 GPQLENQHLKVGYIPDE  157 (584)
T ss_pred             chHhhhhhhhcccCchh
Confidence            99999999999986554

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

Probab=98.89  E-value=4e-09  Score=99.32  Aligned_cols=72  Identities=38%  Similarity=0.637  Sum_probs=67.7

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| +..+++++|.++|.+||.|..+.+.        +|||||+|.+.++|..|++.|++..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL-~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNL-PYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCC-CCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            699999999 8999999999999999999888874        6899999999999999999999999999999999976


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus       194 ~  194 (306)
T COG0724         194 P  194 (306)
T ss_pred             c
Confidence            4

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.85  E-value=3.9e-09  Score=98.53  Aligned_cols=79  Identities=30%  Similarity=0.536  Sum_probs=70.8

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec--------cEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------NFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~--------g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      ....+|.+.|||+.|+| .|+.++|.-+|+.||+|..|.+.+        .||||+|++.+++.+|.-+|++..|+++.|
T Consensus       233 Ad~~PPeNVLFVCKLNP-VTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRI  311 (479)
T KOG0415|consen  233 ADVKPPENVLFVCKLNP-VTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRI  311 (479)
T ss_pred             cccCCCcceEEEEecCC-cccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceE
Confidence            45568889999999965 566999999999999999999973        499999999999999999999999999999


Q ss_pred             EEEEeeeC
Q 014384          216 SVEYAVRD  223 (425)
Q Consensus       216 ~v~~a~~~  223 (425)
                      +|.|+..-
T Consensus       312 HVDFSQSV  319 (479)
T KOG0415|consen  312 HVDFSQSV  319 (479)
T ss_pred             Eeehhhhh
Confidence            99997653

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.84  E-value=5.8e-09  Score=98.31  Aligned_cols=165  Identities=19%  Similarity=0.186  Sum_probs=110.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhh-----cCCeeEEEE------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRR-----YGKVDRVDM------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~-----~G~V~~v~i------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .-.|-+.+||+++|+.|+.+||..     -|++.-+.+      ..|-|||.|..+++|..||. -|...|  ..+-|.|
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~i--GqRYIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNI--GQRYIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHH--hHHHHHH
Confidence            456778899999999999999973     233322333      27999999999999999994 333344  1333333


Q ss_pred             EEeccc--------------cCC-CCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcE-EE--EEE-
Q 014384          123 EWTKHE--------------RGI-RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI-IS--VRI-  183 (425)
Q Consensus       123 ~~a~~~--------------~~~-~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v-~~--v~~-  183 (425)
                      .-+...              ... ..+.................||-+.+| |+.++.++|.++|..|..- ..  |.+ 
T Consensus       238 FRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGL-Py~AtvEdIL~FlgdFa~~i~f~gVHmv  316 (508)
T KOG1365|consen  238 FRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGL-PYEATVEDILDFLGDFATDIRFQGVHMV  316 (508)
T ss_pred             HHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCC-ChhhhHHHHHHHHHHHhhhcccceeEEE
Confidence            211100              000 000000001111222334679999999 9999999999999988743 22  344 


Q ss_pred             ------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          184 ------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       184 ------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                            +.|-|||+|.+.++|..|....+.+..+.+-|.|--+..
T Consensus       317 ~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~  361 (508)
T KOG1365|consen  317 LNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSV  361 (508)
T ss_pred             EcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccH
Confidence                  367999999999999999999998888888888866543

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.83  E-value=1e-08  Score=90.89  Aligned_cols=78  Identities=29%  Similarity=0.494  Sum_probs=70.5

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHh----hhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLER----HFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~----~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ..++.||||.|| ...+..++|+.    +|++||.|..|...     +|.|||.|.+.+.|..|+..|+|..|.|+.+.|
T Consensus         6 ~~pn~TlYInnL-nekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    6 VNPNGTLYINNL-NEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             cCCCceEeehhc-cccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            455669999999 78888888877    99999999999884     799999999999999999999999999999999


Q ss_pred             EEeeeCCC
Q 014384          218 EYAVRDDD  225 (425)
Q Consensus       218 ~~a~~~~~  225 (425)
                      .||+.+.+
T Consensus        85 qyA~s~sd   92 (221)
T KOG4206|consen   85 QYAKSDSD   92 (221)
T ss_pred             ecccCccc
Confidence            99998743

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=7.4e-09  Score=92.63  Aligned_cols=74  Identities=31%  Similarity=0.553  Sum_probs=69.5

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      ..|||++| ++.+.+.+|+.+|..||.|..+.+..+|+||+|.+..+|..|+..||+..|.|..+.|+|+.....
T Consensus         2 ~rv~vg~~-~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    2 PRVYIGRL-PYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             Cceeeccc-CCccchhHHHHHHhhccccccceeecccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            46899999 899999999999999999999999999999999999999999999999999999999999987543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.75  E-value=2.4e-08  Score=94.98  Aligned_cols=74  Identities=24%  Similarity=0.510  Sum_probs=65.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...+|||++|+.++++++|++.|.+||.|..+.+        .+||+||.|.+.+.+.+++ .+.-..|  +++.+.|..
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~--~gk~vevkr  172 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDF--NGKKVEVKR  172 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec-ccceeee--cCceeeEee
Confidence            4679999999999999999999999999888777        3899999999999999998 5666677  899999998


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      |.+..
T Consensus       173 A~pk~  177 (311)
T KOG4205|consen  173 AIPKE  177 (311)
T ss_pred             ccchh
Confidence            87765

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.75  E-value=8.6e-09  Score=92.86  Aligned_cols=78  Identities=18%  Similarity=0.358  Sum_probs=69.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      +..+.+.|||-.||...++.+|.++|-.||.|...++        +|+|+||.|.++.+|..||.+|||..||  =+.|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIG--MKRLK  358 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIG--MKRLK  358 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhh--hhhhh
Confidence            4556799999999999999999999999999988776        5999999999999999999999999995  67889


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.+..++.
T Consensus       359 VQLKRPkd  366 (371)
T KOG0146|consen  359 VQLKRPKD  366 (371)
T ss_pred             hhhcCccc
Confidence            98776543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.73  E-value=1.9e-08  Score=99.13  Aligned_cols=76  Identities=33%  Similarity=0.582  Sum_probs=69.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..+.|||.+|...+...+|+.||++||+|+-.++        .++|+||++.+.++|.+||..|+.+.|  .|+.|.|+-
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTEL--HGrmISVEk  481 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTEL--HGRMISVEK  481 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhh--cceeeeeee
Confidence            3478999999999999999999999999987776        278999999999999999999999999  899999999


Q ss_pred             eccccC
Q 014384          125 TKHERG  130 (425)
Q Consensus       125 a~~~~~  130 (425)
                      ++..+.
T Consensus       482 aKNEp~  487 (940)
T KOG4661|consen  482 AKNEPG  487 (940)
T ss_pred             cccCcc
Confidence            887663

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.73  E-value=2.3e-08  Score=99.31  Aligned_cols=74  Identities=28%  Similarity=0.527  Sum_probs=70.1

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ..|||+|+ |+.+++++|..+|+..|.|..+++.        +||||++|.+.++|..|+..|||.++.|+.|.|.|+..
T Consensus        19 ~~v~vgni-p~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNI-PYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCC-CCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            89999999 8999999999999999999999994        78999999999999999999999999999999999887


Q ss_pred             CCC
Q 014384          223 DDD  225 (425)
Q Consensus       223 ~~~  225 (425)
                      ...
T Consensus        98 ~~~  100 (435)
T KOG0108|consen   98 RKN  100 (435)
T ss_pred             cch
Confidence            543

>smart00361 RRM_1 RNA recognition motif

Probab=98.72  E-value=3.5e-08  Score=73.48  Aligned_cols=53  Identities=28%  Similarity=0.508  Sum_probs=47.1

Q ss_pred             HHHHHhhhc----cCCcEEEEE---Ee--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          165 TRDLERHFE----PYGKIISVR---IR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       165 ~~~L~~~f~----~~G~v~~v~---~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      +++|+++|.    +||.|..|.   +.        +|||||+|.+.++|.+|+..|||..++|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999998884   21        679999999999999999999999999999976

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.72  E-value=3.3e-08  Score=86.32  Aligned_cols=78  Identities=17%  Similarity=0.304  Sum_probs=69.5

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhc-CCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRY-GKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~-G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ........++|..||..+-+.+|..+|.+| |.|..+.|        ++|||||+|++++.|+-|.+.||+..|  .++.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl--~e~l  121 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLL--MEHL  121 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhh--hhhe
Confidence            345566889999999999999999999998 78888888        389999999999999999999999999  7999


Q ss_pred             EEEEEeccc
Q 014384          120 LRVEWTKHE  128 (425)
Q Consensus       120 l~V~~a~~~  128 (425)
                      |.|.+-.+.
T Consensus       122 L~c~vmppe  130 (214)
T KOG4208|consen  122 LECHVMPPE  130 (214)
T ss_pred             eeeEEeCch
Confidence            999886554

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.70  E-value=3.1e-08  Score=101.14  Aligned_cols=73  Identities=33%  Similarity=0.543  Sum_probs=68.9

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ++||||++| +..+++++|.++|+.||.|..|.+.  ++||||.+..-.+|.+|+.+|.+..+.++.|+|.||...
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 SRTLWVGGI-PKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccc-cchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            379999999 7899999999999999999999885  899999999999999999999999999999999998775

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.68  E-value=1.8e-08  Score=95.50  Aligned_cols=161  Identities=17%  Similarity=0.258  Sum_probs=124.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCC-CeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDR-TEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng-~~ig~~gr~l~V  122 (425)
                      ....++||+++...+.+.++..+|..+|.+....+        ++++++|.|...+.+..|+ ++.+ ..+  .+..+..
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l-~~s~~~~~--~~~~~~~  162 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAAL-EESGSKVL--DGNKGEK  162 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHH-Hhhhcccc--ccccccC
Confidence            35789999999999999999999999997766555        4899999999999999999 4555 344  4555555


Q ss_pred             EEeccccCCCCCCCCCCCCCCCCCCCCCcEEE-EEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEc
Q 014384          123 EWTKHERGIRRPGGGSSARRPSTNTRPSKTLF-VINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYE  193 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~  193 (425)
                      .+.........      .........+..++| |.+| ++.++.++|+.+|..+|.|..+.++        ++||||.|.
T Consensus       163 dl~~~~~~~~~------n~~~~~~~~~s~~~~~~~~~-~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~  235 (285)
T KOG4210|consen  163 DLNTRRGLRPK------NKLSRLSSGPSDTIFFVGEL-DFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFS  235 (285)
T ss_pred             ccccccccccc------chhcccccCccccceeeccc-ccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhh
Confidence            54443321000      011122233444555 9999 7999999999999999999999996        689999999


Q ss_pred             CHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          194 VQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +...+..|+.. +...+.+..+.+++....
T Consensus       236 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  236 AGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             hchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            99999999987 888899999999877654

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.67  E-value=2.5e-09  Score=110.29  Aligned_cols=134  Identities=20%  Similarity=0.301  Sum_probs=113.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...++||.||++.+.+.+|..+|..+|.|..|.+        .+|+|||+|..+++|.+||....++.+   |       
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~---g-------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF---G-------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh---h-------
Confidence            3478999999999999999999999998877666        289999999999999999966666655   3       


Q ss_pred             eccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE-------eccEEEEEEcCHHH
Q 014384          125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQED  197 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~-------~~g~afV~f~~~~~  197 (425)
                                               ...|+|.|+ |...|.++|+.++.++|.++.+.+       ++|.|+|.|.++.+
T Consensus       736 -------------------------K~~v~i~g~-pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~  789 (881)
T KOG0128|consen  736 -------------------------KISVAISGP-PFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEAD  789 (881)
T ss_pred             -------------------------hhhhheeCC-CCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcch
Confidence                                     135788889 888999999999999999998876       47899999999999


Q ss_pred             HHHHHHHcCCCccCCeEEEEEEeee
Q 014384          198 ATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       198 A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      |..++..++...+.-..+.|....+
T Consensus       790 ~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  790 ASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhcccchhhhhhhcCccccccCC
Confidence            9999988888777777777766544

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.64  E-value=6.3e-08  Score=97.96  Aligned_cols=78  Identities=21%  Similarity=0.371  Sum_probs=71.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      ....++.|||+||++.+++++|...|+.||+|..|+|.           ..+|||.|-+-.+|+.|+..|||..|  .+.
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv--~~~  247 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV--MEY  247 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee--eee
Confidence            45677899999999999999999999999999999983           67999999999999999999999999  899


Q ss_pred             EEEEEEecccc
Q 014384          119 RLRVEWTKHER  129 (425)
Q Consensus       119 ~l~V~~a~~~~  129 (425)
                      .|++.|++...
T Consensus       248 e~K~gWgk~V~  258 (877)
T KOG0151|consen  248 EMKLGWGKAVP  258 (877)
T ss_pred             eeeeccccccc
Confidence            99999986544

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.62  E-value=3.1e-07  Score=89.77  Aligned_cols=161  Identities=19%  Similarity=0.307  Sum_probs=107.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....+|-+.+||+.||++||.+||.-.-.|.. |.|       +.|-|||+|++.+.|++|| .-|...|  ..+-|.|.
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al-~rhre~i--GhRYIEvF  177 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIAL-GRHRENI--GHRYIEVF  177 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHH-HHHHHhh--ccceEEee
Confidence            35678999999999999999999998765544 333       3799999999999999999 4555566  46677775


Q ss_pred             EeccccC---------------------CCCCC--------------------C-----------------CC-----CC
Q 014384          124 WTKHERG---------------------IRRPG--------------------G-----------------GS-----SA  140 (425)
Q Consensus       124 ~a~~~~~---------------------~~~~~--------------------~-----------------~~-----~~  140 (425)
                      .+.....                     ..+..                    .                 +.     ..
T Consensus       178 ~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~  257 (510)
T KOG4211|consen  178 RSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDP  257 (510)
T ss_pred             hhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccc
Confidence            4321100                     00000                    0                 00     00


Q ss_pred             -CCC-------------CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcE-EEEEE-----eccEEEEEEcCHHHHHH
Q 014384          141 -RRP-------------STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI-ISVRI-----RRNFAFVQYEVQEDATR  200 (425)
Q Consensus       141 -~~~-------------~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v-~~v~~-----~~g~afV~f~~~~~A~~  200 (425)
                       ...             .........++..+| |+..+..++..+|...-.+ +.|.+     ..|-|+|+|.+.++|..
T Consensus       258 ~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGl-py~a~~~di~nfFspl~p~~v~i~ig~dGr~TGEAdveF~t~edav~  336 (510)
T KOG4211|consen  258 NYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGL-PYDATENDIANFFSPLNPYRVHIEIGPDGRATGEADVEFATGEDAVG  336 (510)
T ss_pred             ccCCCCCcccCCCcccccCCCCCCceeeecCC-CccCCCcchhhhcCCCCceeEEEEeCCCCccCCcceeecccchhhHh
Confidence             000             000111267788999 8999999999999977655 33444     26799999999999999


Q ss_pred             HHHHcCCCccCCeEEEE
Q 014384          201 ALDATNMSKLTDRVISV  217 (425)
Q Consensus       201 A~~~l~g~~~~g~~i~v  217 (425)
                      |+- -++..+..+-|.+
T Consensus       337 Ams-kd~anm~hrYVEl  352 (510)
T KOG4211|consen  337 AMG-KDGANMGHRYVEL  352 (510)
T ss_pred             hhc-cCCcccCcceeee
Confidence            986 3555555555444

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.60  E-value=1.4e-07  Score=86.40  Aligned_cols=75  Identities=24%  Similarity=0.455  Sum_probs=67.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...++|+|.||++.|++++|++||..||.++.+.|+       .|.|-|.|...++|.+||+.|||+.+  +|+.|++..
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~l--dG~~mk~~~  158 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVAL--DGRPMKIEI  158 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCccc--CCceeeeEE
Confidence            344789999999999999999999999988888883       79999999999999999999999888  999999987


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      ....
T Consensus       159 i~~~  162 (243)
T KOG0533|consen  159 ISSP  162 (243)
T ss_pred             ecCc
Confidence            6544

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.59  E-value=1.2e-07  Score=93.75  Aligned_cols=76  Identities=29%  Similarity=0.532  Sum_probs=68.5

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .-...|||.+| ...|...+|+.+|.+||+|+-..+.        +.|+||+|.+.++|.+||..||.++|.|+.|.|+.
T Consensus       403 ~~gRNlWVSGL-SstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  403 TLGRNLWVSGL-SSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             ccccceeeecc-ccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34578999999 6888899999999999999888875        46999999999999999999999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      ++.+.
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            88763

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

Probab=98.55  E-value=3.8e-07  Score=71.69  Aligned_cols=73  Identities=14%  Similarity=0.256  Sum_probs=60.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecC--CCcEEEE
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRY--GKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGR--KGRRLRV  122 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~--G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~--~gr~l~V  122 (425)
                      +||+|.|||...|.++|.+++...  |...-+.|+        .|||||.|.+++.|......++|..+..  ..+...|
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            699999999999999999998864  666666663        7999999999999999999999998831  3666677


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .||.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77754

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

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.52  E-value=2.2e-07  Score=87.00  Aligned_cols=77  Identities=25%  Similarity=0.424  Sum_probs=66.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHH-cCCCccCCeEEEEEEee
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDA-TNMSKLTDRVISVEYAV  221 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~-l~g~~~~g~~i~v~~a~  221 (425)
                      .....-.+|||++|. ..+++++|.++|.+||+|..+.+.  +++|||+|.+.++|+.|.+. ++...|+|..|.|.|..
T Consensus       223 PeD~~I~tLyIg~l~-d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLN-DEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CcccceeEEEecccc-cchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            344556899999994 578899999999999999999886  67999999999999988765 56678899999999988


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.47  E-value=2.6e-07  Score=91.33  Aligned_cols=71  Identities=27%  Similarity=0.494  Sum_probs=60.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...+|||.|||.++|+.+|+++|..||.|+...|.        .+||||+|++.++++.||++ +-..|  .++.|.|+-
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~i--g~~kl~Vee  363 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEI--GGRKLNVEE  363 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-Ccccc--CCeeEEEEe
Confidence            34569999999999999999999999999987772        28999999999999999954 45555  799999985


Q ss_pred             ec
Q 014384          125 TK  126 (425)
Q Consensus       125 a~  126 (425)
                      ..
T Consensus       364 k~  365 (419)
T KOG0116|consen  364 KR  365 (419)
T ss_pred             cc
Confidence            43

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.41  E-value=3.3e-07  Score=84.14  Aligned_cols=77  Identities=23%  Similarity=0.444  Sum_probs=69.1

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ....+...|||+|+...+|.++|+..|.-||.|..|.|        .+|||||+|.+.+.++.|+. |||..|  .|..|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i--~~~~i  172 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEI--PGPAI  172 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccc--ccccc
Confidence            45667899999999999999999999999999987777        38999999999999999995 999999  89999


Q ss_pred             EEEEeccc
Q 014384          121 RVEWTKHE  128 (425)
Q Consensus       121 ~V~~a~~~  128 (425)
                      .|.+....
T Consensus       173 ~vt~~r~~  180 (231)
T KOG4209|consen  173 EVTLKRTN  180 (231)
T ss_pred             eeeeeeee
Confidence            99987643

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.39  E-value=1.4e-06  Score=76.98  Aligned_cols=78  Identities=19%  Similarity=0.348  Sum_probs=67.2

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccC---CeEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLT---DRVI  215 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~---g~~i  215 (425)
                      ....||||.+| |.++...+|..+|..|-.-+-+.|.         +-+|||.|.+..+|.+|+.+|||..|+   +..|
T Consensus        32 ~~VRTLFVSGL-P~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   32 GAVRTLFVSGL-PNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             cccceeeeccC-CcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34689999999 9999999999999998766555553         249999999999999999999999998   7899


Q ss_pred             EEEEeeeCCCC
Q 014384          216 SVEYAVRDDDD  226 (425)
Q Consensus       216 ~v~~a~~~~~~  226 (425)
                      ++++|+.+...
T Consensus       111 hiElAKSNtK~  121 (284)
T KOG1457|consen  111 HIELAKSNTKR  121 (284)
T ss_pred             EeeehhcCccc
Confidence            99999886543

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.31  E-value=4e-06  Score=82.99  Aligned_cols=72  Identities=26%  Similarity=0.424  Sum_probs=63.0

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||.|| |..++..+|+++|..||.|+...|.        ..||||+|.+.+++..||++- -..|+|+.|.|+...
T Consensus       288 ~~~i~V~nl-P~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNL-PPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecC-CCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecc
Confidence            356999999 8999999999999999999988874        169999999999999999864 788999999998765


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus       366 ~~  367 (419)
T KOG0116|consen  366 PG  367 (419)
T ss_pred             cc
Confidence            53

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.30  E-value=2.2e-06  Score=75.01  Aligned_cols=76  Identities=18%  Similarity=0.343  Sum_probs=67.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccC-CcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPY-GKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~-G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ......++|..+ |..+.+.+|..+|.+| |.|..+.+.        +|||||+|++.+.|.-|.+.||+..|.|+.|.|
T Consensus        46 ~~~~g~~~~~~~-p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   46 QEIEGVVYVDHI-PHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             cCCccceeeccc-ccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            445567888889 8999899999999988 788888883        689999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      .+-.++
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            997765

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.25  E-value=4e-07  Score=86.43  Aligned_cols=61  Identities=15%  Similarity=0.080  Sum_probs=53.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      +..+||+|++|+..+...+|.++|..+|+|....+.    .-+|.|+|....+...|+ .++|..+
T Consensus       149 eirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~hal-r~~gre~  213 (479)
T KOG4676|consen  149 EIRRTREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHAL-RSHGRER  213 (479)
T ss_pred             HHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHH-Hhcchhh
Confidence            344899999999999999999999999999887772    568889999999999999 6777766

>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=4.1e-06  Score=62.79  Aligned_cols=71  Identities=23%  Similarity=0.379  Sum_probs=49.6

Q ss_pred             ceEEEcCCCCCCCHHH----HHHHHhhcC-CeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           55 RPIFCGNFEYDARQSD----LERLFRRYG-KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~----L~~lF~~~G-~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..|+|.|||.+.+...    |.+|+..|| +|..|  ..+.|+|.|.+++.|..|+.-|+|..+  .|..|.|.|.....
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~~~tAilrF~~~~~A~RA~KRmegEdV--fG~kI~v~~~~~~r   78 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--SGGTAILRFPNQEFAERAQKRMEGEDV--FGNKISVSFSPKNR   78 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE----TT-EEEEESSHHHHHHHHHHHTT--S--SSS--EEESS--S-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--eCCEEEEEeCCHHHHHHHHHhhccccc--ccceEEEEEcCCcc
Confidence            5799999999988655    567888886 56555  689999999999999999999999999  79999999985443

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

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.21  E-value=6.6e-06  Score=61.71  Aligned_cols=71  Identities=25%  Similarity=0.360  Sum_probs=49.6

Q ss_pred             cEEEEEcCCCCCCCHHH----HHhhhccCC-cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          151 KTLFVINFDPYHTRTRD----LERHFEPYG-KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~----L~~~f~~~G-~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ..|+|.|| |...+...    |++++..+| .|..|  ..+.|+|.|.+++.|..|++.|+|..+.|..|.|.|.....
T Consensus         3 s~L~V~NL-P~~~d~~~I~~RL~qLsdNCGGkVl~v--~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~r   78 (90)
T PF11608_consen    3 SLLYVSNL-PTNKDPSSIKNRLRQLSDNCGGKVLSV--SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKNR   78 (90)
T ss_dssp             EEEEEES---TTS-HHHHHHHHHHHHHTTT--EEE----TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S-
T ss_pred             cEEEEecC-CCCCCHHHHHHHHHHHhhccCCEEEEE--eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCcc
Confidence            46899999 77776544    678888887 56655  67999999999999999999999999999999999986653

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

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.18  E-value=6.3e-07  Score=78.86  Aligned_cols=76  Identities=20%  Similarity=0.184  Sum_probs=68.1

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec------cEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR------NFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~------g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..+...||||+|| ...++++-|.++|-+.|+|..|.|+.      .||||.|.++-...-|++.|||..+.+.+|.|.+
T Consensus         5 aae~drtl~v~n~-~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    5 AAEMDRTLLVQNM-YSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             CcchhhHHHHHhh-hhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3455689999999 78899999999999999999999973      3999999999999999999999999999999888


Q ss_pred             eee
Q 014384          220 AVR  222 (425)
Q Consensus       220 a~~  222 (425)
                      -..
T Consensus        84 r~G   86 (267)
T KOG4454|consen   84 RCG   86 (267)
T ss_pred             ccC
Confidence            544

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.14  E-value=1.6e-06  Score=86.16  Aligned_cols=69  Identities=33%  Similarity=0.480  Sum_probs=63.6

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ..+..+|+|.|| +..+++++|..+|+.||+|..|+..   .+..||+|.|..+|+.|+++|++.+|.|+.|.
T Consensus        72 ~~~~~~L~v~nl-~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNL-PRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEec-CCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            455679999999 7899999999999999999998773   78999999999999999999999999999888

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.13  E-value=8.8e-06  Score=74.65  Aligned_cols=76  Identities=26%  Similarity=0.375  Sum_probs=68.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ....+|+|.|| ++.+.+++|+++|..||.++.+.+.       .|.|-|.|...+||..|++.+||..++|..+.+...
T Consensus        81 ~~~~~v~v~NL-~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNL-PYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecC-CcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            33478999999 8999999999999999988888773       689999999999999999999999999999999987


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ....
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            7653

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.12  E-value=4.4e-05  Score=72.61  Aligned_cols=151  Identities=19%  Similarity=0.292  Sum_probs=102.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRY-----GKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~-----G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ....+..|-..+||+..++.+|..+|.-.     |.+.++..   ..|.|.|.|.+++.-+.|++ -+.+.+  .++.|.
T Consensus        56 ~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~--g~ryie  132 (508)
T KOG1365|consen   56 SADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHM--GTRYIE  132 (508)
T ss_pred             ccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhc--cCCcee
Confidence            34556778888999999999999999864     33333333   37899999999999999994 455555  478888


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhcc-----CCc--EEEEEE----eccEEEE
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEP-----YGK--IISVRI----RRNFAFV  190 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~-----~G~--v~~v~~----~~g~afV  190 (425)
                      |--+.......-.++..............-.|-+.+| |+.+++.++..+|..     -|.  |..|.-    +.|-|||
T Consensus       133 vYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGL-Pfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFv  211 (508)
T KOG1365|consen  133 VYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGL-PFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFV  211 (508)
T ss_pred             eeccCchhheEecCCccccCCCCCCcccceEEEecCC-CCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEE
Confidence            8766554433222222211111111122345667899 999999999999962     232  333333    2679999


Q ss_pred             EEcCHHHHHHHHHH
Q 014384          191 QYEVQEDATRALDA  204 (425)
Q Consensus       191 ~f~~~~~A~~A~~~  204 (425)
                      .|..+++|+.|+.+
T Consensus       212 lfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  212 LFACEEDAQFALRK  225 (508)
T ss_pred             EecCHHHHHHHHHH
Confidence            99999999999864

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.06  E-value=3.6e-06  Score=75.84  Aligned_cols=152  Identities=14%  Similarity=0.179  Sum_probs=107.1

Q ss_pred             ceEEEcCCCCCCCHHH-H--HHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           55 RPIFCGNFEYDARQSD-L--ERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~-L--~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      -.++++|+-..+..+- |  ...|+.|-.+....+       ..+++|+.|.....-.++...-+++.++  -..  |..
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~--~~~--VR~  172 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIG--KPP--VRL  172 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhcccccccccc--Ccc--eee
Confidence            3566777766666554 3  667777665544443       2789999999988888888777888772  222  333


Q ss_pred             eccccCCCCCCCCCCCCCC-CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--------eccEEEEEEcCH
Q 014384          125 TKHERGIRRPGGGSSARRP-STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQ  195 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--------~~g~afV~f~~~  195 (425)
                      +-...-         .... .........||.+.| ...++.+.|-..|.+|-......+        .+||+||.|.+.
T Consensus       173 a~gtsw---------edPsl~ew~~~DfRIfcgdl-gNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~p  242 (290)
T KOG0226|consen  173 AAGTSW---------EDPSLAEWDEDDFRIFCGDL-GNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDP  242 (290)
T ss_pred             cccccc---------CCcccccCccccceeecccc-cccccHHHHHHHHHhccchhhccccccccccccccceeeeecCH
Confidence            222110         0111 122344568999999 788999999999999875544444        278999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          196 EDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .++..|+.+|+|..++.+.|++.-+
T Consensus       243 ad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  243 ADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HHHHHHHHhhcccccccchhHhhhh
Confidence            9999999999999999999887543

>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=98.04  E-value=9.8e-06  Score=65.15  Aligned_cols=69  Identities=19%  Similarity=0.388  Sum_probs=43.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCC--EEEEEEcCHHHHHHHHHhcCCC---eecCCCcEEEEE
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRT---EFGRKGRRLRVE  123 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg--~aFV~F~~~~~A~~A~~~lng~---~ig~~gr~l~V~  123 (425)
                      ..|+|.++...++-++|+++|..||.|..|.+..|  .|||-|.+++.|+.|+..+.-.   .+-+.+..+.+.
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            46899999999999999999999999999999754  8999999999999999866433   222245555544

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

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.01  E-value=1.7e-05  Score=63.74  Aligned_cols=69  Identities=20%  Similarity=0.367  Sum_probs=45.2

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEecc--EEEEEEcCHHHHHHHHHHcCCC-----ccCCeEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRALDATNMS-----KLTDRVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g--~afV~f~~~~~A~~A~~~l~g~-----~~~g~~i~v~~a  220 (425)
                      ..|+|.++ ...++.++|+++|.+||.|.+|.+.+|  .|||.|.++++|+.|+..+...     .|.+..+.+..-
T Consensus         2 ~il~~~g~-~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen    2 CILKFSGL-GEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             -EEEEEE---SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             eEEEEecC-CCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            56888998 677789999999999999999999977  9999999999999998876443     566777766653

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

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.95  E-value=2.7e-05  Score=71.55  Aligned_cols=75  Identities=23%  Similarity=0.355  Sum_probs=67.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ......+||+|+ .+.++.++++.+|+.||.|..+.|+        +|||||+|.+.+.+..|+. ||+..|.|..|.|.
T Consensus        98 ~~d~~sv~v~nv-d~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   98 EVDAPSVWVGNV-DFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             ccCCceEEEecc-ccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            455689999999 5777788899999999999877774        6799999999999999999 99999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      +....
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            98775

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.93  E-value=2.2e-05  Score=79.79  Aligned_cols=164  Identities=13%  Similarity=0.133  Sum_probs=114.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------e-CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------K-SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~-kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .+.+.|-+.+++.++.+.++.++|--. .|..+.|       + .|.++|+|..+.++.+|+. -|.+.+  -.+.+.|.
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~--~~R~~q~~  384 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDD--VNRPFQTG  384 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhh--hhcceeec
Confidence            344566677899999999999998653 2344444       2 7999999999999999984 444444  37777774


Q ss_pred             Eecccc--------CCCCCC------CC---------CCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE
Q 014384          124 WTKHER--------GIRRPG------GG---------SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS  180 (425)
Q Consensus       124 ~a~~~~--------~~~~~~------~~---------~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~  180 (425)
                      .+-...        ..+.+.      +.         ........+.....+|||..| |..++..++.++|.....|++
T Consensus       385 P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~l-P~~t~~~~~v~~f~~~~~Ved  463 (944)
T KOG4307|consen  385 PPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQL-PVMTPIVPPVNKFMGAAAVED  463 (944)
T ss_pred             CCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccC-Cccccccchhhhhhhhhhhhh
Confidence            432111        000000      00         001112334556689999999 999999999999998887777


Q ss_pred             -EEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          181 -VRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       181 -v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                       |.|.       .+.|||+|..++++..|+...+...++.+.|.|.-.
T Consensus       464 ~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  464 FIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             eeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence             6663       569999999999999998877777777788888753

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.92  E-value=1.5e-05  Score=81.25  Aligned_cols=73  Identities=26%  Similarity=0.361  Sum_probs=66.4

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      +..+.|||+|| +..++++.|...|..||+|..|.|+           ..|+||.|-+-.||+.|++.|+|..+.+..++
T Consensus       172 P~TTNlyv~Nl-npsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  172 PQTTNLYVGNL-NPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CcccceeeecC-CccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            44678999999 5677799999999999999999985           56999999999999999999999999999999


Q ss_pred             EEEee
Q 014384          217 VEYAV  221 (425)
Q Consensus       217 v~~a~  221 (425)
                      +.|++
T Consensus       251 ~gWgk  255 (877)
T KOG0151|consen  251 LGWGK  255 (877)
T ss_pred             ecccc
Confidence            99973

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.91  E-value=8.5e-06  Score=77.19  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=68.1

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEE--------eCCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--------VDM--------KSGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--------v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      ......+|||-+|+..+|+++|.++|.+||.|..        |+|        .|+-|.|.|+++..|++|+..++++.|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            3556789999999999999999999999998762        333        389999999999999999999999999


Q ss_pred             cCCCcEEEEEEecccc
Q 014384          114 GRKGRRLRVEWTKHER  129 (425)
Q Consensus       114 g~~gr~l~V~~a~~~~  129 (425)
                        .+.+|+|.+|....
T Consensus       142 --~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 --CGNTIKVSLAERRT  155 (351)
T ss_pred             --cCCCchhhhhhhcc
Confidence              89999998886544

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.87  E-value=2e-05  Score=71.20  Aligned_cols=75  Identities=20%  Similarity=0.492  Sum_probs=63.4

Q ss_pred             hhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           47 IAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        47 ~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      ..+.+...-.||+|.|...++.+.|...|.+|-.....++        ++||+||.|.++.++..|+.+|||+.+  ..+
T Consensus       183 l~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyV--gsr  260 (290)
T KOG0226|consen  183 LAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYV--GSR  260 (290)
T ss_pred             cccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccc--ccc
Confidence            3455667789999999999999999999999965544333        489999999999999999999999999  577


Q ss_pred             EEEEE
Q 014384          119 RLRVE  123 (425)
Q Consensus       119 ~l~V~  123 (425)
                      +|++.
T Consensus       261 piklR  265 (290)
T KOG0226|consen  261 PIKLR  265 (290)
T ss_pred             hhHhh
Confidence            77664

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

Probab=97.86  E-value=8.4e-05  Score=58.49  Aligned_cols=72  Identities=24%  Similarity=0.301  Sum_probs=60.7

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhcc--CCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccC----CeEEE
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEP--YGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLT----DRVIS  216 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~--~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~----g~~i~  216 (425)
                      +||.|.|| |...++++|.+++..  .|....+.+|        .|||||-|.+++.|..-.+.++|..+.    .+.+.
T Consensus         2 TTvMirNI-Pn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    2 TTVMIRNI-PNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             eeEEEecC-CCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            68999999 899999999988865  3556666665        689999999999999999999998886    57788


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.||.-+
T Consensus        81 i~yAriQ   87 (97)
T PF04059_consen   81 ISYARIQ   87 (97)
T ss_pred             EehhHhh
Confidence            8888654

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.77  E-value=4.7e-05  Score=71.20  Aligned_cols=70  Identities=19%  Similarity=0.418  Sum_probs=59.9

Q ss_pred             ceEEEcCCCCCCCHHHH------HHHHhhcCCeeEEEEeC---------CEE--EEEEcCHHHHHHHHHhcCCCeecCCC
Q 014384           55 RPIFCGNFEYDARQSDL------ERLFRRYGKVDRVDMKS---------GFA--FIYMDDERDAEDAIRGLDRTEFGRKG  117 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L------~~lF~~~G~V~~v~i~k---------g~a--FV~F~~~~~A~~A~~~lng~~ig~~g  117 (425)
                      .-|||-+|++.+..+++      .++|++||+|..|.+.+         +.+  ||.|.+.++|..||.+.+|..+  +|
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~--DG  192 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL--DG  192 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc--cC
Confidence            45899999998877662      57999999999999842         223  9999999999999999999999  99


Q ss_pred             cEEEEEEec
Q 014384          118 RRLRVEWTK  126 (425)
Q Consensus       118 r~l~V~~a~  126 (425)
                      +.|+..|..
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            999998754

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

Probab=97.77  E-value=5.8e-05  Score=52.62  Aligned_cols=50  Identities=22%  Similarity=0.394  Sum_probs=43.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHH
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAI  105 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~  105 (425)
                      +.|-|.+.++...+..|. .|..||+|..+.+.  ...+||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            568899998877655555 88899999999997  889999999999999996

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.74  E-value=0.00012  Score=72.51  Aligned_cols=73  Identities=19%  Similarity=0.320  Sum_probs=59.5

Q ss_pred             hhhcCCCceEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHH----hcCCCeec
Q 014384           48 AAFEAMMRPIFCGNFEYDARQSDLERLFR-RYGKVDRVDM--------KSGFAFIYMDDERDAEDAIR----GLDRTEFG  114 (425)
Q Consensus        48 ~~~~~~~~~l~V~nL~~~~t~~~L~~lF~-~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~----~lng~~ig  114 (425)
                      .+.-.+.+|||||+||--+|.++|..+|+ .||.|..+-|        ++|-|-|.|.+..+=.+||.    .|+...| 
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~-  442 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDI-  442 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEecccc-
Confidence            34556779999999999999999999999 7999998877        48999999999999888885    3455555 


Q ss_pred             CCCcEEEEE
Q 014384          115 RKGRRLRVE  123 (425)
Q Consensus       115 ~~gr~l~V~  123 (425)
                        .+.|.|+
T Consensus       443 --~KRVEIk  449 (520)
T KOG0129|consen  443 --DKRVEIK  449 (520)
T ss_pred             --ceeeeec
Confidence              4455544

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.70  E-value=3.9e-05  Score=80.29  Aligned_cols=117  Identities=17%  Similarity=0.259  Sum_probs=90.4

Q ss_pred             eeeEEEEeCCCCcccccccCCcceeecccccccchhhhhh-hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeC
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAA-FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS   88 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~k   88 (425)
                      ..|+|+.|.+-.....++.......+..+...   +...+ ....++.|||++|.+-+....|...|..||.|..|.+-+
T Consensus       413 sa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r---~glG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h  489 (975)
T KOG0112|consen  413 SAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR---IGLGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH  489 (975)
T ss_pred             cchhhhhhhccccCcccchhhcCCccccCccc---ccccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc
Confidence            35888888776655555544433333333211   11222 456788999999999999999999999999999999964


Q ss_pred             --CEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           89 --GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        89 --g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                        -||||+|++...|.+|++.|-|..||.-.+.|.|.|+...-
T Consensus       490 gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  490 GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             CCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCC
Confidence              59999999999999999999999998667889999987654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.70  E-value=3.1e-05  Score=77.46  Aligned_cols=77  Identities=12%  Similarity=0.198  Sum_probs=66.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecC-CCcEEEEEEecc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFR-RYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGR-KGRRLRVEWTKH  127 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~-~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~-~gr~l~V~~a~~  127 (425)
                      .....|+|.||---+|.-+|+.|+. .+|.|+++||  .+..|||.|.+.++|.+..++|||+.|.. +.+.|.|.|...
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~  521 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRA  521 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecch
Confidence            4568999999999999999999999 6788888887  48899999999999999999999998852 678888888654


Q ss_pred             c
Q 014384          128 E  128 (425)
Q Consensus       128 ~  128 (425)
                      .
T Consensus       522 d  522 (718)
T KOG2416|consen  522 D  522 (718)
T ss_pred             h
Confidence            3

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.57  E-value=0.00018  Score=67.80  Aligned_cols=77  Identities=17%  Similarity=0.277  Sum_probs=66.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE--------EEE-------eccEEEEEEcCHHHHHHHHHHcCCCccC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS--------VRI-------RRNFAFVQYEVQEDATRALDATNMSKLT  211 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~--------v~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~  211 (425)
                      ...++.|||.|| |..+|.+++.++|.+||.|..        |.|       .+|-|.|.|.-.+.+.-|++.|++..|.
T Consensus       131 ~~~Nt~VYVsgL-P~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGL-PLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCC-CCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            344567999999 899999999999999998753        233       2789999999999999999999999999


Q ss_pred             CeEEEEEEeeeCC
Q 014384          212 DRVISVEYAVRDD  224 (425)
Q Consensus       212 g~~i~v~~a~~~~  224 (425)
                      |+.|.|+.|+-+.
T Consensus       210 g~~~rVerAkfq~  222 (382)
T KOG1548|consen  210 GKKLRVERAKFQM  222 (382)
T ss_pred             CcEEEEehhhhhh
Confidence            9999999987653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.53  E-value=5.3e-05  Score=73.16  Aligned_cols=64  Identities=19%  Similarity=0.261  Sum_probs=56.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------------------CCEEEEEEcCHHHHHHHHHhc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------------------SGFAFIYMDDERDAEDAIRGL  108 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------------------kg~aFV~F~~~~~A~~A~~~l  108 (425)
                      +..+.++|.+.|||.+-..+.|.+||+.||.|..|.|.                     +-+|||+|+..+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            44578999999999999999999999999999999982                     458999999999999999888


Q ss_pred             CCCee
Q 014384          109 DRTEF  113 (425)
Q Consensus       109 ng~~i  113 (425)
                      |....
T Consensus       307 ~~e~~  311 (484)
T KOG1855|consen  307 NPEQN  311 (484)
T ss_pred             chhhh
Confidence            66544

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

Probab=97.48  E-value=0.0003  Score=49.04  Aligned_cols=50  Identities=26%  Similarity=0.610  Sum_probs=42.6

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHH
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRAL  202 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~  202 (425)
                      +.|-|.|+ +... .+.|..+|..||+|..+.+.  ...++|+|.+..+|++||
T Consensus         2 ~wI~V~Gf-~~~~-~~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGF-PPDL-AEEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeE-CchH-HHHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            56889999 4444 56677799999999999998  779999999999999985

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.45  E-value=6.4e-05  Score=68.21  Aligned_cols=58  Identities=22%  Similarity=0.481  Sum_probs=49.8

Q ss_pred             HHHHHHHh-hcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           69 SDLERLFR-RYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        69 ~~L~~lF~-~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ++|...|. +||+|+++++.       .|.+||.|...++|++|+..||+..|  .|++|..++...+
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 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWY--NGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccc--cCCcceeeecCcC
Confidence            44555555 89999999873       79999999999999999999999999  8999999987543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.44  E-value=6.7e-06  Score=85.50  Aligned_cols=154  Identities=20%  Similarity=0.183  Sum_probs=116.1

Q ss_pred             CCCceEEEcCCCCCCCHH-HHHHHHhhcCCeeEEEEeC--------CEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQS-DLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~-~L~~lF~~~G~V~~v~i~k--------g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....+++.|+.+..... .+...|..+|.|+.|.+.+        .++++++....+++.|. ...+..+  .++.+.|
T Consensus       569 ~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat-~pa~~~~--a~~~~av  645 (881)
T KOG0128|consen  569 LERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESAT-VPAGGAL--ANRSAAV  645 (881)
T ss_pred             hhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcc-ccccccc--CCccccC
Confidence            344677888998877766 6788999999999999953        38889999999999998 7777777  5888888


Q ss_pred             EEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--------eccEEEEEEcC
Q 014384          123 EWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEV  194 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--------~~g~afV~f~~  194 (425)
                      ..++........      ...........++||.|| +..+.+.+|...|..+|.+..+.+        .+|+|||+|..
T Consensus       646 ~~ad~~~~~~~~------kvs~n~~R~~~~~fvsnl-~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~  718 (881)
T KOG0128|consen  646 GLADAEEKEENF------KVSPNEIRDLIKIFVSNL-SPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLK  718 (881)
T ss_pred             CCCCchhhhhcc------CcCchHHHHHHHHHHhhc-chhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeec
Confidence            777655422111      111111233468899999 677779999999999998777665        27899999999


Q ss_pred             HHHHHHHHHHcCCCccCCeEE
Q 014384          195 QEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       195 ~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      ++++.+||.....+.++...+
T Consensus       719 ~~~~~aaV~f~d~~~~gK~~v  739 (881)
T KOG0128|consen  719 PEHAGAAVAFRDSCFFGKISV  739 (881)
T ss_pred             CCchhhhhhhhhhhhhhhhhh
Confidence            999999998777666663333

>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=97.43  E-value=0.00056  Score=54.19  Aligned_cols=70  Identities=17%  Similarity=0.178  Sum_probs=52.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEE-------------E--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVD-------------M--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~-------------i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      .+-|.|-+.|+. ....|.++|++||+|.+..             +  -.....|.|.++.+|.+|| ..||..|  .|.
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~--~g~   81 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIF--SGS   81 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEE--TTC
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEE--cCc
Confidence            456888899887 5678889999999998875             2  2568899999999999999 8999999  564


Q ss_pred             -EEEEEEecc
Q 014384          119 -RLRVEWTKH  127 (425)
Q Consensus       119 -~l~V~~a~~  127 (425)
                       .+-|.+++.
T Consensus        82 ~mvGV~~~~~   91 (100)
T PF05172_consen   82 LMVGVKPCDP   91 (100)
T ss_dssp             EEEEEEE-HH
T ss_pred             EEEEEEEcHH
Confidence             455777644

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.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.32  E-value=0.00015  Score=65.77  Aligned_cols=62  Identities=19%  Similarity=0.281  Sum_probs=56.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------------------CCEEEEEEcCHHHHHHHHHhcCCCe
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------------------SGFAFIYMDDERDAEDAIRGLDRTE  112 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------------------kg~aFV~F~~~~~A~~A~~~lng~~  112 (425)
                      .+-.||++|||+.+...-|+++|+.||.|-.|.|.                    -.-|+|+|.+...|..+...|||.+
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            56799999999999999999999999999999982                    1246899999999999999999999


Q ss_pred             ec
Q 014384          113 FG  114 (425)
Q Consensus       113 ig  114 (425)
                      ||
T Consensus       153 Ig  154 (278)
T KOG3152|consen  153 IG  154 (278)
T ss_pred             cC
Confidence            95

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.28  E-value=0.0011  Score=49.99  Aligned_cols=57  Identities=18%  Similarity=0.286  Sum_probs=46.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCC
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR  110 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng  110 (425)
                      -....||+ +|..+...||.+||+.||.|.--+|.-..|||...+.+.|..|+..+.-
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWINDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEEEEEECTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcCCcEEEEeecHHHHHHHHHHhcc
Confidence            34566666 9999999999999999999998889999999999999999999987763

; 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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.27  E-value=0.00057  Score=68.31  Aligned_cols=76  Identities=20%  Similarity=0.310  Sum_probs=60.5

Q ss_pred             hcCCCceEEEcCCCCCCC------HHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCC
Q 014384           50 FEAMMRPIFCGNFEYDAR------QSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRK  116 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t------~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~  116 (425)
                      .+.-...|+|.|+|---.      ..-|..+|+++|+|..+.++       +||+|++|.+..+|+.|++.|||+.|- +
T Consensus        54 ~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld-k  132 (698)
T KOG2314|consen   54 AEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLD-K  132 (698)
T ss_pred             cCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceec-c
Confidence            345567899999985322      23466899999999988884       899999999999999999999999985 5


Q ss_pred             CcEEEEEEec
Q 014384          117 GRRLRVEWTK  126 (425)
Q Consensus       117 gr~l~V~~a~  126 (425)
                      ..++.|..-+
T Consensus       133 nHtf~v~~f~  142 (698)
T KOG2314|consen  133 NHTFFVRLFK  142 (698)
T ss_pred             cceEEeehhh
Confidence            7777775433

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.24  E-value=0.00068  Score=63.64  Aligned_cols=77  Identities=25%  Similarity=0.451  Sum_probs=62.0

Q ss_pred             CCCCcEEEEEcCCCCCCCHH---HH--HhhhccCCcEEEEEEec---------c--EEEEEEcCHHHHHHHHHHcCCCcc
Q 014384          147 TRPSKTLFVINFDPYHTRTR---DL--ERHFEPYGKIISVRIRR---------N--FAFVQYEVQEDATRALDATNMSKL  210 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~---~L--~~~f~~~G~v~~v~~~~---------g--~afV~f~~~~~A~~A~~~l~g~~~  210 (425)
                      ....+-+||-+|+|..+.++   .|  .++|.+||.|..|.+.+         +  -.||+|.+.++|..||.+++|..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            34456789999966665554   23  47899999999999852         2  248999999999999999999999


Q ss_pred             CCeEEEEEEeeeC
Q 014384          211 TDRVISVEYAVRD  223 (425)
Q Consensus       211 ~g~~i~v~~a~~~  223 (425)
                      +|+.|+..|...+
T Consensus       191 DGr~lkatYGTTK  203 (480)
T COG5175         191 DGRVLKATYGTTK  203 (480)
T ss_pred             cCceEeeecCchH
Confidence            9999999996543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.22  E-value=0.00083  Score=68.72  Aligned_cols=70  Identities=20%  Similarity=0.423  Sum_probs=60.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKV-DRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V-~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++|-|.|+|.+++.+||.+||.-|-.+ .+|.+       ..|-|.|.|++.++|..|...|++..|  ..++|.|.+
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 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKI--RNRVVSLRI  943 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcc--cceeEEEEe
Confidence            44699999999999999999999999755 34555       379999999999999999999999999  688887754

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.14  E-value=0.0018  Score=54.42  Aligned_cols=56  Identities=25%  Similarity=0.433  Sum_probs=48.2

Q ss_pred             HHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           69 SDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        69 ~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .+|.+.|..||+|.-|++--+.-+|.|.+-+.|-+|+ .|+|..|  .|+.|+|.+..+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~~mwVTF~dg~sALaal-s~dg~~v--~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGDTMWVTFRDGQSALAAL-SLDGIQV--NGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETTCEEEEESSCHHHHHHH-HGCCSEE--TTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCCeEEEEECccHHHHHHH-ccCCcEE--CCEEEEEEeCCc
Confidence            3678889999999999998899999999999999999 8999999  799999987654

; PDB: 1UFW_A 2DNR_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.12  E-value=0.002  Score=53.36  Aligned_cols=76  Identities=14%  Similarity=0.244  Sum_probs=61.1

Q ss_pred             hhhcCCCceEEEcCCCCCCC----HHHHHHHHhhcCCeeEEEEe-CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           48 AAFEAMMRPIFCGNFEYDAR----QSDLERLFRRYGKVDRVDMK-SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        48 ~~~~~~~~~l~V~nL~~~~t----~~~L~~lF~~~G~V~~v~i~-kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ...+.++.||.|.=|..++.    ...|...++.||+|..|.+. +..|.|.|.|..+|-.|+.+++...-   |..+.+
T Consensus        80 ~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s~~p---gtm~qC  156 (166)
T PF15023_consen   80 NTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQSRAP---GTMFQC  156 (166)
T ss_pred             cCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcCCCC---CceEEe
Confidence            34567789999987766654    23455667889999999996 88999999999999999999988654   888888


Q ss_pred             EEec
Q 014384          123 EWTK  126 (425)
Q Consensus       123 ~~a~  126 (425)
                      .|-.
T Consensus       157 sWqq  160 (166)
T PF15023_consen  157 SWQQ  160 (166)
T ss_pred             eccc
Confidence            8854

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.07  E-value=0.0025  Score=53.63  Aligned_cols=77  Identities=18%  Similarity=0.288  Sum_probs=55.3

Q ss_pred             CCCCCCcEEEEEcCC---CC--CCC---HHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFD---PY--HTR---TRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~---p~--~~~---~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ..++|..||.|.=+.   +.  ...   -.+|.+.|..||.|.-+++..+.-+|+|.+-+.|.+|+. |+|.+++|+.|+
T Consensus        22 ~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~~mwVTF~dg~sALaals-~dg~~v~g~~l~  100 (146)
T PF08952_consen   22 SQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGDTMWVTFRDGQSALAALS-LDGIQVNGRTLK  100 (146)
T ss_dssp             ----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTCEEEEESSCHHHHHHHH-GCCSEETTEEEE
T ss_pred             hcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCCeEEEEECccHHHHHHHc-cCCcEECCEEEE
Confidence            345666677766552   11  121   136788899999999999999999999999999999997 899999999999


Q ss_pred             EEEeee
Q 014384          217 VEYAVR  222 (425)
Q Consensus       217 v~~a~~  222 (425)
                      |....+
T Consensus       101 i~LKtp  106 (146)
T PF08952_consen  101 IRLKTP  106 (146)
T ss_dssp             EEE---
T ss_pred             EEeCCc
Confidence            987654

; PDB: 1UFW_A 2DNR_A.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.03  E-value=0.00035  Score=66.47  Aligned_cols=75  Identities=23%  Similarity=0.446  Sum_probs=64.6

Q ss_pred             CCCceEE-EcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIF-CGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~-V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++| |+||+.++|.++|..+|..+|.|..|.+        .+|||||+|.+...+..|+.. +...+  .+.++.|
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~--~~~~~~~  258 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSI--GGRPLRL  258 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcc--cCccccc
Confidence            3345565 9999999999999999999999999998        389999999999999999966 77777  6899999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      +......
T Consensus       259 ~~~~~~~  265 (285)
T KOG4210|consen  259 EEDEPRP  265 (285)
T ss_pred             ccCCCCc
Confidence            8876553

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.93  E-value=0.00069  Score=64.47  Aligned_cols=77  Identities=25%  Similarity=0.254  Sum_probs=66.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEE--------EE--------eccEEEEEEcCHHHHHHHHHHcCCCcc
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV--------RI--------RRNFAFVQYEVQEDATRALDATNMSKL  210 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v--------~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~  210 (425)
                      .....+|||-+| +..+++++|.++|.++|.|..-        .|        +|+-|.|.|.+...|+.|+..+++..|
T Consensus        63 ~s~~~ti~v~g~-~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   63 KSDNETIFVWGC-PDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             ccccccceeecc-CccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            455679999999 7888899999999999987432        11        278999999999999999999999999


Q ss_pred             CCeEEEEEEeeeCC
Q 014384          211 TDRVISVEYAVRDD  224 (425)
Q Consensus       211 ~g~~i~v~~a~~~~  224 (425)
                      .|..|+|.+|....
T Consensus       142 ~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  142 CGNTIKVSLAERRT  155 (351)
T ss_pred             cCCCchhhhhhhcc
Confidence            99999999987764

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.88  E-value=0.0023  Score=64.17  Aligned_cols=69  Identities=23%  Similarity=0.384  Sum_probs=55.5

Q ss_pred             CcEEEEEcCCCCCCC------HHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccC-CeEE
Q 014384          150 SKTLFVINFDPYHTR------TRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLT-DRVI  215 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~------~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i  215 (425)
                      ..+|+|.|+ |..-.      ...|..+|+++|+|..+.++       +||.|++|.+..+|+.|++.|||..|+ +++.
T Consensus        58 D~vVvv~g~-PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGA-PVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCC-cccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            467788887 54321      23466899999999999997       789999999999999999999999887 5666


Q ss_pred             EEEE
Q 014384          216 SVEY  219 (425)
Q Consensus       216 ~v~~  219 (425)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.86  E-value=0.0025  Score=57.93  Aligned_cols=97  Identities=28%  Similarity=0.317  Sum_probs=75.9

Q ss_pred             HHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEE
Q 014384          100 DAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII  179 (425)
Q Consensus       100 ~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~  179 (425)
                      -|..|..+|++...  .++.|.|-|+..                       ..|+|.|| ...++.+.|.+.|..||+|.
T Consensus         6 ~ae~ak~eLd~~~~--~~~~lr~rfa~~-----------------------a~l~V~nl-~~~~sndll~~~f~~fg~~e   59 (275)
T KOG0115|consen    6 LAEIAKRELDGRFP--KGRSLRVRFAMH-----------------------AELYVVNL-MQGASNDLLEQAFRRFGPIE   59 (275)
T ss_pred             HHHHHHHhcCCCCC--CCCceEEEeecc-----------------------ceEEEEec-chhhhhHHHHHhhhhcCccc
Confidence            46777778999998  899999999864                       46999999 67788999999999999876


Q ss_pred             EEEE-------eccEEEEEEcCHHHHHHHHHHcCCCc----cCCeEEEEEEeee
Q 014384          180 SVRI-------RRNFAFVQYEVQEDATRALDATNMSK----LTDRVISVEYAVR  222 (425)
Q Consensus       180 ~v~~-------~~g~afV~f~~~~~A~~A~~~l~g~~----~~g~~i~v~~a~~  222 (425)
                      ...+       +.+-++|+|...-.|.+|+..+...-    ..+.++.|+-...
T Consensus        60 ~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~eq  113 (275)
T KOG0115|consen   60 RAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPMEQ  113 (275)
T ss_pred             hheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChhhc
Confidence            5444       25689999999999999998874433    3355565555443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.86  E-value=0.00042  Score=62.99  Aligned_cols=57  Identities=26%  Similarity=0.373  Sum_probs=49.3

Q ss_pred             HHHHhhhc-cCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          166 RDLERHFE-PYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       166 ~~L~~~f~-~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ++|...|+ +||+|+.+.+.       .|.+||.|...++|++|++.||+..|.|++|..++..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            44555555 99999999773       68999999999999999999999999999999999654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.68  E-value=0.0017  Score=63.01  Aligned_cols=61  Identities=33%  Similarity=0.481  Sum_probs=53.6

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------------------ccEEEEEEcCHHHHHHHHHHc
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------------------RNFAFVQYEVQEDATRALDAT  205 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------------------~g~afV~f~~~~~A~~A~~~l  205 (425)
                      ..+..+|++.|| |..-..+.|.++|..+|.|+.|.|.                     +-+|+|+|...+.|.+|.+.|
T Consensus       228 el~srtivaenL-P~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  228 ELPSRTIVAENL-PLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             ccccceEEEecC-CcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            357899999999 7877789999999999999999983                     238999999999999999988


Q ss_pred             CCC
Q 014384          206 NMS  208 (425)
Q Consensus       206 ~g~  208 (425)
                      +..
T Consensus       307 ~~e  309 (484)
T KOG1855|consen  307 NPE  309 (484)
T ss_pred             chh
Confidence            653

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.66  E-value=0.0048  Score=57.11  Aligned_cols=74  Identities=19%  Similarity=0.260  Sum_probs=56.4

Q ss_pred             CCceEEEcCC--CCCCC---HHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           53 MMRPIFCGNF--EYDAR---QSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        53 ~~~~l~V~nL--~~~~t---~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      .++.|.+.|+  +-.+.   ++++.+..++||+|..|.|.         .--.||+|+..++|.+|+-.|||..|  .|+
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyF--GGr  357 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYF--GGR  357 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCcee--cce
Confidence            3344555554  22333   45678889999999988883         23579999999999999999999999  599


Q ss_pred             EEEEEEeccc
Q 014384          119 RLRVEWTKHE  128 (425)
Q Consensus       119 ~l~V~~a~~~  128 (425)
                      .+...|.+..
T Consensus       358 ~v~A~Fyn~e  367 (378)
T KOG1996|consen  358 VVSACFYNLE  367 (378)
T ss_pred             eeeheeccHH
Confidence            9988887644

>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=96.64  E-value=0.007  Score=48.00  Aligned_cols=68  Identities=25%  Similarity=0.437  Sum_probs=50.9

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEE-------------Ee--ccEEEEEEcCHHHHHHHHHHcCCCccCCe-
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVR-------------IR--RNFAFVQYEVQEDATRALDATNMSKLTDR-  213 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~-------------~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~-  213 (425)
                      ...|.|.|+ |... ...|.++|++||.|.+..             ++  .+...|+|.++.+|.+||. .||..|.|. 
T Consensus         6 ~~wVtVFGf-p~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    6 ETWVTVFGF-PPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             CCEEEEE----GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CeEEEEEcc-CHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            457889999 5554 778999999999998885             33  4588999999999999997 699999885 


Q ss_pred             EEEEEEe
Q 014384          214 VISVEYA  220 (425)
Q Consensus       214 ~i~v~~a  220 (425)
                      .+-|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4556665

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.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.60  E-value=0.002  Score=64.94  Aligned_cols=78  Identities=15%  Similarity=0.259  Sum_probs=66.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhc-cCCcEEEEEE--eccEEEEEEcCHHHHHHHHHHcCCCccC---CeEEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFE-PYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMSKLT---DRVISVE  218 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~-~~G~v~~v~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~---g~~i~v~  218 (425)
                      ....+.+.|+|.|| -...|.-+|+.++. ..|.|..++|  .+..|||.|.+.++|.+...+|||..+-   ++.|.+.
T Consensus       439 sR~~~SnvlhI~nL-vRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNL-VRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CCCCccceEeeecc-cccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            35567799999999 68888999999998 6777887776  4789999999999999999999998763   6889999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      |+...
T Consensus       518 f~~~d  522 (718)
T KOG2416|consen  518 FVRAD  522 (718)
T ss_pred             ecchh
Confidence            97654

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.56  E-value=0.0047  Score=57.12  Aligned_cols=58  Identities=28%  Similarity=0.294  Sum_probs=50.3

Q ss_pred             HHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          165 TRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       165 ~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      +++++..+++||+|..|.|.         .--.||+|+..+.|.+|+-.|||..|+|+.+...|...
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            45677889999999988874         12689999999999999999999999999999888654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.39  E-value=0.0021  Score=58.38  Aligned_cols=64  Identities=16%  Similarity=0.273  Sum_probs=56.1

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec--------------------cEEEEEEcCHHHHHHHHHHcCCCc
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------------------NFAFVQYEVQEDATRALDATNMSK  209 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~--------------------g~afV~f~~~~~A~~A~~~l~g~~  209 (425)
                      ...||+++| |..+...-|+++|.+||.|-.|.+..                    .-|+|+|.+...|..+...||+..
T Consensus        74 ~GVvylS~I-Pp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   74 TGVVYLSNI-PPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             ceEEEeccC-CCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            468999999 66777999999999999999999941                    158899999999999999999999


Q ss_pred             cCCeE
Q 014384          210 LTDRV  214 (425)
Q Consensus       210 ~~g~~  214 (425)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.31  E-value=0.0029  Score=62.21  Aligned_cols=60  Identities=22%  Similarity=0.392  Sum_probs=52.4

Q ss_pred             CCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          162 HTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       162 ~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .-+-.+|..+|.+||.|..|.+.  ...|.|+|.+..+|-.|.. .++..|+|+.|+|-|-+.
T Consensus       384 lnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  384 LNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             CchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            34467899999999999999885  4689999999999988875 799999999999999776

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=96.30  E-value=0.0025  Score=65.22  Aligned_cols=73  Identities=18%  Similarity=0.154  Sum_probs=63.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ...+.-+|||+||...+..+-+..++..||-|..+..-+ |+|++|..+..+..|+..|+-..+  +|..|.+..-
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-fgf~~f~~~~~~~ra~r~~t~~~~--~~~kl~~~~d  108 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-FGFCEFLKHIGDLRASRLLTELNI--DDQKLIENVD  108 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-hcccchhhHHHHHHHHHHhcccCC--Ccchhhccch
Confidence            445667999999999999999999999999998776655 999999999999999998988888  7887777654

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.27  E-value=0.025  Score=40.48  Aligned_cols=54  Identities=17%  Similarity=0.234  Sum_probs=44.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhc----CCeeEEEEeCCEEEEEEcCHHHHHHHHHhc
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRY----GKVDRVDMKSGFAFIYMDDERDAEDAIRGL  108 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~----G~V~~v~i~kg~aFV~F~~~~~A~~A~~~l  108 (425)
                      ...|+|.++ .+++.++|+.+|..|    ++..-=+|.-..|=|.|.+.+.|..||.+|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHcC
Confidence            357899998 458899999999999    654434456778899999999999999765

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.88  E-value=0.0074  Score=57.12  Aligned_cols=71  Identities=14%  Similarity=0.284  Sum_probs=58.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGK--VDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~--V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....+|||||-+-+|+++|.+.+...|-  |.++++        +||||+|...+...+++.|+.|-.+.|  +|+.-.
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~i--HGQ~P~  155 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTI--HGQSPT  155 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhccccee--cCCCCe
Confidence            33467999999999999999999888774  333443        499999999999999999999999999  787666


Q ss_pred             EEE
Q 014384          122 VEW  124 (425)
Q Consensus       122 V~~  124 (425)
                      |--
T Consensus       156 V~~  158 (498)
T KOG4849|consen  156 VLS  158 (498)
T ss_pred             eec
Confidence            643

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.65  E-value=0.056  Score=38.70  Aligned_cols=53  Identities=26%  Similarity=0.326  Sum_probs=41.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccC----CcEEEEEEeccEEEEEEcCHHHHHHHHHHc
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPY----GKIISVRIRRNFAFVQYEVQEDATRALDAT  205 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~----G~v~~v~~~~g~afV~f~~~~~A~~A~~~l  205 (425)
                      ..|+|.|++  .++.++|+.+|..|    ++..-=.|--.-|-|.|.+.+.|..|+.+|
T Consensus         6 eavhirGvd--~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD--ELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC--CCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHcC
Confidence            579999994  56689999999998    544333444568889999999999999765

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.61  E-value=0.008  Score=59.25  Aligned_cols=74  Identities=15%  Similarity=0.322  Sum_probs=62.0

Q ss_pred             CCceEEEcCCCCCC-CHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           53 MMRPIFCGNFEYDA-RQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        53 ~~~~l~V~nL~~~~-t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      +.+.|.+.-++..+ |.++|...|.+||+|..|.+.  .-.|.|+|.+..+|-.|. ...+..|  +++.|+|.|.+...
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~-~s~~avl--nnr~iKl~whnps~  447 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAY-ASHGAVL--NNRFIKLFWHNPSP  447 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchh-cccccee--cCceeEEEEecCCc
Confidence            34556666666655 468999999999999999884  568999999999998887 7899999  99999999998754

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.51  E-value=0.034  Score=55.94  Aligned_cols=69  Identities=16%  Similarity=0.225  Sum_probs=54.6

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhcc--CCcEEEEEEe-ccEEEEEEcCHHHHHHHHHHcCC--CccCCeEEEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEP--YGKIISVRIR-RNFAFVQYEVQEDATRALDATNM--SKLTDRVISVEY  219 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~--~G~v~~v~~~-~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~i~v~~  219 (425)
                      .+.|.|.-| +..+..++|+.||..  |-++..|.+. ..-=||+|++..||+.|.+.|..  ++|.|+.|...+
T Consensus       175 RcIvilREI-pettp~e~Vk~lf~~encPk~iscefa~N~nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  175 RCIVILREI-PETTPIEVVKALFKGENCPKVISCEFAHNDNWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eeEEEEeec-CCCChHHHHHHHhccCCCCCceeeeeeecCceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            456677888 899999999999975  7789999886 56778999999999999877644  456666655444

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.24  E-value=0.1  Score=38.95  Aligned_cols=59  Identities=24%  Similarity=0.438  Sum_probs=38.8

Q ss_pred             CCCCHHHHHHHHhhcC-----CeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           64 YDARQSDLERLFRRYG-----KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        64 ~~~t~~~L~~lF~~~G-----~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ..++..+|..+|...+     .|-.|.|...|+||+-... .|..++..|++..+  .|+.|.|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDNFSFVEVPEE-VAEKVLEALNGKKI--KGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT--HHHHHHHHTT--S--SS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeeeEEEEEECHH-HHHHHHHHhcCCCC--CCeeEEEEEC
Confidence            5688899999998764     4668889999999998765 78889999999999  8999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=95.16  E-value=0.015  Score=61.20  Aligned_cols=75  Identities=21%  Similarity=0.180  Sum_probs=64.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .+.++.|.+-.+|..-|..||..||.|..++.-  -..|.|+|...+.|..|+.+|+|+++...|-+.+|.+|+...
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            445556666678888999999999999999983  578999999999999999999999887679999999998655

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.02  E-value=0.13  Score=38.93  Aligned_cols=55  Identities=24%  Similarity=0.438  Sum_probs=44.5

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                      +..+|. + |......||.++|..||.|.--.|.-.-|||...+.+.|..|+..+.-
T Consensus        10 HVFhlt-F-PkeWK~~DI~qlFspfG~I~VsWi~dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-F-PKEWKTSDIYQLFSPFGQIYVSWINDTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE----TT--HHHHHHHCCCCCCEEEEEECTTEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-C-chHhhhhhHHHHhccCCcEEEEEEcCCcEEEEeecHHHHHHHHHHhcc
Confidence            344454 8 677778999999999999999999999999999999999999988763

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.85  E-value=0.17  Score=42.17  Aligned_cols=75  Identities=21%  Similarity=0.279  Sum_probs=55.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHH---HhhhccCCcEEEEEEe-ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDL---ERHFEPYGKIISVRIR-RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L---~~~f~~~G~v~~v~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|-.+|.|.=|.......+||   .+.+..||+|..|.+. +..|.|.|.+...|.+|+.+++. ..-|..+.+.|..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            35666788886653233334454   4566789999999986 77999999999999999999876 5566777776643

>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=94.70  E-value=0.098  Score=46.43  Aligned_cols=61  Identities=25%  Similarity=0.316  Sum_probs=45.0

Q ss_pred             CHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcC--CCeecCCCcEEEEEEecccc
Q 014384           67 RQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLD--RTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        67 t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~ln--g~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..+.|+++|..|+.+..+.+-  -+=..|.|.+.+.|..|...|+  +..|  .|..|+|.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~--~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSF--NGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEE--TTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhccccccc--CCCceEEEEccccc
Confidence            358899999999988776663  4567899999999999999999  8999  89999999985443

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.70  E-value=0.031  Score=49.40  Aligned_cols=77  Identities=9%  Similarity=0.015  Sum_probs=50.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhh-cCCe---eEEEE----------eCCEEEEEEcCHHHHHHHHHhcCCCeecC--
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRR-YGKV---DRVDM----------KSGFAFIYMDDERDAEDAIRGLDRTEFGR--  115 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~-~G~V---~~v~i----------~kg~aFV~F~~~~~A~~A~~~lng~~ig~--  115 (425)
                      .....|.|.+||+++|++++.+.+.. ++..   ..+.-          .-.-|||.|.+.+++...+..++|..|-.  
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            34569999999999999999997776 5554   23331          13579999999999999999999987730  


Q ss_pred             -CCcEEEEEEeccc
Q 014384          116 -KGRRLRVEWTKHE  128 (425)
Q Consensus       116 -~gr~l~V~~a~~~  128 (425)
                       .--...|++|...
T Consensus        85 g~~~~~~VE~Apyq   98 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQ   98 (176)
T ss_dssp             S-EEEEEEEE-SS-
T ss_pred             CCCcceeEEEcchh
Confidence             1235567777653

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.61  E-value=0.15  Score=38.13  Aligned_cols=59  Identities=27%  Similarity=0.291  Sum_probs=38.1

Q ss_pred             CCCCHHHHHhhhccCC-----cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          161 YHTRTRDLERHFEPYG-----KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G-----~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ..++..+|..++...+     .|-.|.+...|+||+-... .|..++..|++..+.|+.|.|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeeeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4566788888777654     5789999999999998765 788999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=94.56  E-value=0.032  Score=52.95  Aligned_cols=70  Identities=11%  Similarity=0.233  Sum_probs=54.4

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCC--cEEEEEE--------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYG--KIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G--~v~~v~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...++||+|| .+++|+++|.+.+...|  .+.++++        .+|||+|...+....++.++.|...+|.|..-.|-
T Consensus        79 rk~~~YvGNL-~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   79 RKYCCYVGNL-LWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ceEEEEecce-eEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3468999999 67777888887776665  3444444        27899999999999999999999999998765554


Q ss_pred             E
Q 014384          219 Y  219 (425)
Q Consensus       219 ~  219 (425)
                      -
T Consensus       158 ~  158 (498)
T KOG4849|consen  158 S  158 (498)
T ss_pred             c
Confidence            3

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.26  E-value=0.015  Score=55.29  Aligned_cols=71  Identities=20%  Similarity=0.377  Sum_probs=57.4

Q ss_pred             ceEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEeC-----------CEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           55 RPIFCGNFEYDARQSDLE---RLFRRYGKVDRVDMKS-----------GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~---~lF~~~G~V~~v~i~k-----------g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      .-+||-+|+..+..+.+.   +.|.+||.|..|.+.+           .-+||.|+..++|..||...+|+.+  +|+.|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~--dg~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVD--DGRAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHh--hhhhh
Confidence            557888898877655443   5899999999998842           3589999999999999999999999  89987


Q ss_pred             EEEEecc
Q 014384          121 RVEWTKH  127 (425)
Q Consensus       121 ~V~~a~~  127 (425)
                      +..+...
T Consensus       156 ka~~gtt  162 (327)
T KOG2068|consen  156 KASLGTT  162 (327)
T ss_pred             HHhhCCC
Confidence            7776543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=93.92  E-value=0.061  Score=52.41  Aligned_cols=72  Identities=22%  Similarity=0.280  Sum_probs=59.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhcc--CCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCC-ccCCeEEEEEEeeeC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEP--YGKIISVRIRRNFAFVQYEVQEDATRALDATNMS-KLTDRVISVEYAVRD  223 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~--~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~a~~~  223 (425)
                      +.||++|| ...++..+|..+|..  .+.-..+-+..||+||.+.+..-|.+|++.++|. ++.|..+.+++...+
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 NKLYIGNL-SPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             Cccccccc-CCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            46899999 456669999999974  3444556667899999999999999999999985 578999999997665

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.81  E-value=0.09  Score=53.03  Aligned_cols=56  Identities=16%  Similarity=0.186  Sum_probs=47.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEe-CCEEEEEEcCHHHHHHHHHhcC
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRR--YGKVDRVDMK-SGFAFIYMDDERDAEDAIRGLD  109 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~--~G~V~~v~i~-kg~aFV~F~~~~~A~~A~~~ln  109 (425)
                      -+.|.|.-||.++.+++|+.||..  |-++.+|.+- ..-=||.|++..||.+|...|.
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDNWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCceEEEeecchhHHHHHHHHH
Confidence            367888899999999999999985  7788888873 5567999999999999987554

>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=93.72  E-value=0.29  Score=39.59  Aligned_cols=60  Identities=10%  Similarity=0.108  Sum_probs=43.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      ...+.+...|.-++.++|..+...+- .|..+.|-      +-.+.|.|.+.++|......+||+.|
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            34444445555556667766666654 45666662      45889999999999999999999988

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.37  E-value=0.068  Score=48.88  Aligned_cols=70  Identities=26%  Similarity=0.385  Sum_probs=55.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeec--CCCcEEEEEE
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFG--RKGRRLRVEW  124 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig--~~gr~l~V~~  124 (425)
                      ..|||.||..-+..+.|.+-|..||.|..-.+       ..+-++|+|...-.|.+|+..++..-|+  ..+.+..|+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            78999999999999999999999999875443       3688999999999999999877433221  2455655654

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.23  E-value=0.42  Score=44.85  Aligned_cols=73  Identities=16%  Similarity=0.102  Sum_probs=54.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..=|.|-++++..+ .-|..+|.+||+|......  -.+-+|.|...-+|.+|| ..||+.|. ..-.|-|..+..+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KAL-skng~ii~-g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKAL-SKNGTIID-GDVMIGVKPCTDKS  271 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhh-hhcCeeec-cceEEeeeecCCHH
Confidence            45577778877554 5677899999999887774  458899999999999999 88999993 33344455544443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.06  E-value=0.032  Score=53.01  Aligned_cols=74  Identities=22%  Similarity=0.355  Sum_probs=58.5

Q ss_pred             CcEEEEEcCCCCCCCHHHHH--hhhccCCcEEEEEEecc-----------EEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLE--RHFEPYGKIISVRIRRN-----------FAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~--~~f~~~G~v~~v~~~~g-----------~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .+-+||-+|++....+..|+  ..|.+||.|..|.+.++           -++|+|...++|..||...+|..++|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            34567778855555555665  56899999999988542           589999999999999999999999999987


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      ..+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7775554

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=92.53  E-value=4.5  Score=38.09  Aligned_cols=155  Identities=14%  Similarity=0.162  Sum_probs=97.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------------CCEEEEEEcCHHHHHHHHH----hcCC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------------SGFAFIYMDDERDAEDAIR----GLDR  110 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------------kg~aFV~F~~~~~A~~A~~----~lng  110 (425)
                      ..-.++.|.+.||...++--.+...|-+||+|+.|.|-               ...+.+-|-+.+.|-.+..    .|+.
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsE   90 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSE   90 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHH
Confidence            45567899999999999999999999999999999992               3578899999998876542    2322


Q ss_pred             --CeecCCCcEEEEEEeccccCCCC--CCCCC--------CCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHh---hhccC
Q 014384          111 --TEFGRKGRRLRVEWTKHERGIRR--PGGGS--------SARRPSTNTRPSKTLFVINFDPYHTRTRDLER---HFEPY  175 (425)
Q Consensus       111 --~~ig~~gr~l~V~~a~~~~~~~~--~~~~~--------~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~---~f~~~  175 (425)
                        +.+  +-..|.|.|..-.-....  +....        .....-........|.|.=-+ ....++-|.+   ++..-
T Consensus        91 fK~~L--~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~~-~~~~~dl~~~kL~fL~~~  167 (309)
T PF10567_consen   91 FKTKL--KSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFKD-PVDKDDLIEKKLPFLKNS  167 (309)
T ss_pred             HHHhc--CCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEecC-ccchhHHHHHhhhhhccC
Confidence              233  677778877653211100  11000        001112233445566665432 2222332332   22233


Q ss_pred             Cc----EEEEEEe----------ccEEEEEEcCHHHHHHHHHHcCC
Q 014384          176 GK----IISVRIR----------RNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       176 G~----v~~v~~~----------~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                      +.    ++.|.+.          ++||.+.|-+...|.+.++.|..
T Consensus       168 ~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~  213 (309)
T PF10567_consen  168 NNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKS  213 (309)
T ss_pred             CCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHh
Confidence            32    4556653          67999999999999999887763

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.50  E-value=0.091  Score=54.18  Aligned_cols=76  Identities=17%  Similarity=0.175  Sum_probs=65.3

Q ss_pred             CCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          142 RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       142 ~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      +...+.++..++||+|+ .+.+.++-++.+...+|.|..+...+ |+|++|..+..+..|+..|+...++|..+.+..
T Consensus        32 p~~~~~~~~~~vfv~~~-~~~~s~~~~~~il~~~g~v~s~kr~~-fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   32 PVFQPLPPRDTVFVGNI-SYLVSQEFWKSILAKSGFVPSWKRDK-FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             ccccCCCCCceeEecch-hhhhhHHHHHHHHhhCCcchhhhhhh-hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            33456677889999999 78888888999999999998887766 999999999999999999999999888776655

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.46  E-value=0.56  Score=46.46  Aligned_cols=63  Identities=13%  Similarity=0.174  Sum_probs=53.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      +...+.|+|-.+|..+|..||..|...|- .|..|.|-      +-.+.|.|.+.++|..+...+||+.|
T Consensus        71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~F  140 (493)
T KOG0804|consen   71 ASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQF  140 (493)
T ss_pred             CCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcC
Confidence            33478999999999999999999988764 46777772      45789999999999999999999988

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.30  E-value=0.38  Score=45.13  Aligned_cols=67  Identities=21%  Similarity=0.319  Sum_probs=52.2

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec--cEEEEEEcCHHHHHHHHHHcCCCccCCeE-EEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--NFAFVQYEVQEDATRALDATNMSKLTDRV-ISVEY  219 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~--g~afV~f~~~~~A~~A~~~l~g~~~~g~~-i~v~~  219 (425)
                      ..-|-|.++.|..  ..-|..+|++||.|++.....  ++.+|.|.+..+|.+||. .||+.|+|.. |-|.-
T Consensus       197 D~WVTVfGFppg~--~s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ--VSIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCccc--hhHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeee
Confidence            4567788884443  467889999999999887763  488999999999999997 5888888754 44443

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=92.30  E-value=0.56  Score=34.09  Aligned_cols=56  Identities=13%  Similarity=0.192  Sum_probs=44.6

Q ss_pred             CCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          161 YHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ..++-++|+..+..|+... |..-+.--||.|.+..+|.++....+|+.+.+..|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~~-I~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWDR-IRDDRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcce-EEecCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4567899999999997644 3344444579999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=92.16  E-value=0.29  Score=43.50  Aligned_cols=58  Identities=19%  Similarity=0.243  Sum_probs=45.6

Q ss_pred             HHHHHhhhccCCcEEEEEEecc--EEEEEEcCHHHHHHHHHHcC--CCccCCeEEEEEEeee
Q 014384          165 TRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRALDATN--MSKLTDRVISVEYAVR  222 (425)
Q Consensus       165 ~~~L~~~f~~~G~v~~v~~~~g--~afV~f~~~~~A~~A~~~l~--g~~~~g~~i~v~~a~~  222 (425)
                      .+.|+++|..|+.+..+.+.+.  -..|.|.+.++|..|...|+  +..|.|..|.|-|+..
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             HHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            5789999999999888888765  57899999999999999999  9999999999999854

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=92.13  E-value=3.5  Score=33.31  Aligned_cols=70  Identities=23%  Similarity=0.333  Sum_probs=49.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEecc------EEEEEEcCHHHHHHHHHHcCCCccCC---eEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRN------FAFVQYEVQEDATRALDATNMSKLTD---RVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~~g------~afV~f~~~~~A~~A~~~l~g~~~~g---~~i~v~~a  220 (425)
                      ..|.|-...|..++.++|..+...+- .|..++|.+.      .+.|+|.++++|.+-...+||+.|.-   ..++|-|.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~ChvvfV   92 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVVFV   92 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEEEE
Confidence            34444444378887888877777665 5667777532      67799999999999999999998874   34544443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=91.72  E-value=0.93  Score=32.96  Aligned_cols=56  Identities=25%  Similarity=0.388  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           64 YDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        64 ~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ..++.++|+..+..|+- ..|...+.=-||.|.+.++|+.+....+|..+  .+-.|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~-~~I~~d~tGfYIvF~~~~Ea~rC~~~~~~~~~--f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW-DRIRDDRTGFYIVFNDSKEAERCFRAEDGTLF--FTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCc-ceEEecCCEEEEEECChHHHHHHHHhcCCCEE--EEEEEEe
Confidence            35788999999999984 45556544458999999999999999999988  4555543

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=91.08  E-value=0.45  Score=36.72  Aligned_cols=74  Identities=16%  Similarity=0.204  Sum_probs=46.9

Q ss_pred             EEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHh
Q 014384           91 AFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLER  170 (425)
Q Consensus        91 aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~  170 (425)
                      |+|.|.++.-|...+. +....+.+++..+.|...........       ...........+|.|.|| |....+++|++
T Consensus         1 AlITF~e~~VA~~i~~-~~~~~v~l~~~~~~V~v~P~~~~~~~-------k~qv~~~vs~rtVlvsgi-p~~l~ee~l~D   71 (88)
T PF07292_consen    1 ALITFEEEGVAQRILK-KKKHPVPLEDCCVRVKVSPVTLGHLQ-------KFQVFSGVSKRTVLVSGI-PDVLDEEELRD   71 (88)
T ss_pred             CEEEeCcHHHHHHHHh-CCEEEEEECCEEEEEEEEeEecCCce-------EEEEEEcccCCEEEEeCC-CCCCChhhhee
Confidence            7899999999999884 33333333566666654433221100       000112345678999999 78888999988


Q ss_pred             hhc
Q 014384          171 HFE  173 (425)
Q Consensus       171 ~f~  173 (425)
                      .++
T Consensus        72 ~Le   74 (88)
T PF07292_consen   72 KLE   74 (88)
T ss_pred             eEE
Confidence            765

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.60  E-value=1  Score=46.01  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=62.7

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccC----CcEEEEEEe----------------c--------------------
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPY----GKIISVRIR----------------R--------------------  185 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~----G~v~~v~~~----------------~--------------------  185 (425)
                      ...+++.|-|.||++..+...+|..+|.-|    |.|..|.|-                .                    
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            356778999999999999999999988754    478888871                0                    


Q ss_pred             -----------------c--EEEEEEcCHHHHHHHHHHcCCCccC--CeEEEEEEeee
Q 014384          186 -----------------N--FAFVQYEVQEDATRALDATNMSKLT--DRVISVEYAVR  222 (425)
Q Consensus       186 -----------------g--~afV~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~a~~  222 (425)
                                       +  ||.|+|.+.+.|....+.++|.+|.  +..|-+.|...
T Consensus       250 ~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPD  307 (650)
T KOG2318|consen  250 EEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPD  307 (650)
T ss_pred             hhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCC
Confidence                             1  8999999999999999999999998  45566666444

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.60  E-value=1.7  Score=44.50  Aligned_cols=77  Identities=19%  Similarity=0.329  Sum_probs=62.7

Q ss_pred             hcCCCceEEEcCCCCC-CCHHHHHHHHhhc----CCeeEEEEe-------------------------------------
Q 014384           50 FEAMMRPIFCGNFEYD-ARQSDLERLFRRY----GKVDRVDMK-------------------------------------   87 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~-~t~~~L~~lF~~~----G~V~~v~i~-------------------------------------   87 (425)
                      ....++.|-|.||.|+ |...+|.-+|+.|    |.|..|.|.                                     
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            3566789999999984 6789999999987    689888871                                     


Q ss_pred             ------------------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           88 ------------------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        88 ------------------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                                        --||.|+|.+.+.|.+....|+|..|+.-+..|-+-|-.
T Consensus       250 ~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIP  306 (650)
T KOG2318|consen  250 EEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIP  306 (650)
T ss_pred             hhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecC
Confidence                              028999999999999999999999996556666666543

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=88.02  E-value=0.34  Score=41.38  Aligned_cols=107  Identities=14%  Similarity=0.080  Sum_probs=68.8

Q ss_pred             CCCHHHHHHHHhh----cCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCC
Q 014384           65 DARQSDLERLFRR----YGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSA  140 (425)
Q Consensus        65 ~~t~~~L~~lF~~----~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~  140 (425)
                      .++-..|.+.+.+    .|.+.-..+..++..++|.+.+++..++. .....|  ++..|.++.-.+......       
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l~~~~fl~~F~~~~d~~~vl~-~~p~~~--~~~~~~l~~W~~~~~~~~-------   97 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDLGDNLFLFQFESEEDRQRVLK-GGPWNF--NGHFLILQRWSPDFNPSE-------   97 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEeCCCeEEEEEEeccceeEEEe-cccccc--cccchhhhhhcccccccc-------
Confidence            3555555555544    45666666779999999999999998883 333344  566666654432210000       


Q ss_pred             CCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe
Q 014384          141 RRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR  184 (425)
Q Consensus       141 ~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~  184 (425)
                         ........-|.|.||+....+++.|+.+.+.+|.+..+...
T Consensus        98 ---~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen   98 ---VKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             ---cceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence               00111223456789955567788899999999999998774

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=86.90  E-value=0.59  Score=43.28  Aligned_cols=101  Identities=17%  Similarity=0.244  Sum_probs=54.6

Q ss_pred             EEEEe-CCEEEEEEcCHHH----HHHHHHhcCCCeecC--CCcEEEEEEeccccCCCCCCC------CCCCCCCCCCCCC
Q 014384           83 RVDMK-SGFAFIYMDDERD----AEDAIRGLDRTEFGR--KGRRLRVEWTKHERGIRRPGG------GSSARRPSTNTRP  149 (425)
Q Consensus        83 ~v~i~-kg~aFV~F~~~~~----A~~A~~~lng~~ig~--~gr~l~V~~a~~~~~~~~~~~------~~~~~~~~~~~~~  149 (425)
                      .|.|. ..+-||.|+-.-.    .+..+.+|+|..|.+  ..-+|+|.-+..+........      .........+..-
T Consensus        69 sckiresnid~iifeael~n~gimkk~l~~ldgfsiklsgfad~lkvka~eakidfpsrhdwdd~fm~~kdmdemkpger  148 (445)
T KOG2891|consen   69 SCKIRESNIDFIIFEAELENKGIMKKFLACLDGFSIKLSGFADILKVKAAEAKIDFPSRHDWDDFFMDAKDMDEMKPGER  148 (445)
T ss_pred             ceeecccccceEEeeHhhhhhhHHHHHHHHhcCCeeeecccchHHhhhHHhhcCCCCcccchHHHHhhhhhhhccCCCCC
Confidence            44553 5688898875433    556777888876622  223444433322211100000      0000011123333


Q ss_pred             CcEEEEEcCCC------------CCCCHHHHHhhhccCCcEEEEEEe
Q 014384          150 SKTLFVINFDP------------YHTRTRDLERHFEPYGKIISVRIR  184 (425)
Q Consensus       150 ~~~l~V~nl~p------------~~~~~~~L~~~f~~~G~v~~v~~~  184 (425)
                      ..||++.+| |            ...+++-|...|+.||.|..|.|+
T Consensus       149 pdti~la~i-p~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdip  194 (445)
T KOG2891|consen  149 PDTIHLAGI-PCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIP  194 (445)
T ss_pred             CCceeecCC-cceeeeecccccccCChHHHHHHHHHHhccceecCCc
Confidence            456777666 3            224577899999999999999985

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=86.59  E-value=0.39  Score=50.99  Aligned_cols=62  Identities=24%  Similarity=0.296  Sum_probs=53.1

Q ss_pred             CCCHHHHHhhhccCCcEEEEEEecc--EEEEEEcCHHHHHHHHHHcCCCccC--CeEEEEEEeeeC
Q 014384          162 HTRTRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRALDATNMSKLT--DRVISVEYAVRD  223 (425)
Q Consensus       162 ~~~~~~L~~~f~~~G~v~~v~~~~g--~afV~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~a~~~  223 (425)
                      ..+-..|..+|.+||.|..++..++  .|.|+|...+.|..|+++|+|+++-  |-+.+|.+|+.-
T Consensus       309 ~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  309 NLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             cchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            3344568889999999999999654  8999999999999999999998754  888999998774

>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=85.66  E-value=2  Score=37.98  Aligned_cols=73  Identities=14%  Similarity=0.156  Sum_probs=49.7

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhcc-CCcE---EEEEE--e--------ccEEEEEEcCHHHHHHHHHHcCCCccCC--
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEP-YGKI---ISVRI--R--------RNFAFVQYEVQEDATRALDATNMSKLTD--  212 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~-~G~v---~~v~~--~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g--  212 (425)
                      ....|.|.+| |-.+|++++.+.+.. ++..   ..+.-  .        -.-|||.|.+.+++..-...++|..|-+  
T Consensus         6 ~~~KvVIR~L-PP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    6 EGTKVVIRRL-PPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ---EEEEEEE--TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             cCceEEEeCC-CCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            3468999999 777889999998877 6655   33431  1        2379999999999999999999976643  


Q ss_pred             ---eEEEEEEeee
Q 014384          213 ---RVISVEYAVR  222 (425)
Q Consensus       213 ---~~i~v~~a~~  222 (425)
                         ....|++|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence               3566777655

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=83.62  E-value=3.6  Score=40.96  Aligned_cols=62  Identities=23%  Similarity=0.379  Sum_probs=52.8

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEecc------EEEEEEcCHHHHHHHHHHcCCCccCC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRN------FAFVQYEVQEDATRALDATNMSKLTD  212 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~~g------~afV~f~~~~~A~~A~~~l~g~~~~g  212 (425)
                      ...|+|-.+ |..++..||..|+..|- .|..|.+.+.      .++|+|.+.++|..-.+.+||..|..
T Consensus        74 ~~mLcilaV-P~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAV-PAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEec-cccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            788999999 88888999999887654 6778887532      67799999999999999999999884

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=80.76  E-value=29  Score=37.15  Aligned_cols=61  Identities=7%  Similarity=0.096  Sum_probs=47.8

Q ss_pred             CCCCHHHHHhhhccCC-----cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          161 YHTRTRDLERHFEPYG-----KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G-----~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ..++..+|..++..-+     .|-.|.|...|.||+... ..|...+..|++..+.|+.|.|+.+..
T Consensus       497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        497 DGVEVRHIVGAIANEGDISSRYIGNIKLFASHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             cCCCHHHHHHHHHhhcCCChhhCCcEEEeCCceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            4666777777766554     356778889999999765 457888889999999999999998753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	425
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-07
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		1e-06
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-06
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		8e-06
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		3e-05
1wf2_A	98	Solution Structure Of Rrm Domain In Hnrpc Protein L		4e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		4e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		6e-05
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		8e-05
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		9e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		4e-04
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		5e-04

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 7/73 (9%)
Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRGLDRT 111
           I+ GN   D R  D+E +F +YG +  +D+K+      FAF+  +D RDAEDA+ G D  
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 112 EFGRKGRRLRVEW 124
           ++   G RLRVE+
Sbjct: 85  DY--DGYRLRVEF 95

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 60  GNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
           GN        +L   F  YG V   D+   +AF++M+   DA +AIRGLD TEF  +G+R
Sbjct: 16  GNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF--QGKR 73
Query: 120 LRVEWT 125
           + V+ +
Sbjct: 74  MHVQLS 79

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN    A + +LER F  YG +  V +     GFAF+  +D RDAEDA+RGLD    
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 114 GRKGRRLRVEWT 125
              G R+RVE +
Sbjct: 63  --CGSRVRVELS 72

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L   + 
Sbjct: 8   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 114 GRKGRRLRVEWTKHE 128
              G  + VE +K++
Sbjct: 68  --HGVNINVEASKNK 80

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           IF GN        +L  LF R G+V   D+   +AF++M+ E DA+ AI  L+  E   K
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV--K 69
Query: 117 GRRLRVE 123
           G+R+ VE
Sbjct: 70  GKRINVE 76

>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein Length = 98

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTD 212
           +F+ N +    +  D+E  F  YGKI+   + + FAFVQY  + +A  A+   +   +  
Sbjct: 18  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 213 RVISVEYA 220
           +V+ +  A
Sbjct: 78  QVLDINLA 85

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 75/181 (41%), Gaps = 37/181 (20%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 105
           M  ++ G+   D  ++ L   F   G +  +    DM +    G+A++      DAE   
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE--- 71
Query: 106 RGLDRTEFGR-KGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKT--LFVINFDPYH 162
           R LD   F   KG+ +R+ W++ +                 + R S    +F+ N D   
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRD----------------PSLRKSGVGNIFIKNLDK-S 114
Query: 163 TRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 216
              + L   F  +G I+S ++       + + FV +E QE A RA++  N   L DR + 
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Query: 217 V 217
           V
Sbjct: 175 V 175

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 9/90 (10%)
Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           P  +L+V +  P  T     E+ F P G I+S+R+ R+        +A+V ++   DA R
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEK-FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNG 230
           ALD  N   +  + + + ++ RD   R++G
Sbjct: 73  ALDTMNFDVIKGKPVRIMWSQRDPSLRKSG 102

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 61  NFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTE 112
           N   D R++DL+ LFR +G + R+ +          GFAFI      DA  AI G+  + 
Sbjct: 22  NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV--SG 79
Query: 113 FGRKGRRLRVEWTK 126
           FG     L VEW K
Sbjct: 80  FGYDHLILNVEWAK 93

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN   +  +++LER F  YG +  V +     GFAF+  +D RDA DA+R LD    
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLD---- 131
Query: 114 GRK--GRRLRVEWTKHE 128
           GR   G R+RVE +  E
Sbjct: 132 GRTLCGCRVRVELSNGE 148

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN   +  +++LER F  YG +  V +     GFAF+  +D RDA DA+R LD    
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELD---- 131
Query: 114 GRK--GRRLRVEWTKHE 128
           GR   G R+RVE +  E
Sbjct: 132 GRTLCGCRVRVELSNGE 148

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 75/181 (41%), Gaps = 37/181 (20%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 105
           M  ++ G+   D  ++ L   F   G +  +    DM +    G+A++      DAE   
Sbjct: 10  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE--- 66
Query: 106 RGLDRTEFGR-KGRRLRVEWTKHEXXXXXXXXXXXXXXXXTNTRPSKT--LFVINFDPYH 162
           R LD   F   KG+ +R+ W++ +                 + R S    +F+ N D   
Sbjct: 67  RALDTMNFDVIKGKPVRIMWSQRD----------------PSLRKSGVGNIFIKNLDK-S 109
Query: 163 TRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 216
              + L   F  +G I+S ++       + + FV +E QE A RA++  N   L DR + 
Sbjct: 110 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 217 V 217
           V
Sbjct: 170 V 170

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F P+G I  ++I         R FAFV++E+ EDA  A+D  N S+L  R I V  
Sbjct: 29  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 88
Query: 220 A 220
           A
Sbjct: 89  A 89

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 11/77 (14%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMK-SGFAFIYMDDERDAEDAI 105
           MR I+ GN  Y A    ++ LF ++GKV       DR   K  GF F+ M +E  +E AI
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AI 59
Query: 106 RGLDRTEFGRKGRRLRV 122
             LD T+F   GR +RV
Sbjct: 60  AKLDNTDF--MGRTIRV 74

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 10/82 (12%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAI 105
           M  +   N  Y      L R+F +YG+V       DR   +S GFAF+   D+RDAEDA+
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 106 RGLDRTEFGRKGRRLRVEWTKH 127
             +D       GR LRV+  ++
Sbjct: 107 DAMDGAVL--DGRELRVQMARY 126

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F P+G I  ++I         R FAFV++E+ EDA  A+D  N S+L  R I V  
Sbjct: 80  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 220 A 220
           A
Sbjct: 140 A 140

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F P+G I  ++I         R FAFV++E+ EDA  A+D  N S+L  R I V  
Sbjct: 24  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 220 A 220
           A
Sbjct: 84  A 84

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F P+G I  ++I         R FAFV++E+ EDA  A+D  N S+L  R I V  
Sbjct: 22  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 220 A 220
           A
Sbjct: 82  A 82

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F P+G I  ++I         R FAFV++E+ EDA  A+D  N S+L  R I V  
Sbjct: 19  LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 220 A 220
           A
Sbjct: 79  A 79

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 57  IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRG 107
           +F GN      ++SD+E +F +YG+V    +  G+AF+   +ER A  A+ G
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLG 81

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 10/82 (12%)
Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAI 105
           M  +   N  Y      L R+F +YG+V       DR   +S GFAF+   D+RDAEDA+
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 106 RGLDRTEFGRKGRRLRVEWTKH 127
             +D       GR LRV+  ++
Sbjct: 130 DAMDGAVL--DGRELRVQMARY 149

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	425
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-31
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-29
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-29
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-13
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-26
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-26
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-15
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-25
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-24
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-23
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-20
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-13
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-22
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-21
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	8e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-21
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-21
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-21
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-19
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	9e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-17
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-16
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-16
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-15
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	7e-15
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	8e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-12
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-14
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-13
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-14
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	7e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-13
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-12
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-13
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-10
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-09
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-12
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	6e-12
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-05
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-12
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-12
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-10
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-11
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	8e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-08
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-10
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-05
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-09
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-07
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	8e-07
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-04
2div_A	99	TRNA selenocysteine associated protein; structural	7e-06
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	5e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	8e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	8e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-04

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  120 bits (303), Expect = 2e-31
 Identities = 35/202 (17%), Positives = 56/202 (27%), Gaps = 30/202 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +   N      Q   E L R +G +            +S G+ F     +  A  A   L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
                G   R L V W             + A + +     S+ L V    P       L
Sbjct: 158 LGKPLG--PRTLYVHW-------------TDAGQLTPALLHSRCLCVDRLPPGFNDVDAL 202

Query: 169 ERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV 221
            R           ++          FA ++YE  E A  A    +   L    + V +  
Sbjct: 203 CRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCA 262

Query: 222 RDDDDRRNGHSPDRNRDRSPDR 243
                R    +    +  + +R
Sbjct: 263 PGPPGRSMLAALIAAQATALNR 284

>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 =  102 bits (256), Expect = 7e-25
 Identities = 32/185 (17%), Positives = 52/185 (28%), Gaps = 34/185 (18%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGR 115
           I       D    ++  L   Y        K  G AF+ + +   AE AI    ++    
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRL-- 82

Query: 116 KGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPY 175
           + R L V+                             L V N  P     +  E    P+
Sbjct: 83  RERELSVQLQPT----------------------DALLCVANL-PPSLTQQQFEELVRPF 119

Query: 176 GKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDR 227
           G +    +  +        + F +Y  ++ A RA        L  R + V +        
Sbjct: 120 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP 179

Query: 228 RNGHS 232
              HS
Sbjct: 180 ALLHS 184

>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 = 58.1 bits (141), Expect = 1e-09
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 142 RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDAT 199
                 R  + + +    P     +++      Y  +    + +    AFV     E A 
Sbjct: 14  HTERQFRNRRKILIRGL-PGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAE 71

Query: 200 RALDATNMSKLTDRVISVEYAVRD 223
            A++A + S+L +R +SV+    D
Sbjct: 72  AAINAFHQSRLRERELSVQLQPTD 95

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score =  112 bits (281), Expect = 2e-29
 Identities = 30/199 (15%), Positives = 58/199 (29%), Gaps = 36/199 (18%)

Query: 57  IFCGNFEYDARQSD-LERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTE 112
           +     +      D +  +F  YG V++V     K G A + M D    + AI  L+   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNF 66

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNT---------------------RPSK 151
              +  ++ V  +K    +     G      S                         PS 
Sbjct: 67  MFGQ--KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSN 124

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALD 203
            L   N  P      +     +  G      +        R +   ++++ + DA   L 
Sbjct: 125 VLHFFNA-PLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLG 183

Query: 204 ATNMSKLTDRVISVEYAVR 222
             N  ++ +      Y ++
Sbjct: 184 FLNHYQMKNPNGPYPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 72.8 bits (178), Expect = 4e-15
 Identities = 18/125 (14%), Positives = 39/125 (31%), Gaps = 3/125 (2%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDAT 205
            S  L V   D        +   F  YG +  V+    +   A V+        RA+   
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62

Query: 206 NMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGS 265
           N + +  + ++V  + +        +  +       D    R+      E+ + +  +  
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 266 SRSPY 270
           S   +
Sbjct: 123 SNVLH 127

>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 =  113 bits (286), Expect = 6e-29
 Identities = 38/183 (20%), Positives = 66/183 (36%), Gaps = 29/183 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGL 108
           ++  NF     Q ++  L +    V         R +    FA+I +  + DA   +  L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
           +  +    G  L  + +              ++R  + T   + + + N          L
Sbjct: 180 NGLKIE--GYTLVTKVSNPLE---------KSKRTDSATLEGREIMIRNLSTELLDENLL 228

Query: 169 ERHFEPYGKIISVRI---------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
              FE +G I  + I             AF+ +E ++ A RAL   N S L +R ISV  
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSL 287

Query: 220 AVR 222
           A +
Sbjct: 288 ADK 290

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 91.6 bits (228), Expect = 5e-21
 Identities = 30/187 (16%), Positives = 62/187 (33%), Gaps = 41/187 (21%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KSGFAFIYMDDERDAEDAIRGLDR 110
           +   N      Q+ + + F+  G +  VD+         FA I       A  AI    +
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLER 170
                +   + V                             TL++ NF P +T+  ++  
Sbjct: 104 VVGQNE---IIVSHLT-----------------------ECTLWMTNFPPSYTQR-NIRD 136

Query: 171 HFEPYGKI-ISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR 222
             +    + +S+R+        R FA++    +EDA   ++  N  K+    +  + +  
Sbjct: 137 LLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 196

Query: 223 DDDDRRN 229
            +  +R 
Sbjct: 197 LEKSKRT 203

>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 =  106 bits (267), Expect = 2e-27
 Identities = 31/176 (17%), Positives = 66/176 (37%), Gaps = 28/176 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV------DRVDMKS-GFAFIYMDDERDAEDAIRGLD 109
           +F GN   +   ++L+               D     +  F ++  +   D E A+  L 
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 74

Query: 110 RTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLE 169
             +    G  +++E  K               R S   R ++TL   N   ++    +L+
Sbjct: 75  GLKVF--GNEIKLEKPK--------------GRDSKKVRAARTLLAKNL-SFNITEDELK 117

Query: 170 RHFEPYGKIISVR---IRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR 222
             FE   +I  V      +  A+++++ + DA + L+    +++  R +S+ Y   
Sbjct: 118 EVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  107 bits (269), Expect = 2e-27
 Identities = 39/199 (19%), Positives = 78/199 (39%), Gaps = 24/199 (12%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAE 102
            A+M  ++ G+  Y+  +  + + F  +G +       D V MK  GFAF+  +    A+
Sbjct: 25  LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84

Query: 103 DAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYH 162
            A+  ++    G  GR ++V                   + +   R    ++V +     
Sbjct: 85  LALEQMNSVMLG--GRNIKVGRP-----SNIGQAQPIIDQLAEEARAFNRIYVASVHQ-D 136

Query: 163 TRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRV 214
               D++  FE +GKI S  +         + + F++YE  + +  A+ + N+  L  + 
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196

Query: 215 ISVEYAVRDDDDRRNGHSP 233
           + V  AV          +P
Sbjct: 197 LRVGKAVTPPMPLLTPATP 215

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 67.0 bits (164), Expect = 5e-13
 Identities = 28/130 (21%), Positives = 44/130 (33%), Gaps = 20/130 (15%)

Query: 132 RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------- 183
            +  G  SA +          ++V +          + + F P+G I S+ +        
Sbjct: 10  GQQMGRGSAAQRQGALAIMSRVYVGSIYY-ELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68

Query: 184 RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDR 243
            + FAFV+YEV E A  AL+  N   L  R I V              S         D+
Sbjct: 69  HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV-----------GRPSNIGQAQPIIDQ 117

Query: 244 GRRRSPSPYR 253
               + +  R
Sbjct: 118 LAEEARAFNR 127

>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 =  101 bits (253), Expect = 1e-26
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 4/86 (4%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           M  +F GN   +A + ++  LF +YGKV   D+   + F++++D+  AEDAIR L   + 
Sbjct: 8   MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKL 67

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSS 139
              G  + VE +K++   +   G SS
Sbjct: 68  H--GVNINVEASKNKS--KASSGPSS 89

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 66.8 bits (164), Expect = 3e-14
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 2/89 (2%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 203
           S+ +     LF+ N  P     +++   FE YGK++   I +N+ FV  E +  A  A+ 
Sbjct: 2   SSGSSGMVKLFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIR 60

Query: 204 ATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
             +  KL    I+VE + ++     +G S
Sbjct: 61  NLHHYKLHGVNINVEAS-KNKSKASSGPS 88

>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 =  100 bits (251), Expect = 3e-26
 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 52  AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRT 111
                IF GN        +L  LF R G+V   D+   +AF++M+ E DA+ AI  L+  
Sbjct: 7   GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGK 66

Query: 112 EFGRKGRRLRVEWTKHERGIRRPGGG 137
           E    G+R+ VE +   +    P  G
Sbjct: 67  EVK--GKRINVELSTKGQKKSGPSSG 90

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 68.8 bits (169), Expect = 7e-15
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALD 203
           S ++  +  +FV N       +++L   FE  G++I   + +++AFV  E + DA  A+ 
Sbjct: 3   SGSSGNTWKIFVGNV-SAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIA 61

Query: 204 ATNMSKLTDRVISVEYAVRDDDDRRNG 230
             N  ++  + I+VE + +        
Sbjct: 62  QLNGKEVKGKRINVELSTKGQKKSGPS 88

>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 =  101 bits (252), Expect = 4e-25
 Identities = 43/192 (22%), Positives = 71/192 (36%), Gaps = 31/192 (16%)

Query: 57  IFCGNF-EYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTE 112
           +   N          L  LF  YG V RV +   K   A + M D   A+ A+  L+  +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65

Query: 113 FGRKGRRLRVEWTKH-----------ERGIRRPGGGSSARRPSTNTR--------PSKTL 153
               G+ +R+  +KH           ++G+ +  G S   R              PS TL
Sbjct: 66  LH--GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATL 123

Query: 154 FVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSK 209
            + N  P  +   DL+  F   G ++         R  A +Q    E+A +AL   +   
Sbjct: 124 HLSNIPPSVSEE-DLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182

Query: 210 LTD-RVISVEYA 220
           L +   + V ++
Sbjct: 183 LGENHHLRVSFS 194

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 70.3 bits (172), Expect = 3e-14
 Identities = 23/121 (19%), Positives = 39/121 (32%), Gaps = 11/121 (9%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATN 206
           +  L V N +P     + L   F  YG +  V+I   ++  A VQ      A  A+   N
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 207 MSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSS 266
             KL  + I +  +           +    R+   D+G  +        R      +   
Sbjct: 63  GHKLHGKPIRITLS--------KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQ 114

Query: 267 R 267
            
Sbjct: 115 N 115

>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 =   99 bits (250), Expect = 4e-25
 Identities = 44/182 (24%), Positives = 67/182 (36%), Gaps = 37/182 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +       D    +L  LFR  G +       D     S G+AF+    E D++ AI+ L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
           +      + +RL+V +                 RP   +     L+V N     T    L
Sbjct: 66  NGITV--RNKRLKVSY----------------ARPGGESIKDTNLYVTNLPRTIT-DDQL 106

Query: 169 ERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKL--TDRVISVE 218
           +  F  YG I+   I         R  AFV+Y  +E+A  A+ A N        + +SV 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

Query: 219 YA 220
            A
Sbjct: 167 LA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 57.2 bits (139), Expect = 5e-10
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 9/90 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRA 201
           +  L V          R+L   F   G I + RI R+        +AFV +  + D+ RA
Sbjct: 3   NTNLIVNYLPQ-DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 202 LDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
           +   N   + ++ + V YA    +  ++ +
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTN 91

>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 = 95.4 bits (238), Expect = 2e-24
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           +  GN        +L   F  YG V   D+   +AF++M+   DA +AIRGLD TEF   
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQ-- 70

Query: 117 GRRLRVEWTKH-ERGIRRPGGG 137
           G+R+ V+ +    R    P  G
Sbjct: 71  GKRMHVQLSTSRLRTASGPSSG 92

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 68.0 bits (167), Expect = 1e-14
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQE 196
           GSS        + S  L V N        ++L   FE YG +I   I +++AFV  E  E
Sbjct: 1   GSSGSSG----KASTKLHVGNI-SPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAE 55

Query: 197 DATRALDATNMSKLTDRVISVEYA 220
           DA  A+   + ++   + + V+ +
Sbjct: 56  DAVEAIRGLDNTEFQGKRMHVQLS 79

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 96.6 bits (241), Expect = 1e-23
 Identities = 29/194 (14%), Positives = 64/194 (32%), Gaps = 29/194 (14%)

Query: 52  AMMRPIFCGNFEYDARQSDLERLFRRYGKV------------DRVDMKS-GFAFIYMDDE 98
           AM R ++ GN  +   +  +   F    ++                 +   FAF+     
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 99  RDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTR----PSKTLF 154
            +   A+   D   F   G+ L++      + +       S   P   +      +  LF
Sbjct: 62  DETTQAM-AFDGIIFQ--GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLF 118

Query: 155 VINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATN 206
           +     Y      ++     +G + +  + ++        +AF +Y       +A+   N
Sbjct: 119 IGGLPNYLN-DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177

Query: 207 MSKLTDRVISVEYA 220
             +L D+ + V+ A
Sbjct: 178 GMQLGDKKLLVQRA 191

>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 = 94.9 bits (237), Expect = 2e-23
 Identities = 31/183 (16%), Positives = 73/183 (39%), Gaps = 32/183 (17%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRG 107
           R ++ GN +    +  L++ F+  G +       D+ +    +AF+      DA  A++ 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 108 LDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRD 167
           L+  +   +   +++ W              + +   +++  +  LFV + +  +     
Sbjct: 61  LNGKQI--ENNIVKINW--------------AFQSQQSSSDDTFNLFVGDLNV-NVDDET 103

Query: 168 LERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           L   F+ +   +S  +         R + FV +  Q+DA  A+D+     L  R + + +
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163

Query: 220 AVR 222
           A +
Sbjct: 164 AAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 58.7 bits (143), Expect = 1e-10
 Identities = 20/88 (22%), Positives = 41/88 (46%), Gaps = 8/88 (9%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALD 203
           + L+V N D   T    L+++F+  G I +++I  +       +AFV+Y    DA  AL 
Sbjct: 1   RVLYVGNLDKAITED-ILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59

Query: 204 ATNMSKLTDRVISVEYAVRDDDDRRNGH 231
             N  ++ + ++ + +A +      +  
Sbjct: 60  TLNGKQIENNIVKINWAFQSQQSSSDDT 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 91.5 bits (228), Expect = 7e-23
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 10/102 (9%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRAL 202
              N  P   LF+ N    +    DL R F PYG I+ + I+  F F+Q++  +    A+
Sbjct: 3   EMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 62

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           +  +      + + +E +           S  R +    D G
Sbjct: 63  ECESQEMNFGKKLILEVS----------SSNARPQFDHGDHG 94

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 84.2 bits (209), Expect = 2e-20
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 57  IFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F GN    +  + DL R+F  YG + ++++K+ F FI  D+ +   DAI    +     
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN-- 70

Query: 116 KGRRLRVEWTKHERGIRRPGGGSSAR 141
            G++L +E +       RP       
Sbjct: 71  FGKKLILEVS---SSNARPQFDHGDH 93

>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 = 94.7 bits (236), Expect = 8e-23
 Identities = 44/208 (21%), Positives = 80/208 (38%), Gaps = 31/208 (14%)

Query: 43  SQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIY 94
             ++ +A    M  ++ G+   D  ++ L   F   G +       D +  +S G+A++ 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 95  MDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLF 154
                DAE A+  ++      KG+ +R+ W              S R PS        +F
Sbjct: 64  FQQPADAERALDTMNFDVI--KGKPVRIMW--------------SQRDPSLRKSGVGNIF 107

Query: 155 VINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALDATNMS 208
           + N D      + L   F  +G I+S ++       + + FV +E QE A RA++  N  
Sbjct: 108 IKNLDKSID-NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGM 166

Query: 209 KLTDRVISVEYAVRDDDDRRNGHSPDRN 236
            L DR + V       +      +  + 
Sbjct: 167 LLNDRKVFVGRFKSRKEREAELGARAKE 194

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 66.5 bits (163), Expect = 7e-13
 Identities = 29/104 (27%), Positives = 50/104 (48%), Gaps = 9/104 (8%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------F 187
           G   +  PS  + P  +L+V +  P  T    L   F P G I+S+R+ R+        +
Sbjct: 1   GPLGSMNPSAPSYPMASLYVGDLHPDVT-EAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
           A+V ++   DA RALD  N   +  + + + ++ RD   R++G 
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV 103

>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 = 93.4 bits (233), Expect = 1e-22
 Identities = 40/182 (21%), Positives = 76/182 (41%), Gaps = 37/182 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +       +  Q +   LF   G++       D++  +S G+ F+   D +DAE AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
           +      + + ++V +               AR  S + R +  L+V       T  ++L
Sbjct: 65  NGLRL--QTKTIKVSY---------------ARPSSASIRDAN-LYVSGLPKTMT-QKEL 105

Query: 169 ERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKL--TDRVISVE 218
           E+ F  YG+II+ RI  +          F++++ + +A  A+   N  K       I+V+
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

Query: 219 YA 220
           +A
Sbjct: 166 FA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 55.7 bits (135), Expect = 2e-09
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 10/91 (10%)

Query: 150 SKT-LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           SKT L V      +    +    F   G+I S ++ R+        + FV Y   +DA +
Sbjct: 1   SKTNLIVNYLPQ-NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
           A++  N  +L  + I V YA       R+ +
Sbjct: 60  AINTLNGLRLQTKTIKVSYARPSSASIRDAN 90

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 95.5 bits (238), Expect = 1e-22
 Identities = 50/222 (22%), Positives = 82/222 (36%), Gaps = 41/222 (18%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVD-MKS-GFAFIYMDDERDAEDAIRGLDRTEFG 114
           +F GN   D  + D +RLF RYG+   V   +  GF FI ++    AE A   LD T   
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL- 83

Query: 115 RKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEP 174
            K R LR+ +                            L V N  P  +    LE+ F  
Sbjct: 84  -KSRPLRIRF----------------------ATHGAALTVKNLSPVVS-NELLEQAFSQ 119

Query: 175 YGKIISVRI-------RRNFAFVQYEVQEDATRALDATN----MSKLTDRVISVEYAVRD 223
           +G +    +            FV++  +  A +AL+       +   T R + VE   + 
Sbjct: 120 FGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF 179

Query: 224 DDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGS 265
           DD+      P++   ++    + R   P   + G+ ++   S
Sbjct: 180 DDED---GLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYAS 218

>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 = 62.8 bits (153), Expect = 2e-11
 Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 3/89 (3%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEV 194
            S  +           LFV N     T   D +R FE YG+   V I   R F F++ E 
Sbjct: 9   KSFLKPGEKTYTQRCRLFVGNLPTDIT-EEDFKRLFERYGEPSEVFINRDRGFGFIRLES 67

Query: 195 QEDATRALDATNMSKLTDRVISVEYAVRD 223
           +  A  A    + + L  R + + +A   
Sbjct: 68  RTLAEIAKAELDGTILKSRPLRIRFATHG 96

>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 = 90.7 bits (226), Expect = 8e-22
 Identities = 37/185 (20%), Positives = 65/185 (35%), Gaps = 37/185 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRV--DMKS-GFAFIYMDDERDAEDAIR 106
           +F G       + DL  LF +YG V       DR     +S G  F+     + A +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 107 GLDRTE-FGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRT 165
            L   +        ++++    E+                N    + LF+       T  
Sbjct: 66  ALHNMKVLPGMHHPIQMKPADSEK---------------NNAVEDRKLFIGMISKKCT-E 109

Query: 166 RDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTD---RVI 215
            D+   F  +G+I   RI R         AFV +  +  A  A+ A + ++  +     +
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM 169

Query: 216 SVEYA 220
            V++A
Sbjct: 170 VVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 59.9 bits (146), Expect = 6e-11
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 12/97 (12%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN----------FAFVQYEVQEDAT 199
           +  +FV          +DL   FE YG +  + + R+            FV +  ++ A 
Sbjct: 3   AIKMFVGQVPR-TWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRN 236
            A +A +  K+   +      ++  D  +N    DR 
Sbjct: 62  EAQNALHNMKVLPGMHHPIQ-MKPADSEKNNAVEDRK 97

>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 = 88.6 bits (220), Expect = 1e-21
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 57  IFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F GN      ++SD+E +F +YG+V    +  G+AF+   +ER A  A+ G +      
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVL-- 87

Query: 116 KGRRLRVEWTKHERGIRRPGGGS 138
            G+ L +      +   R G  S
Sbjct: 88  AGQTLDINMAGEPKP-DRSGPSS 109

>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 = 74.7 bits (184), Expect = 8e-17
 Identities = 22/103 (21%), Positives = 41/103 (39%)

Query: 130 GIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAF 189
           G+      S+    +     +  +F+ N +    +  D+E  F  YG++    + + +AF
Sbjct: 7   GMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAF 66

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           VQY  +  A  A+   N   L  + + +  A     DR    S
Sbjct: 67  VQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109

>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 = 89.6 bits (223), Expect = 2e-21
 Identities = 25/187 (13%), Positives = 56/187 (29%), Gaps = 41/187 (21%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------------GFAFIYMDDERDA 101
           R ++ GN  +   +  +   F    ++  +                  FAF+      + 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 102 EDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPY 161
             A+   D   F   G+ L++                           +  LF+     Y
Sbjct: 65  TQAM-AFDGIIFQ--GQSLKIRRPH----------------DYQPLPGAHKLFIGGLPNY 105

Query: 162 HTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDR 213
                 ++     +G + +  +         + +AF +Y       +A+   N  +L D+
Sbjct: 106 LN-DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 164

Query: 214 VISVEYA 220
            + V+ A
Sbjct: 165 KLLVQRA 171

>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 = 90.8 bits (225), Expect = 3e-21
 Identities = 43/192 (22%), Positives = 72/192 (37%), Gaps = 31/192 (16%)

Query: 57  IFCGNFEYDA-RQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTE 112
           +   N   +      L  LF  YG V RV +   K   A + M D   A+ A+  L+  +
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 96

Query: 113 FGRKGRRLRVEWTKH-----------ERGIRRPGGGSSARR--------PSTNTRPSKTL 153
               G+ +R+  +KH           ++G+ +  G S   R              PS TL
Sbjct: 97  LH--GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATL 154

Query: 154 FVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSK 209
            + N  P  +   DL+  F   G ++         R  A +Q    E+A +AL   +   
Sbjct: 155 HLSNIPPSVSEE-DLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213

Query: 210 LTD-RVISVEYA 220
           L +   + V ++
Sbjct: 214 LGENHHLRVSFS 225

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 69.3 bits (169), Expect = 1e-13
 Identities = 26/142 (18%), Positives = 41/142 (28%), Gaps = 9/142 (6%)

Query: 133 RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAF 189
           R         P      +  L V N +P     + L   F  YG +  V+I   ++  A 
Sbjct: 17  RGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENAL 76

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSP 249
           VQ      A  A+   N  KL  + I +  +   +          R         +    
Sbjct: 77  VQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV------QLPREGQEDQGLTKDYGN 130

Query: 250 SPYRRERGSPDYGRGSSRSPYR 271
           SP  R +        +   P  
Sbjct: 131 SPLHRFKKPGSKNFQNIFPPSA 152

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 86.2 bits (214), Expect = 5e-21
 Identities = 32/91 (35%), Positives = 45/91 (49%), Gaps = 5/91 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---GFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN    A + +LER F  YG +  V +     GFAF+  +D RDAEDA+RGLD    
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPS 144
              G R+RVE +       R     + R+  
Sbjct: 63  C--GSRVRVELSTGMPRRSRFDRPPARRKLL 91

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 6/93 (6%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYEVQEDATRALDATNMSKLTDRVIS 216
                  +LER F  YG + +V I RN   FAFV++E   DA  A+   +   +    + 
Sbjct: 9   GTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR 68

Query: 217 VEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSP 249
           VE +       R    P R   R         P
Sbjct: 69  VELSTGMPRRSRFDRPPAR---RKLLEVLFNGP 98

>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 = 85.8 bits (213), Expect = 7e-21
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 3/74 (4%)

Query: 57  IFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F GN    +  + DL R+F  YG + ++++K+ F FI  D+ +   DAI    +     
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMN-- 82

Query: 116 KGRRLRVEWTKHER 129
            G++L +E +    
Sbjct: 83  FGKKLILEVSSSNA 96

>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 = 76.6 bits (189), Expect = 1e-17
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 132 RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQ 191
                G   R     +R    LF+ N    +    DL R F PYG I+ + I+  F F+Q
Sbjct: 8   HHHSSGLVPRGSHMKSR----LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQ 63

Query: 192 YEVQEDATRALDATNMSKLTDRVISVEYA 220
           ++  +    A++  +      + + +E +
Sbjct: 64  FDNPQSVRDAIEXESQEMNFGKKLILEVS 92

>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 = 81.6 bits (202), Expect = 3e-19
 Identities = 35/88 (39%), Positives = 50/88 (56%), Gaps = 9/88 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRGLDRT 111
           I+ GN   D R  D+E +F +YG +  +D+K+      FAF+  +D RDAEDA+ G D  
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84

Query: 112 EFGRKGRRLRVEWTKHERGIRRPGGGSS 139
           ++   G RLRVE+ +  RG     G SS
Sbjct: 85  DYD--GYRLRVEFPRSGRG--TGSGPSS 108

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 25/118 (21%), Positives = 38/118 (32%), Gaps = 17/118 (14%)

Query: 132 RRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RN 186
              G                 ++V N  P   RT+D+E  F  YG I  + ++       
Sbjct: 4   GSSGMSGGGVIRGPAGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP 62

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           FAFV++E   DA  A+   +        + VE+               R     P  G
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP-----------RSGRGTGSGPSSG 109

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 81.2 bits (201), Expect = 4e-19
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 1/103 (0%)

Query: 126 KHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR 185
            H         GS           +  LFV  F P   +  +L   F P+G +  V+I  
Sbjct: 7   HHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPF-PLDVQESELNEIFGPFGPMKEVKILN 65

Query: 186 NFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRR 228
            FAFV++E  E A +A++  +     ++ + V Y+       R
Sbjct: 66  GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 75.0 bits (185), Expect = 7e-17
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           +F   F  D ++S+L  +F  +G +  V + +GFAF+  ++   A  AI  +    F   
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFA-- 91

Query: 117 GRRLRVEWTKHERGIRR 133
            + L V ++K      R
Sbjct: 92  NQPLEVVYSKLPAKRYR 108

>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 = 81.5 bits (201), Expect = 9e-19
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 52  AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGL 108
            +   ++ GN   +  +++LER F  YG +  V +     GFAF+  +D RDA DA+R L
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130

Query: 109 DRTEFGRKGRRLRVEWTKHER 129
           D       G R+RVE +  E+
Sbjct: 131 DGRTLC--GCRVRVELSNGEK 149

>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 = 67.6 bits (165), Expect = 8e-14
 Identities = 29/135 (21%), Positives = 42/135 (31%), Gaps = 6/135 (4%)

Query: 89  GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTR 148
           G       D   AE   +                                   R S    
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC--P 71

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYEVQEDATRALDAT 205
               ++V N    +    +LER F  YG + SV + RN   FAFV++E   DA  A+   
Sbjct: 72  LDCKVYVGNL-GNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 130

Query: 206 NMSKLTDRVISVEYA 220
           +   L    + VE +
Sbjct: 131 DGRTLCGCRVRVELS 145

>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 = 80.0 bits (198), Expect = 1e-18
 Identities = 28/108 (25%), Positives = 48/108 (44%), Gaps = 5/108 (4%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQE 196
           GSS    S+     K LFV N          LE+ F  +GK+  V+  +++AF+ ++ ++
Sbjct: 1   GSSG---SSGMAKVKVLFVRNL-ANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERD 56

Query: 197 DATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
            A +A++  N   L    I + +A +  D +R      R     P  G
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFA-KPPDQKRKERKAQRQAASGPSSG 103

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 4/91 (4%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRK 116
           +F  N      +  LE+ F ++GK++RV     +AFI+ D+   A  A+  ++  +    
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLE-- 71

Query: 117 GRRLRVEW--TKHERGIRRPGGGSSARRPST 145
           G  + + +     ++   R     +A  PS+
Sbjct: 72  GENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>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 = 78.1 bits (193), Expect = 3e-18
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 7/89 (7%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV--DRVDMKSGFAFIYMDDERDAEDAIRGLD-R 110
           M  ++ GN        DL +LF         +V +KSG+AF+   D+  A  AI  L  +
Sbjct: 8   MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 67

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGSS 139
            E    G+ + V+++  ++   R  G SS
Sbjct: 68  VEL--HGKIMEVDYSVSKK--LRSSGPSS 92

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 4/92 (4%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRA 201
           S+ +     L++ N         DL + F      ++ ++  +  +AFV Y  Q  A RA
Sbjct: 2   SSGSSGMNKLYIGNL-SPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRA 60

Query: 202 LDATN-MSKLTDRVISVEYAVRDDDDRRNGHS 232
           ++  +   +L  +++ V+Y+V          S
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSSGPSS 92

>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 = 74.6 bits (184), Expect = 7e-17
 Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           +F GN   D  + ++ +LF +YGK   V +    GF FI ++    AE A   LD     
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 77

Query: 115 RKGRRLRVEWTKHERGIRRPGGGS 138
             G++LRV +  H       G  S
Sbjct: 78  --GKQLRVRFACH-SASLTSGPSS 98

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 4/97 (4%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYE 193
           G S +            LFV N  P      ++ + FE YGK   V I   + F F++ E
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLE 59

Query: 194 VQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNG 230
            +  A  A    +   L  + + V +A        +G
Sbjct: 60  TRTLAEIAKVELDNMPLRGKQLRVRFA-CHSASLTSG 95

>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 = 74.4 bits (183), Expect = 7e-17
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG-KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           I   N   D+   ++  L + Y  K   VD     AF+ + +   A++AI+   +  F  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF-- 65

Query: 116 KGRRLRVEWTKHERGIRR-PGGG 137
           +G+ L V+    +  +   P  G
Sbjct: 66  RGKDLIVQLQPTDALLCSGPSSG 88

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRNFAFVQYEVQEDATRALDATNMS 208
           S  + V N  P  +  +++    + Y  K   V   +  AFV     E A  A+   +  
Sbjct: 5   SSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 209 KLTDRVISVEYAVRD 223
               + + V+    D
Sbjct: 64  SFRGKDLIVQLQPTD 78

>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 = 73.8 bits (182), Expect = 1e-16
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRTEFG 114
           ++ G    +   + L R F R+G +  +D   G  FA+I  +    A+ A   +     G
Sbjct: 20  LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLG 79

Query: 115 RKGRRLRVEWTKHERG 130
              RRLRV++ K    
Sbjct: 80  GPDRRLRVDFAKSGPS 95

>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 = 70.7 bits (174), Expect = 2e-15
 Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 5/90 (5%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQY 192
             GSS +       P+  L+V    P  T    L R F+ +G I ++      +FA++QY
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPN-TSLAALAREFDRFGSIRTIDHVKGDSFAYIQY 60

Query: 193 EVQEDATRALDATNMSKL--TDRVISVEYA 220
           E  + A  A        L   DR + V++A
Sbjct: 61  ESLDAAQAACAKMRGFPLGGPDRRLRVDFA 90

>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 = 73.1 bits (180), Expect = 3e-16
 Identities = 27/99 (27%), Positives = 38/99 (38%), Gaps = 3/99 (3%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYE 193
           G S +          K L+V N     T    +E+ F         R++  R++AFV + 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFS 59

Query: 194 VQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            +EDA  A+ A N   L    I V  A   D D     S
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98

>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 = 68.1 bits (167), Expect = 1e-14
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYG--KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTE 112
           + ++  N      +  +E+ F       V+RV     +AF++  +  DA +A++ L+   
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 75

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSS 139
               G  + V   K     +   G SS
Sbjct: 76  LD--GSPIEVTLAKPVD--KDSSGPSS 98

>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 = 71.6 bits (176), Expect = 8e-16
 Identities = 29/99 (29%), Positives = 40/99 (40%), Gaps = 7/99 (7%)

Query: 137 GSSARRPSTNTRPSK-TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYE 193
           GSS             TL+V   D        L   F P+G II + +   RN AFV YE
Sbjct: 1   GSSGSSGERRAPRKGNTLYVYGED---MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYE 57

Query: 194 VQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
             E A +A+   N +++    + V  A R      +G S
Sbjct: 58  KMESADQAVAELNGTQVESVQLKVNIA-RKQPMLDSGPS 95

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++    +     + L   F  +G +  + M      AF+  +    A+ A+  L+ T+  
Sbjct: 18  LYVYGEDMT--PTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 75

Query: 115 RKGRRLRVEWTKHERGIRRPGGGS 138
               +L+V   + ++ +   G  S
Sbjct: 76  --SVQLKVNIAR-KQPMLDSGPSS 96

>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 = 70.7 bits (174), Expect = 2e-15
 Identities = 29/89 (32%), Positives = 38/89 (42%), Gaps = 11/89 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           I   N   D R++DL+ LFR +G + R+    D  +    GFAFI      DA  AI G+
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGG 137
               +      L VEW K       P  G
Sbjct: 78  SGFGYD--HLILNVEWAK-PSTNSGPSSG 103

>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 = 65.3 bits (160), Expect = 2e-13
 Identities = 26/104 (25%), Positives = 47/104 (45%), Gaps = 10/104 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------F 187
           G S +  P+     + T+ V N     TR  DL+  F P+G I  + + ++        F
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAV-RDDDDRRNG 230
           AF+ +  +EDA RA+   +       +++VE+A    +    +G
Sbjct: 60  AFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>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 = 69.9 bits (172), Expect = 3e-15
 Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 10/89 (11%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERH----FEPYGKIISVRIRRN-----FAFVQYEVQE 196
            TRP+ T+++ N      +  +L++     F  +G+I+ + + R+      AFV ++   
Sbjct: 4   ETRPNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62

Query: 197 DATRALDATNMSKLTDRVISVEYAVRDDD 225
            AT AL +       D+ + ++YA  D D
Sbjct: 63  SATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 11/79 (13%)

Query: 57  IFCGNFEYDARQSDLER----LFRRYGKVDRV----DMKS-GFAFIYMDDERDAEDAIRG 107
           I+  N     ++ +L++    +F R+G++  +     +K  G AF+   +   A +A+R 
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70

Query: 108 LDRTEFGRKGRRLRVEWTK 126
           +    F    + +R+++ K
Sbjct: 71  MQGFPFY--DKPMRIQYAK 87

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 71.3 bits (175), Expect = 3e-15
 Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

Query: 129 RGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI----- 183
                 GG   +     +    + L+V          + L   F P+G I  ++I     
Sbjct: 42  TERHVDGGSGGSGGSGGSATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYE 100

Query: 184 ---RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
               R FAFV++E+ EDA  A+D  N S+L  R I V  A
Sbjct: 101 TEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 64.8 bits (158), Expect = 7e-13
 Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ G    +     L   F  +G +       D    K  GFAF+  +   DA  AI  +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

Query: 109 DRTEFGRKGRRLRVEW 124
           + +E    GR +RV  
Sbjct: 126 NESELF--GRTIRVNL 139

>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 = 70.5 bits (173), Expect = 4e-15
 Identities = 22/113 (19%), Positives = 47/113 (41%), Gaps = 11/113 (9%)

Query: 53  MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRG 107
           + R ++  N  Y     ++  +F +YG + ++ + +     G A++  +D  DA++A+  
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66

Query: 108 LDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDP 160
           L         R L V +    R  ++       ++     +  K  + IN DP
Sbjct: 67  LSGFNVS--NRYLVVLYYNANRAFQK----MDTKKKEEQLKLLKEKYGINTDP 113

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 68.6 bits (168), Expect = 2e-14
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-----FAFVQYEVQEDATRAL 202
             ++ L++ N  PY     ++   F  YG I  +R+         A+V YE   DA  A+
Sbjct: 6   EVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAV 64

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRRN 229
           D  +   +++R + V Y   +   ++ 
Sbjct: 65  DHLSGFNVSNRYLVVLYYNANRAFQKM 91

>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 = 69.5 bits (171), Expect = 5e-15
 Identities = 30/93 (32%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNF 187
           G S +     N  P+  L V      +T  RDL   F  YG I  V I         R F
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           AFV +E  +DA  A +  N  +L  R I V   
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 10/81 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 105
              +          + DL  +F +YG +  V    D +S    GFAF+Y ++  DA++A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 106 RGLDRTEFGRKGRRLRVEWTK 126
              +  E    GRR+RV    
Sbjct: 75  ERANGMELD--GRRIRVSGPS 93

>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 = 69.2 bits (170), Expect = 8e-15
 Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 8/103 (7%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAF 189
           G S +     +    +TL+V N     T    + + F   G   S ++         + F
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEV-LILQLFSQIGPCKSCKMITEHTSNDPYCF 59

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           V++    DA  AL A N  K+  + + V +A      +++G S
Sbjct: 60  VEFYEHRDAAAALAAMNGRKILGKEVKVNWA-TTPSSQKSGPS 101

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 9/88 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KSGFAFIYMDDERDAEDAIRGLDR 110
           ++ GN   D  +  + +LF + G      M         + F+   + RDA  A+  ++ 
Sbjct: 18  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGS 138
            +    G+ ++V W       ++ G  S
Sbjct: 78  RKI--LGKEVKVNWAT-TPSSQKSGPSS 102

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 13/100 (13%)

Query: 48  AAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDER 99
              + M+  +   N  Y      L R+F +YG+V  V +          GFAF+   D R
Sbjct: 8   PDVDGMIT-LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66

Query: 100 DAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSS 139
           DA+DA   +D  E    GR LRV+  ++ R  R   G SS
Sbjct: 67  DAQDAEAAMDGAELD--GRELRVQVARYGR--RDLSGPSS 102

>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 = 63.0 bits (154), Expect = 1e-12
 Identities = 32/104 (30%), Positives = 43/104 (41%), Gaps = 10/104 (9%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFA 188
           GSS      +     TL V N   Y T    L R FE YG++  V I         R FA
Sbjct: 1   GSSGSSGP-DVDGMITLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           FV++  + DA  A  A + ++L  R + V+ A     D     S
Sbjct: 59  FVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSS 102

>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 = 68.7 bits (168), Expect = 1e-14
 Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           I   N       ++++  F R+G + RV +      A +   +  +A  A R L  ++F 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF- 71

Query: 115 RKGRRLRVEW 124
                L +EW
Sbjct: 72  -HHVPLYLEW 80

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 67.1 bits (164), Expect = 4e-14
 Identities = 20/121 (16%), Positives = 40/121 (33%), Gaps = 15/121 (12%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRA 201
            ++ R    +   N  P  T   +++  F  +G +  V +      A V++    +A +A
Sbjct: 4   GSSGRSKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKA 62

Query: 202 LDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDY 261
                 SK     + +E+A            P      +P +   +   P  +    P  
Sbjct: 63  FRHLAYSKFHHVPLYLEWA------------PIGVFGAAPQKKDSQHEQPAEKAESGPSS 110

Query: 262 G 262
           G
Sbjct: 111 G 111

>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 = 68.1 bits (167), Expect = 3e-14
 Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 9/116 (7%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FA 188
           G S +       R   T+FV N D Y    + L+  F   G ++   I  +         
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLD-YKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIG 59

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
            V +E   +A +A+   N   L DR + V+        + +   P+R +   P  G
Sbjct: 60  TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD-ERALPKGDFFPPERPQQSGPSSG 114

>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 = 55.0 bits (133), Expect = 9e-10
 Identities = 21/98 (21%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS-GFAFIYMDDERDAEDAIRGLD 109
           +F  N +Y      L+ +F   G V R D+      KS G   +  +   +A  AI   +
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77

Query: 110 RTEFGRKGRRLRVEW--TKHERGIRRPGGGSSARRPST 145
                   R + V+       +G   P        PS+
Sbjct: 78  GQLLF--DRPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 68.0 bits (166), Expect = 3e-14
 Identities = 14/110 (12%), Positives = 34/110 (30%), Gaps = 10/110 (9%)

Query: 125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERH----FEPYGKIIS 180
           T   +  R+            +T PS+ + + N          L+          G I+ 
Sbjct: 4   TAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNI-NPEVPKEKLQALLYALASSQGDILD 62

Query: 181 VRIRRN-----FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
           + +  +      A++ +  QE A   ++A          + + ++     
Sbjct: 63  IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 50.3 bits (120), Expect = 5e-08
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 11/79 (13%)

Query: 57  IFCGNFEYDARQSDLER----LFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRG 107
           +   N   +  +  L+     L    G +  + +       G A+I    +  A+  +  
Sbjct: 32  VLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEA 91

Query: 108 LDRTEFGRKGRRLRVEWTK 126
                F  +G  L + +++
Sbjct: 92  FQGYPF--QGNPLVITFSE 108

>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 = 66.9 bits (164), Expect = 4e-14
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 41  SHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAF 92
           S S             ++  N  +    +DL R+F +YGKV +V +       KS G AF
Sbjct: 3   SGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 93  IYMDDERDAEDAIRGLDRTEFGRKGRRLRV 122
           I   D+  A++  R ++  +    GR ++ 
Sbjct: 63  ILFLDKDSAQNCTRAINNKQLF--GRVIKA 90

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 9/95 (9%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRN 186
           G   S+           T++V N  P+     DL R F  YGK++ V I         + 
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV 221
            AF+ +  ++ A     A N  +L  RVI    A+
Sbjct: 60  VAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI 94

>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 = 66.0 bits (162), Expect = 5e-14
 Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ G    +     L   F  +G +       D    K  GFAF+  +   DA  AI  +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69

Query: 109 DRTEFGRKGRRLRVEWTK 126
           + +E    GR +RV   K
Sbjct: 70  NESELF--GRTIRVNLAK 85

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 9/81 (11%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDAT 199
              + L+V          + L   F P+G I  ++I         R FAFV++E+ EDA 
Sbjct: 5   TTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 200 RALDATNMSKLTDRVISVEYA 220
            A+D  N S+L  R I V  A
Sbjct: 64  AAIDNMNESELFGRTIRVNLA 84

>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 = 71.1 bits (173), Expect = 5e-14
 Identities = 29/218 (13%), Positives = 62/218 (28%), Gaps = 19/218 (8%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERH----FEPYGKIISVRIRRN-----FAFVQYE 193
               TRP+ T+++ N +    +  +L++     F  +G+I+ + + R+      AFV ++
Sbjct: 2   AVPETRPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60

Query: 194 VQEDATRALDATNMSKLTDRVISVEYAVRDDD---------DRRNGHSPDRNRDRSPDRG 244
               AT AL +       D+ + ++YA  D D           R+     R         
Sbjct: 61  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120

Query: 245 RRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRS 304
            +++                    P   +     +     P         P  G    + 
Sbjct: 121 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180

Query: 305 PYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPY 342
           P                +    +         ++    
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEE 218

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.9 bits (118), Expect = 5e-07
 Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATNMSKLT-DRVI 215
           P  T    L   F  +     VR+   R + AFV+++ +  A  A DA    K+T +  +
Sbjct: 216 PEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275

Query: 216 SVEYA 220
            + +A
Sbjct: 276 KISFA 280

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.5 bits (117), Expect = 7e-07
 Identities = 18/104 (17%), Positives = 44/104 (42%), Gaps = 11/104 (10%)

Query: 57  IFCGNFEYDARQSDLER----LFRRYGKVDRV----DMKS-GFAFIYMDDERDAEDAIRG 107
           I+  N     ++ +L++    +F ++G++  +     +K  G AF+   +   A +A+R 
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71

Query: 108 LDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSK 151
           +    F    + +R+++ K +  I     G+   R     +   
Sbjct: 72  MQGFPFY--DKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKP 113

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.0 bits (108), Expect = 9e-06
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 53  MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLD 109
               +F  N   +  +  L  LF ++     V +   +   AF+  D+E  A  A   L 
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQ 265

Query: 110 RTEFGRKGRRLRVEWTK 126
             +   +   +++ + K
Sbjct: 266 GFKIT-QNNAMKISFAK 281

>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 = 66.9 bits (164), Expect = 6e-14
 Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           ++  N      + DL  LF R+ +         M +    G AFI   ++  A  A+  +
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           +  +    G+ L +E+ K+++  R  G  S
Sbjct: 88  NGYKLY--GKILVIEFGKNKKQ-RSSGPSS 114

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 10/93 (10%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
           P+K L++ N        RDL   F  + +     I         R  AF+ +  +E A +
Sbjct: 24  PNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           AL   N  KL  +++ +E+  ++   R +G S 
Sbjct: 83  ALHLVNGYKLYGKILVIEFG-KNKKQRSSGPSS 114

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.2 bits (162), Expect = 7e-14
 Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
            + GN  + A ++DL  LF+ +G +         G  FI  D    A   I  L    F 
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQ 89

Query: 115 RKGRRLRVEWTKH 127
             GR LR  W K 
Sbjct: 90  --GRNLRTGWGKE 100

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATR 200
           P   T    T ++ N   + T   DL   F+ +G I+  +    +   F++Y+  E A  
Sbjct: 24  PPRVT----TAYIGNIPHFAT-EADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAV 78

Query: 201 ALDATNMSKLTDRVISVEYA 220
            + A        R +   + 
Sbjct: 79  CIVALANFPFQGRNLRTGWG 98

>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 = 66.5 bits (163), Expect = 7e-14
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ G    +     L   F  +G +       D    K  GFAF+  +   DA  AI  +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           + +E    GR +RV   K    I+  G  S
Sbjct: 75  NESELF--GRTIRVNLAK-PMRIKESGPSS 101

>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 = 66.1 bits (162), Expect = 7e-14
 Identities = 29/101 (28%), Positives = 44/101 (43%), Gaps = 10/101 (9%)

Query: 140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQ 191
           +   S      + L+V          + L   F P+G I  ++I         R FAFV+
Sbjct: 2   SSGSSGMATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 192 YEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           +E+ EDA  A+D  N S+L  R I V  A +    + +G S
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRVNLA-KPMRIKESGPS 100

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 142 RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDA 198
             S   R ++TL   N   ++    +L+  FE   +I  V      +  A+++++ + DA
Sbjct: 8   CTSKKVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA 66

Query: 199 TRALDATNMSKLTDRVISVEYA 220
            + L+    +++  R +S+ Y 
Sbjct: 67  EKNLEEKQGAEIDGRSVSLYYT 88

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV--DRVDMKS-GFAFIYMDDERDAEDAIRGLDRT 111
           R +   N  ++  + +L+ +F    ++     D KS G A+I    E DAE  +      
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

Query: 112 EFGRKGRRLRVEWTKHERGIRR 133
           E    GR + + +T  E+G  R
Sbjct: 77  EID--GRSVSLYYTG-EKGGTR 95

>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 = 65.8 bits (161), Expect = 1e-13
 Identities = 31/103 (30%), Positives = 44/103 (42%), Gaps = 8/103 (7%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAF 189
           G S +   S +    K L V N  P+  R  DL + F  +GKI+ V I       + F F
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGF 59

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           V +E   DA RA +  + + +  R I V  A        +G S
Sbjct: 60  VTFENSADADRAREKLHGTVVEGRKIEVNNA-TARVMTNSGPS 101

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 9/94 (9%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS------GFAFIYMDDERDAEDA 104
           ++  + +   N  +  R  DL ++F ++GK+  V++        GF F+  ++  DA+ A
Sbjct: 12  KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRA 71

Query: 105 IRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
              L  T     GR++ V      R +   G  S
Sbjct: 72  REKLHGTVVE--GRKIEVNNAT-ARVMTNSGPSS 102

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 11/107 (10%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---------RRN 186
           G S +       + +  + V N  P+    R++   F  +G++ +VR+          R 
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59

Query: 187 FAFVQYEVQEDATRALDA-TNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           F FV +  ++DA +A +A  + + L  R + +E+A  +   +    S
Sbjct: 60  FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 61.6 bits (150), Expect = 4e-12
 Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 13/92 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS-----GFAFIYMDDERDAEDAIRG 107
           I   N  + A Q ++  LF  +G++  V     M       GF F+    ++DA+ A   
Sbjct: 18  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77

Query: 108 L-DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           L   T     GRRL +EW        + G  S
Sbjct: 78  LCHSTHLY--GRRLVLEWAD-SEVTVQSGPSS 106

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 65.1 bits (159), Expect = 3e-13
 Identities = 12/88 (13%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           P K +        + R   L+     YG++  V I  +         A V +     A  
Sbjct: 5   PLKEVTFARL-NDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRR 228
            +   +++ +   +I  +  ++     +
Sbjct: 64  TVKNLHLTSVMGNIIHAQLDIKGQQRMK 91

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 61.6 bits (150), Expect = 4e-12
 Identities = 17/105 (16%), Positives = 41/105 (39%), Gaps = 10/105 (9%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERDAEDAI 105
           ++ +       + R++ L+ + R+YG+V+ V++       K  G A +     R A++ +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPS 150
           + L  T     G  +  +     +   +          +  T P+
Sbjct: 66  KNLHLTSV--MGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPT 108

>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 = 64.4 bits (157), Expect = 3e-13
 Identities = 17/104 (16%), Positives = 29/104 (27%), Gaps = 5/104 (4%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYE 193
           G S +         S  + V           DL    E +G I  V +   +  A V++E
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFE 59

Query: 194 VQEDATRALDATNMSKLT--DRVISVEYAVRDDDDRRNGHSPDR 235
             + A   +       +    +     Y+      R     P  
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>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 = 60.6 bits (147), Expect = 7e-12
 Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           +          ++DL     ++G +  V M      A +  ++   A++ +         
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77

Query: 115 RKGRRLRVEWTKHERGIRRPGGGSSAR 141
             G++    ++  +R I RPG    + 
Sbjct: 78  IAGQQAFFNYSTSKR-ITRPGNSGPSS 103

>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 = 64.2 bits (157), Expect = 3e-13
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 15/101 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERDAEDAI 105
            R ++ G+  YD  +  +  L    G V  + M       +S G+AFI   D   +  A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTN 146
           R L+  + G   R L+  ++           G S      +
Sbjct: 62  RNLNGYQLG--SRFLKCGYSS-----NSDISGVSLEHHHHH 95

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 15/96 (15%), Positives = 38/96 (39%), Gaps = 9/96 (9%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
           PS+ +++ +  PY      +       G +I++++         + +AF+++   E +  
Sbjct: 1   PSRVVYLGSI-PYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRN 236
           A+   N  +L  R +   Y+   D    +      +
Sbjct: 60  AVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>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 = 64.1 bits (157), Expect = 3e-13
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 11/76 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS---------GFAFIYMDDERDAEDAIRG 107
           +  G    +  +  +  +F  YGK+  +DM           G+A++  ++  +AE A++ 
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 108 LDRTEFGRKGRRLRVE 123
           +D  +    G+ +   
Sbjct: 67  MDGGQID--GQEITAT 80

>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 = 55.2 bits (134), Expect = 4e-10
 Identities = 12/83 (14%), Positives = 32/83 (38%), Gaps = 10/83 (12%)

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---------RRNFAFVQYEVQED 197
           +     + +      +     +   F  YGKI  + +          + +A+V++E  ++
Sbjct: 1   SMKPTKVHIGRL-TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59

Query: 198 ATRALDATNMSKLTDRVISVEYA 220
           A +AL   +  ++  + I+    
Sbjct: 60  AEKALKHMDGGQIDGQEITATAV 82

>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 = 64.2 bits (157), Expect = 4e-13
 Identities = 25/90 (27%), Positives = 38/90 (42%), Gaps = 10/90 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           +F  N  Y + + DLE+LF  YG +  +    D  +    GFAF+       A  A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           D   F   GR L V  +  ++   + G  S
Sbjct: 71  DGQVFQ--GRMLHVLPSTIKKEASQSGPSS 98

>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 = 62.6 bits (153), Expect = 1e-12
 Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 10/98 (10%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQ 195
           S+ +  S  LFV N   Y +   DLE+ F  YG +  +           + FAFV +   
Sbjct: 2   SSGSSGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 196 EDATRALDATNMSKLTDRVISVEYAV-RDDDDRRNGHS 232
           E A +A    +      R++ V  +  + +  +    S
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.3 bits (157), Expect = 5e-13
 Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 9/101 (8%)

Query: 126 KHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-- 183
            H            +   + N    K L V N  P+  R  DL + F  +GKI+ V I  
Sbjct: 7   HHHH--SSGLVPRGSHMNTENKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIF 63

Query: 184 ----RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
                + F FV +E   DA RA +  + + +  R I V  A
Sbjct: 64  NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS------GFAFIYMDDERDAEDAIRGLDR 110
           +   N  +  R  DL ++F ++GK+  V++        GF F+  ++  DA+ A   L  
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91

Query: 111 TEFGRKGRRLRV 122
           T     GR++ V
Sbjct: 92  TVVE--GRKIEV 101

>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 = 64.2 bits (157), Expect = 5e-13
 Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI------RRNFAFVQYEVQEDATRALD 203
           S  +F+ N D      + L   F  +G I+S ++       + + FV +E QE A RA++
Sbjct: 5   SGNIFIKNLD-KSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE 63

Query: 204 ATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRN 236
             N   L DR + V       +      +  + 
Sbjct: 64  KMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>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 = 60.3 bits (147), Expect = 1e-11
 Identities = 22/114 (19%), Positives = 41/114 (35%), Gaps = 18/114 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           IF  N +       L   F  +G +       D  +   G+ F++ + +  AE AI  ++
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMN 66

Query: 110 RTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHT 163
                   R++ V     +    R     +  +  TN      +++ NF P  T
Sbjct: 67  GMLLN--DRKVFVGR--FKSRKEREAELGARAKEFTN------VYIKNFGPGST 110

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 7/86 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS----GFAFIYMDDERDAEDAIRGLDRTE 112
           +   N  Y A +  L+ +F +   +     ++    G+AFI      DA++A+   ++ E
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE 77

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGS 138
               GR +R+E     RG    G  S
Sbjct: 78  IE--GRAIRLELQG-PRGSPNSGPSS 100

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 16/113 (14%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQ 191
           G S +   ST +  SKTL + N   Y      L+  FE    I   + +    + +AF++
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNL-SYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIE 59

Query: 192 YEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           +   EDA  AL++ N  ++  R I +E              P  + +  P  G
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRLELQ-----------GPRGSPNSGPSSG 101

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 63.7 bits (155), Expect = 5e-13
 Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV---DMKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           ++ GN   DAR SDL+R  R  G V            AF++  D   A+ A+  L     
Sbjct: 22  VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRL 81

Query: 114 GRKGRRLRVEWTKHER 129
           G     LRV   + +R
Sbjct: 82  G--TDTLRVALARQQR 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 18/90 (20%), Positives = 29/90 (32%), Gaps = 4/90 (4%)

Query: 134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFV 190
            G       P      +  ++V N  P   R  DL+R     G +      +     AF+
Sbjct: 3   SGSSGPGSPPGEGAPLAADVYVGNL-PRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYA 220
            Y     A +A+      +L    + V  A
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 64.4 bits (157), Expect = 6e-13
 Identities = 34/112 (30%), Positives = 45/112 (40%), Gaps = 9/112 (8%)

Query: 117 GRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG 176
           G   R        G ++ G GS       N  P+  L V      +T  RDL   F  YG
Sbjct: 13  GLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGL-SLYTTERDLREVFSKYG 71

Query: 177 KIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            I  V I         R FAFV +E  +DA  A +  N  +L  R I V+++
Sbjct: 72  PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 56.7 bits (137), Expect = 4e-10
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 10/84 (11%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAI 105
              +          + DL  +F +YG +  V    D +S    GFAF+Y ++  DA++A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 106 RGLDRTEFGRKGRRLRVEWTKHER 129
              +  E    GRR+RV+++  +R
Sbjct: 106 ERANGMELD--GRRIRVDFSITKR 127

>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 = 65.2 bits (159), Expect = 6e-13
 Identities = 36/162 (22%), Positives = 58/162 (35%), Gaps = 17/162 (10%)

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFE 173
           G   + LR +        R               + S TL+V N   ++T    +   F 
Sbjct: 3   GGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNL-SFYTTEEQIYELFS 61

Query: 174 PYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
             G I  + +           F FV+Y  + DA  A+   N ++L DR+I  ++     +
Sbjct: 62  KSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121

Query: 226 DRRNGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSR 267
            R+ G      R RS  + R      Y   RG   YG+ +  
Sbjct: 122 GRQYG------RGRSGGQVRDEYRQDYDAGRGG--YGKLAQN 155

>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 = 59.4 bits (144), Expect = 7e-11
 Identities = 26/123 (21%), Positives = 49/123 (39%), Gaps = 13/123 (10%)

Query: 39  RRSHSQLSIAAFEAMMRP---IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------K 87
           R  H +      E +++    ++ GN  +   +  +  LF + G + ++ M         
Sbjct: 21  RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80

Query: 88  SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNT 147
            GF F+      DAE+A+R ++ T      R +R +W    +  R+ G G S  +     
Sbjct: 81  CGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138

Query: 148 RPS 150
           R  
Sbjct: 139 RQD 141

>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 = 63.4 bits (155), Expect = 6e-13
 Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 8/93 (8%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNF 187
           G   S+          +T+FV N +    R   L   F   G +  V I        ++F
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLE-ARVREEILYELFLQAGPLTKVTICKDREGKPKSF 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            FV ++  E  + A+   N  +L  R I+V   
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 60.3 bits (147), Expect = 7e-12
 Identities = 24/91 (26%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 41  SHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS-GFAFI 93
           S S     A E   R +F GN E   R+  L  LF + G + +V +      K   F F+
Sbjct: 3   SGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFV 62

Query: 94  YMDDERDAEDAIRGLDRTEFGRKGRRLRVEW 124
                     AI  L+       GR + V  
Sbjct: 63  CFKHPESVSYAIALLNGIRLY--GRPINVSG 91

>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 = 65.6 bits (161), Expect = 6e-13
 Identities = 34/181 (18%), Positives = 60/181 (33%), Gaps = 38/181 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F G   +D  + +L   F +YG V       D    +S GF F+  +     ++ ++  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
            +      G+ +           +R       R        +  +FV    P      + 
Sbjct: 64  TQHILD--GKVIDP---------KRA----IPRDEQ---DKTGKIFVGGIGPDVRPK-EF 104

Query: 169 ERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           E  F  +G II  ++         R F FV Y+  +   R           DR I ++ A
Sbjct: 105 EEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRA 163

Query: 221 V 221
            
Sbjct: 164 E 164

>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 = 44.1 bits (105), Expect = 2e-05
 Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 12/91 (13%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDAT 199
           + S  +F+     + T   +L  +F  YG +  ++I ++        F F+ +E      
Sbjct: 1   KESCKMFIGGL-NWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVD 59

Query: 200 RALDATNMSKLTDRVISVEYAV-RDDDDRRN 229
             +   +   L  +VI  + A+ RD+ D+  
Sbjct: 60  EVVKTQH--ILDGKVIDPKRAIPRDEQDKTG 88

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 63.9 bits (156), Expect = 7e-13
 Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 13/103 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS-GFAFIYMDDERDAEDAIRGLD 109
           +F G    +  +  L+ +F ++G +  V +      KS GFAFI  ++  DA++A + ++
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69

Query: 110 RTEFGRKGRRLRVEW----TKHERGIRRPGGGSSARRPSTNTR 148
                  G+ ++VE     +    G RRP   S  R PS +  
Sbjct: 70  GKSLH--GKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110

>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 = 63.1 bits (154), Expect = 2e-12
 Identities = 27/107 (25%), Positives = 37/107 (34%), Gaps = 9/107 (8%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRA 201
               LF+       T  + L+  F  +G I  V +        R FAF+ +E   DA  A
Sbjct: 6   HPGKLFIGGL-NRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64

Query: 202 LDATNMSKLTDRVISVEYAV-RDDDDRRNGHSPDRNRDRSPDRGRRR 247
               N   L  + I VE A             P  +R+RSP      
Sbjct: 65  AKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111

>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 = 63.4 bits (155), Expect = 7e-13
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           +F G   +D  +  LE++F +YG++  V    D ++    GF F+  ++  DA+DA+  +
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           +       GR++RV+    +    R G  S
Sbjct: 75  NGKSVD--GRQIRVDQAG-KSSDNRSGPSS 101

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 33/104 (31%), Positives = 45/104 (43%), Gaps = 11/104 (10%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------R-RNFA 188
           GSS    S        LFV     + T  + LE+ F  YG+I  V +       R R F 
Sbjct: 1   GSSG--SSGMASDEGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           FV +E  +DA  A+ A N   +  R I V+ A +  D+R    S
Sbjct: 58  FVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>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 = 63.4 bits (155), Expect = 7e-13
 Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 12/101 (11%)

Query: 49  AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERD 100
           A +  +R +F GN  Y+A +  L+ +F   G V    +       K  G+ F    D+  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 101 AEDAIRGLDRTEFGRKGRRLRVEW--TKHERGIRRPGGGSS 139
           A  A+R L+  EF   GR LRV+   ++  +   +  G  +
Sbjct: 63  ALSAMRNLNGREFS--GRALRVDNAASEKNKEELKSLGTGA 101

>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 = 55.7 bits (135), Expect = 3e-10
 Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 20/106 (18%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDAT 199
           R  +++FV N  PY      L+  F   G ++S R+         + + F +Y+ QE A 
Sbjct: 6   RSLRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGR 245
            A+   N  + + R + V+ A           + ++N++     G 
Sbjct: 65  SAMRNLNGREFSGRALRVDNA-----------ASEKNKEELKSLGT 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 23/90 (25%), Positives = 40/90 (44%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++ G  +    +  L  LF + G V       DRV  +  G+ F+    E DA+ AI+ +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 109 DRTEFGRKGRRLRVEW-TKHERGIRRPGGG 137
           D  +    G+ +RV   + H + +  P  G
Sbjct: 78  DMIKL--YGKPIRVNKASAHNKNLSGPSSG 105

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 21/105 (20%), Positives = 39/105 (37%), Gaps = 10/105 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNF 187
           G S +  P +      T++V   D        L   F   G +++  +         + +
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLD-EKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYA-VRDDDDRRNGH 231
            FV++  +EDA  A+   +M KL  + I V  A   + +      
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>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 = 63.5 bits (155), Expect = 1e-12
 Identities = 27/106 (25%), Positives = 43/106 (40%), Gaps = 10/106 (9%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
               LFV           D+   F  YG+I ++ +         + +  V+YE  ++A  
Sbjct: 21  EGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRR 246
           A++  N   L  + ISV++        +      R R RSPDR RR
Sbjct: 80  AMEGLNGQDLMGQPISVDWC-FVRGPPKGKRRGGRRRSRSPDRRRR 124

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 58.5 bits (142), Expect = 7e-11
 Identities = 19/102 (18%), Positives = 42/102 (41%), Gaps = 10/102 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           +F      +A + D+   F  YG++  +    D ++    G+  +  +  ++A+ A+ GL
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPS 150
           +  +    G+ + V+W       +    G   R  S + R  
Sbjct: 85  NGQDLM--GQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR 124

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 62.5 bits (152), Expect = 1e-12
 Identities = 13/77 (16%), Positives = 27/77 (35%), Gaps = 7/77 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV-----DMKSGFAFIYMDDERDAEDAIRGLDRT 111
           +   N     +   L+ L  +YG V+       D ++    +    +  A  A+  L+  
Sbjct: 18  LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGF 77

Query: 112 EFGRKGRRLRVEWTKHE 128
           +       L+V +   E
Sbjct: 78  QLE--NFTLKVAYIPDE 92

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.7 bits (150), Expect = 3e-12
 Identities = 23/95 (24%), Positives = 34/95 (35%), Gaps = 7/95 (7%)

Query: 137 GSSARRPSTNTRPSKT-LFVINFDPYHTRTRDLERHFEPYGKIISVRI-----RRNFAFV 190
           GSS    S   R     L + N  P H +   L+     YG + S              V
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNI-PPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
            Y  ++ A +ALD  N  +L +  + V Y   +  
Sbjct: 60  TYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMA 94

>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 = 63.7 bits (155), Expect = 2e-12
 Identities = 29/165 (17%), Positives = 55/165 (33%), Gaps = 24/165 (14%)

Query: 95  MDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE----RGIRRPGGGSSARRPSTNTRPS 150
            + + D +  I  L      RKGR    +    E        R             +   
Sbjct: 13  FEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEG 72

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRAL 202
             LFV +      +  +++  F  YG+I ++ +         + +A V+YE  + A  A 
Sbjct: 73  WILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRR 247
           +A N +++  + I V++                 +       RRR
Sbjct: 132 EALNGAEIMGQTIQVDWC-----------FVKGPKRVKKSEKRRR 165

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 59.5 bits (144), Expect = 7e-11
 Identities = 18/94 (19%), Positives = 41/94 (43%), Gaps = 11/94 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           +F  +   +A++ +++  F  YG++  + +          G+A +  +  + A  A   L
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARR 142
           +  E    G+ ++V+W    +G +R       RR
Sbjct: 135 NGAEIM--GQTIQVDWCF-VKGPKRVKKSEKRRR 165

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 22/95 (23%), Positives = 32/95 (33%), Gaps = 12/95 (12%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-----------FAFVQYEVQED 197
            S  LF+ N   + T    L+  F   G I S  I +            F FV+Y+  E 
Sbjct: 4   GSSGLFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 198 ATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           A +AL       +    + V  + R         S
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>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 = 54.6 bits (132), Expect = 8e-10
 Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 15/95 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----------GFAFIYMDDERDAEDAI 105
           +F  N  +   +  L+ +F + G +    +             GF F+       A+ A+
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSA 140
           + L        G +L V  +  ER  +   G SS 
Sbjct: 68  KQLQGHTVD--GHKLEVRIS--ERATKPASGPSSG 98

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 61.4 bits (150), Expect = 3e-12
 Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 11/77 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAI 105
           MR I+ GN  Y A    ++ LF ++GKV  V +          GF F+ M +E    +AI
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAI 59

Query: 106 RGLDRTEFGRKGRRLRV 122
             LD T+F   GR +RV
Sbjct: 60  AKLDNTDFM--GRTIRV 74

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 48.7 bits (117), Expect = 8e-08
 Identities = 17/90 (18%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRAL 202
           + ++V N   Y   +  ++  F  +GK+ +V++         + F FV+ + +E  + A+
Sbjct: 2   RNIYVGNL-VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAI 59

Query: 203 DATNMSKLTDRVISVEYAV-RDDDDRRNGH 231
              + +    R I V  A  +   +  + H
Sbjct: 60  AKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 3e-12
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQY 192
            R    N   ++++++  F P      D++   E  G+++++++RR          FV +
Sbjct: 1   GRWILKNDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 59

Query: 193 EVQEDATRALDATNMSKLTDRVISV 217
           +  E A + +  T   K  +  + +
Sbjct: 60  DSIESAKKFV-ETPGQKYKETDLLI 83

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 10/81 (12%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAED 103
           +   R ++   F  DA   D++      G+V  + M+        G  F+  D    A+ 
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 67

Query: 104 AIRGLDRTEFGRKGRRLRVEW 124
            +      ++  K   L + +
Sbjct: 68  FVE-TPGQKY--KETDLLILF 85

>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 = 62.0 bits (151), Expect = 3e-12
 Identities = 24/108 (22%), Positives = 43/108 (39%), Gaps = 16/108 (14%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNF 187
           G S +    ++    KT+F+ N   + +    L    + +G +  VR+         +  
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGC 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTD------RVISVEYAV-RDDDDRR 228
           AF Q+  QE A + L A ++           R + V+ AV RD+    
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 52.7 bits (127), Expect = 5e-09
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 13/94 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERDAEDAIRGL 108
           +F  N  +D+ +  L  + +++G +  V +        S G AF     +  A+  +   
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77

Query: 109 DRTEFGRK----GRRLRVEW-TKHERGIRRPGGG 137
                G      GR+L+V+     +     P  G
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 9/94 (9%)

Query: 134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRN 186
             G S   R ST+      LF+    P+     +LE   + +G +  +R+        + 
Sbjct: 2   SSGSSGVFRYSTSL-EKHKLFISGL-PFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            A+V+YE +  A++A+   +   + + +I V  +
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 61.1 bits (149), Expect = 5e-12
 Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS-GFAFIYMDDERDAEDAIRGLD 109
           +F     +   + +LE + + +G V  + +      K  G A++  ++E  A  A+  +D
Sbjct: 20  LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79

Query: 110 RTEFGRKGRRLRVE 123
                     ++V 
Sbjct: 80  GMTIK--ENIIKVA 91

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 62.0 bits (151), Expect = 3e-12
 Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATR 200
              N     T++        T    + + F P+G+I+ +R+   + ++FV++   E A  
Sbjct: 22  SPKNC----TVYCGGIASGLTDQ-LMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAH 76

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           A+ + N + +   V+   +  ++  D  +G S
Sbjct: 77  AIVSVNGTTIEGHVVKCYWG-KESPDMTSGPS 107

>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 = 62.0 bits (151), Expect = 3e-12
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 5/84 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVD--RVDMKSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++CG          + + F  +G++   RV  + G++F+       A  AI  ++ T   
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE 87

Query: 115 RKGRRLRVEWTKHERGIRRPGGGS 138
             G  ++  W K        G  S
Sbjct: 88  --GHVVKCYWGKE-SPDMTSGPSS 108

>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 = 60.6 bits (148), Expect = 5e-12
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 10/75 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           ++    +      DL +L + YGK+       D+   K  G+ F+  D    A+ A+  L
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 109 DRTEFGRKGRRLRVE 123
             +      +  +  
Sbjct: 68  KASGVQ--AQMAKQS 80

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRA 201
           S  L++       T  +DL +  +PYGKI+S +          + + FV ++    A +A
Sbjct: 5   SSGLYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 202 LDATNMSKLTDRVISVE 218
           + A   S +  ++    
Sbjct: 64  VTALKASGVQAQMAKQS 80

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 61.0 bits (149), Expect = 5e-12
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           ++ G+  ++  +  L  +F  +GK+D +    D  +    G+ FI   D   A  A+  L
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

Query: 109 DRTEFGRKGRRLRV-EWTKHERGIRRPGGG 137
           +  E    GR +RV   T+   G   P  G
Sbjct: 68  NGFELA--GRPMRVGHVTERLDGGSGPSSG 95

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 10/92 (10%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
            S  L+V +   ++     L   FEP+GKI ++ +         + + F+ +   E A R
Sbjct: 4   GSSGLYVGSL-HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           AL+  N  +L  R + V +   +  D  +G S
Sbjct: 63  ALEQLNGFELAGRPMRVGHV-TERLDGGSGPS 93

>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 = 61.2 bits (149), Expect = 5e-12
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 11/82 (13%)

Query: 49  AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERD 100
                MR ++ G+  ++  +  L  +F  +G+++ + +       +S G+ FI   D   
Sbjct: 22  GSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80

Query: 101 AEDAIRGLDRTEFGRKGRRLRV 122
           A+ A+  L+  E    GR ++V
Sbjct: 81  AKKALEQLNGFELA--GRPMKV 100

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 138 SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAF 189
           + A      +     L+V +   ++     L   FEP+G+I S+++         + + F
Sbjct: 14  AMANNLQKGSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGF 72

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           + +   E A +AL+  N  +L  R + V + 
Sbjct: 73  ITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 61.2 bits (149), Expect = 5e-12
 Identities = 16/85 (18%), Positives = 39/85 (45%), Gaps = 11/85 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           +F  +   +A++ +++  F  YG++  + +          G+A +  +  + A  A   L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRR 133
           +  E    G+ ++V+W    +G +R
Sbjct: 89  NGAEIM--GQTIQVDWCF-VKGPKR 110

>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 = 58.1 bits (141), Expect = 7e-11
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 9/96 (9%)

Query: 133 RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------R 184
           R             +     LFV +      +  +++  F  YG+I ++ +         
Sbjct: 9   RNEDDDELEPGPQRSVEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67

Query: 185 RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           + +A V+YE  + A  A +A N +++  + I V++ 
Sbjct: 68  KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103

>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 = 60.6 bits (148), Expect = 6e-12
 Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 15/95 (15%)

Query: 49  AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERD 100
             EA  R I+ GN +Y A   +LE  F   G V+RV    D  S    GFA+I   D+  
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 101 AEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPG 135
              ++  LD + F  +GR+++V   +      RPG
Sbjct: 61  VRTSLA-LDESLF--RGRQIKVIPKRT----NRPG 88

>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 = 52.5 bits (127), Expect = 4e-09
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDAT 199
             +++++V N   Y     +LE HF   G +  V I         + FA++++  +E   
Sbjct: 4   ADARSIYVGNV-DYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 200 RALDATNMSKLTDRVISVEYA 220
            +L A + S    R I V   
Sbjct: 63  TSL-ALDESLFRGRQIKVIPK 82

>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 = 61.0 bits (148), Expect = 6e-12
 Identities = 17/89 (19%), Positives = 40/89 (44%), Gaps = 5/89 (5%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYE 193
           G S +     +  PS+ L +    P      ++     P+GK+ ++ +   +N AF++  
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELA 59

Query: 194 VQEDATRALD--ATNMSKLTDRVISVEYA 220
            +E A   ++  +     L ++ I ++Y+
Sbjct: 60  TEEAAITMVNYYSAVTPHLRNQPIYIQYS 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 = 53.3 bits (128), Expect = 2e-09
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTE 112
           R +       +  ++++  L   +GKV  + M      AF+ +  E  A   +       
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75

Query: 113 FGRKGRRLRVEWTKHER 129
              + + + ++++ H+ 
Sbjct: 76  PHLRNQPIYIQYSNHKE 92

>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 = 63.5 bits (155), Expect = 6e-12
 Identities = 38/196 (19%), Positives = 66/196 (33%), Gaps = 31/196 (15%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAI 105
           +R +F G   ++     L   F ++G +       D    +S GF F+      + + A+
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRT 165
                   GR      VE        +R      ++RP  +    K +FV          
Sbjct: 73  NARPHKVDGRV-----VE-------PKRAVSREDSQRPGAHLTVKK-IFVGGIKEDTEEH 119

Query: 166 RDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISV 217
             L  +FE YGKI  + I        +R FAFV ++  +   + +       +      V
Sbjct: 120 -HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEV 177

Query: 218 EYAVRDDDDRRNGHSP 233
             A+   +      S 
Sbjct: 178 RKALSKQEMASASSSQ 193

>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 = 42.3 bits (100), Expect = 8e-05
 Identities = 28/107 (26%), Positives = 44/107 (41%), Gaps = 12/107 (11%)

Query: 138 SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAF 189
           S +  P    +  K LF+     + T    L  HFE +G +    + R+        F F
Sbjct: 2   SKSESPKEPEQLRK-LFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 59

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAV-RDDDDRRNGHSPDR 235
           V Y   E+   A++A    K+  RV+  + AV R+D  R   H   +
Sbjct: 60  VTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 105

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 60.3 bits (147), Expect = 7e-12
 Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAFVQYEVQED 197
           S+ +  +  +FV N  P+    + L+  F   G ++   I+           V++E  E 
Sbjct: 2   SSGSSGACQIFVRNL-PFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV 60

Query: 198 ATRALDATNMSKLTDRVISVEYAVRDDDDRRNG 230
           A RA    N  KL+ R I V    R+     +G
Sbjct: 61  AERACRMMNGMKLSGREIDVRID-RNASGPSSG 92

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 11/87 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS------GFAFIYMDDERDAEDAIRGLDR 110
           IF  N  +D     L+  F   G V   D+K       G   +  +    AE A R ++ 
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGG 137
            +    GR + V   + +R    P  G
Sbjct: 71  MKLS--GREIDV---RIDRNASGPSSG 92

>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 = 60.0 bits (146), Expect = 7e-12
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 8/89 (8%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQY 192
           G   S+    T T    TL+V       T   DL  HF  +G+I ++ +  R+  AF+Q+
Sbjct: 1   GSSGSSGEDKTIT----TLYVGGLGDTIT-ETDLRNHFYQFGEIRTITVVQRQQCAFIQF 55

Query: 193 EVQEDATRALDAT-NMSKLTDRVISVEYA 220
             ++ A  A + + N   +  R ++V++ 
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84

>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 = 60.0 bits (146), Expect = 9e-12
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAI-RGLDRTEF 113
           ++ G       ++DL   F ++G++  + +  +   AFI     + AE A  +  ++   
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIV 74

Query: 114 GRKGRRLRVEWTK 126
              GRRL V+W +
Sbjct: 75  N--GRRLNVKWGR 85

>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 = 60.8 bits (148), Expect = 8e-12
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 10/104 (9%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FA 188
              A            LF+ +  P     +DL + F P+G ++S ++  +        F 
Sbjct: 12  SIGAAGSQKEGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           FV Y+    A  A+ + N  ++  + + V+   R  +D ++G S
Sbjct: 71  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-RSKNDSKSGPS 113

>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 = 53.9 bits (130), Expect = 3e-09
 Identities = 21/90 (23%), Positives = 40/90 (44%), Gaps = 11/90 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F  +   +    DL ++F  +G V       D+    S  F F+  D+   A+ AI+ +
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           +  + G   +RL+V+  K  +   + G  S
Sbjct: 88  NGFQIG--MKRLKVQL-KRSKNDSKSGPSS 114

>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 = 60.4 bits (147), Expect = 1e-11
 Identities = 24/105 (22%), Positives = 40/105 (38%), Gaps = 12/105 (11%)

Query: 137 GSSARRPSTNTRPSKT-LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FA 188
           GSS    S +       LFV           D+ R F+P+G I    + R         A
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGML-NKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCA 59

Query: 189 FVQYEVQEDATRALDATNMSKL---TDRVISVEYAVRDDDDRRNG 230
           FV++    +A  A+ A + S+        + V++A  D +   + 
Sbjct: 60  FVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSS 104

>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 = 49.2 bits (118), Expect = 9e-08
 Identities = 19/84 (22%), Positives = 30/84 (35%), Gaps = 10/84 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           +F G       + D+ RLF+ +G +              G AF+      +A+ AI  L 
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77

Query: 110 -RTEFGRKGRRLRVEW--TKHERG 130
                      L V++  T  E G
Sbjct: 78  GSQTMPGASSSLVVKFADTDKESG 101

>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 = 59.9 bits (146), Expect = 1e-11
 Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 8/103 (7%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAF 189
           G S +            L+V N D        L + F P+G I S ++         F F
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLD-DGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGF 59

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           V +   E+AT+A+   N   +  + + V  A +  ++R++G S
Sbjct: 60  VCFSSPEEATKAVTEMNGRIVATKPLYVALA-QRKEERQSGPS 101

>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 = 51.8 bits (125), Expect = 8e-09
 Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 10/90 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVD--RVDMKS----GFAFIYMDDERDAEDAIRGLDR 110
           ++  N +       L + F  +G +   +V M+     GF F+      +A  A+  ++ 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGSSA 140
                  + L V     +R   R  G SS 
Sbjct: 78  RIVA--TKPLYVAL--AQRKEERQSGPSSG 103

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 15/86 (17%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGK--IISVRIRRN--------FAFVQYEVQEDA 198
              T+ + N  P HT    +     PY    + ++R+ ++        FAFVQ     DA
Sbjct: 8   HMDTIILRNIAP-HTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 199 TRALDATN----MSKLTDRVISVEYA 220
           ++ L          K+  + I V++A
Sbjct: 67  SQLLQILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 12/82 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV---------DRVDMKS-GFAFIYMDDERDAEDAIR 106
           I   N         +      Y  +         D+   ++ GFAF+ +    DA   ++
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 107 GLDRTEFGRK--GRRLRVEWTK 126
            L       K  G+ + V++ K
Sbjct: 72  ILQSLHPPLKIDGKTIGVDFAK 93

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 59.0 bits (144), Expect = 2e-11
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F G+   +     L   F+ +          D     S G+ F+    + DA++A+  +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 109 DRTEFGRKGRRLRVEW 124
              +    GR LR+ W
Sbjct: 64  QGQDLN--GRPLRINW 77

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 52.1 bits (126), Expect = 4e-09
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------R-RNFAFVQYEVQEDATRA 201
           +  LFV +    +     L   F+ +   +S  +         R + FV +  Q+DA  A
Sbjct: 1   TFNLFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59

Query: 202 LDATNMSKLTDRVISVEYAVR 222
           +D+     L  R + + +A +
Sbjct: 60  MDSMQGQDLNGRPLRINWAAK 80

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 61.0 bits (148), Expect = 2e-11
 Identities = 32/99 (32%), Positives = 44/99 (44%), Gaps = 11/99 (11%)

Query: 39  RRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GF 90
             SH        E M   +   N  Y      L R+F +YG+V  V    D  +    GF
Sbjct: 56  EGSHHHHHHMDVEGMTS-LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 114

Query: 91  AFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER 129
           AF+   D+RDAEDA+  +D       GR LRV+  ++ R
Sbjct: 115 AFVRFHDKRDAEDAMDAMDGAVLD--GRELRVQMARYGR 151

>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 = 59.1 bits (143), Expect = 1e-10
 Identities = 35/144 (24%), Positives = 49/144 (34%), Gaps = 15/144 (10%)

Query: 97  DERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVI 156
           D   AE   +                              GS       +     +L V 
Sbjct: 22  DAATAEKVFKQYANDNGVDGEWTYD-----DATKTFTVTEGSHHHHHHMDVEGMTSLKVD 76

Query: 157 NFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMS 208
           N   Y T    L R FE YG++  V I         R FAFV++  + DA  A+DA + +
Sbjct: 77  NL-TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA 135

Query: 209 KLTDRVISVEYAVRDDDDRRNGHS 232
            L  R + V+ A R      + HS
Sbjct: 136 VLDGRELRVQMA-RYGRPPDSHHS 158

>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 = 60.1 bits (146), Expect = 3e-11
 Identities = 21/103 (20%), Positives = 35/103 (33%), Gaps = 12/103 (11%)

Query: 48  AAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDER 99
              + +   +          +  L +LF RYG +       DR   +S G+ F+      
Sbjct: 37  PEPDVLRN-LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95

Query: 100 DAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARR 142
            A+ AI GL+        +RL+V         R    G+    
Sbjct: 96  SAQQAIAGLNGFNIL--NKRLKVALAA-SGHQRPGIAGAVGDG 135

>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 = 54.0 bits (130), Expect = 3e-09
 Identities = 21/121 (17%), Positives = 42/121 (34%), Gaps = 10/121 (8%)

Query: 125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI- 183
            + ++  ++        + +      + L V    P       L + FE YG I SV+I 
Sbjct: 17  AQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYI-PTTVDEVQLRQLFERYGPIESVKIV 75

Query: 184 -------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRN 236
                   R + FV+++    A +A+   N   + ++ + V  A      R        +
Sbjct: 76  CDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA-ASGHQRPGIAGAVGD 134

Query: 237 R 237
            
Sbjct: 135 G 135

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 15/100 (15%), Positives = 41/100 (41%), Gaps = 5/100 (5%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEV 194
           GS       +  PS+ + +    P      ++     P+GK+ ++ +   +N AF++   
Sbjct: 3   GSHHHHHHGSGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNT 61

Query: 195 QEDATRALDA--TNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           +E A   ++   +    L  + I ++++   +    +  +
Sbjct: 62  EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPN 101

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 3/89 (3%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTE 112
           R I       D  + ++  L   +GKV  + M      AFI M+ E  A   +       
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSSAR 141
              +G+ + ++++ H+  ++     + AR
Sbjct: 77  PVLRGQPIYIQFSNHKE-LKTDSSPNQAR 104

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 5/81 (6%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRA 201
              T  S  + +           DL    + +G I  V +  ++  A V++E    A  A
Sbjct: 15  PHKTPASPVVHIRGL-IDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNA 73

Query: 202 LDATNMSKLT--DRVISVEYA 220
           ++    +++        V Y+
Sbjct: 74  VNYAADNQIYIAGHPAFVNYS 94

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.5 bits (139), Expect = 9e-11
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           +          ++DL    + +G +  V +  K   A +  +D   A +A+      +  
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIY 83

Query: 115 RKGRRLRVEWTKHER 129
             G    V ++  ++
Sbjct: 84  IAGHPAFVNYSTSQK 98

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----DMKS----GFAFIYMDDERDAEDAIRGL 108
           +F      +A + D+   F  YG++  +    D ++    G+  +  +  ++A+ A+ GL
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85

Query: 109 DRTEFGRKGRRLRVEW 124
           +  +    G+ + V+W
Sbjct: 86  NGQDLM--GQPISVDW 99

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 58.4 bits (142), Expect = 5e-11
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
               LFV           D+   F  YG+I ++ +         + +  V+YE  ++A  
Sbjct: 22  EGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 201 ALDATNMSKLTDRVISVEYA 220
           A++  N   L  + ISV++ 
Sbjct: 81  AMEGLNGQDLMGQPISVDWC 100

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 59.4 bits (144), Expect = 5e-11
 Identities = 31/108 (28%), Positives = 43/108 (39%), Gaps = 10/108 (9%)

Query: 30  PRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS- 88
                    R S S          M  +   N  Y      L R+F +YG+V  V +   
Sbjct: 23  SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82

Query: 89  -------GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER 129
                  GFAF+   D+RDAEDA+  +D       GR LRV+  ++ R
Sbjct: 83  RYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD--GRELRVQMARYGR 128

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 55.9 bits (135), Expect = 6e-10
 Identities = 32/109 (29%), Positives = 46/109 (42%), Gaps = 9/109 (8%)

Query: 129 RGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI----- 183
            G +   G  S  RP  +     +L V N   Y T    L R FE YG++  V I     
Sbjct: 26  GGQQMGRGSMSYGRPPPDVEGMTSLKVDNL-TYRTSPDTLRRVFEKYGRVGDVYIPRDRY 84

Query: 184 ---RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
               R FAFV++  + DA  A+DA + + L  R + V+ A        +
Sbjct: 85  TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 30/108 (27%), Positives = 46/108 (42%), Gaps = 16/108 (14%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FA 188
           GSS      +    K LF+    P +   +DL+  FE +GKI  + + ++         A
Sbjct: 1   GSSGSSGMKDHDAIK-LFIGQI-PRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCA 58

Query: 189 FVQYEVQEDATRALDATNMSKLTD---RVISVEYAVRDDDDRRNGHSP 233
           F+ Y  +E A +A  A +  K      R I V+ A   D + R G  P
Sbjct: 59  FLTYCERESALKAQSALHEQKTLPGMNRPIQVKPA---DSESRGGSGP 103

>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 = 53.9 bits (130), Expect = 2e-09
 Identities = 23/91 (25%), Positives = 35/91 (38%), Gaps = 10/91 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F G    +  + DL+ LF  +GK+       DR      G AF+   +   A  A   L
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 109 DRTE-FGRKGRRLRVEWTKHE-RGIRRPGGG 137
              +      R ++V+    E RG   P  G
Sbjct: 76  HEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 58.8 bits (142), Expect = 5e-11
 Identities = 14/100 (14%), Positives = 39/100 (39%), Gaps = 5/100 (5%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEV 194
           GS      +   PS+ + +    P      ++     P+GK+ ++ +   +N AF++   
Sbjct: 18  GSHMGDSRSAGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNT 76

Query: 195 QEDATRALDATNMSKLT--DRVISVEYAVRDDDDRRNGHS 232
           +E A   ++           + I ++++   +    +  +
Sbjct: 77  EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPN 116

>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 = 54.5 bits (131), Expect = 2e-09
 Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 3/89 (3%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTE 112
           R I       D  + ++  L   +GKV  + M      AFI M+ E  A   +       
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSSAR 141
              +G+ + ++++ H+  ++     + AR
Sbjct: 92  PVLRGQPIYIQFSNHKE-LKTDSSPNQAR 119

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 13/88 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIR 106
           ++ GN  +     DL       G  D +++K           GFA + +  E  ++  + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 107 GLDRTEFGRKGRRLRVEWTKHERGIRRP 134
            L + E    G+   V  +  +      
Sbjct: 64  LLPKRELH--GQNPVVTPSN-KLEHHHH 88

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 14/89 (15%), Positives = 30/89 (33%), Gaps = 12/89 (13%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYG--KIISVRI--------RRNFAFVQYEVQEDATRAL 202
           L++ N   + T   DL       G   I+ ++          + FA V    +  + + +
Sbjct: 4   LYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRRNGH 231
           D     +L  +   V  +    +   + H
Sbjct: 63  DLLPKRELHGQNPVVTPS-NKLEHHHHHH 90

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 22/98 (22%), Positives = 33/98 (33%), Gaps = 15/98 (15%)

Query: 138 SSARRPSTNTR--PSKTLFVINFDPYHTRTRDLERH--FEPYGKIISVRIRRN------- 186
            S+     + R      +FV+           L+R   F  +GKI  V I  +       
Sbjct: 1   GSSGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQ 60

Query: 187 ----FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
                A+V Y   EDA RA+   N   +  R +     
Sbjct: 61  GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.6 bits (126), Expect = 7e-09
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 18/86 (20%)

Query: 57  IFCGNFEYDARQSDLER---LFRRYGKVDRVDM-----------KSGFAFIYMDDERDAE 102
           +F           ++ +    F ++GK+ +V +            S  A++      DA 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 103 DAIRGLDRTEFGRKGRRLRVEW--TK 126
            AI+ ++       GR L+     TK
Sbjct: 78  RAIQCVNNVVVD--GRTLKASLGTTK 101

>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 = 57.3 bits (139), Expect = 8e-11
 Identities = 19/83 (22%), Positives = 28/83 (33%), Gaps = 18/83 (21%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV---------------DRVDMKS-GFAFIYMDDERD 100
           IF      +     +   F++ G +               DR   K  G A +  DD   
Sbjct: 16  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75

Query: 101 AEDAIRGLDRTEFGRKGRRLRVE 123
           A+ AI   D  EF   G  ++V 
Sbjct: 76  AKAAIDWFDGKEF--SGNPIKVS 96

>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 = 50.0 bits (120), Expect = 4e-08
 Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 17/97 (17%)

Query: 140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS------VRIR--------- 184
                 +   + T+FV      +     +  +F+  G I +        I          
Sbjct: 3   HHHHHHSHSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 185 -RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            +  A V ++    A  A+D  +  + +   I V +A
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 57.8 bits (140), Expect = 1e-10
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 15/99 (15%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAE 102
           E   R ++ GN +Y +   DLE  F   G ++R+ +          G+A+I   +  ++ 
Sbjct: 33  EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSV 91

Query: 103 DAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSAR 141
           DA   +D T F  +GR ++V   +       PG  S+ R
Sbjct: 92  DAAVAMDETVF--RGRTIKVLPKR----TNMPGISSTDR 124

>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 = 54.0 bits (130), Expect = 3e-09
 Identities = 20/111 (18%), Positives = 40/111 (36%), Gaps = 10/111 (9%)

Query: 118 RRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK 177
             ++   +K   G    G               ++++V N   Y +  +DLE HF   G 
Sbjct: 4   PCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNV-DYGSTAQDLEAHFSSCGS 62

Query: 178 IISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           I  + I         + +A++++  +     A+ A + +    R I V   
Sbjct: 63  INRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 112

>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 = 57.1 bits (138), Expect = 1e-10
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 10/83 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGK-VDRVDMK---------SGFAFIYMDDERDAEDAIR 106
           +F G      ++ ++     +  + V  V +           GFAF+  +  R A  A R
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 107 GLDRTEFGRKGRRLRVEWTKHER 129
            L        G ++ V+W + E 
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEI 93

>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 = 50.2 bits (120), Expect = 4e-08
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 17/103 (16%)

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIR---------RNFAFVQYEVQE 196
           +  +  LF+    P   +  ++        + +  V +          R FAFV+YE   
Sbjct: 5   SSGNCRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 197 DATRALDATNMS--KLTDRVISVEYAV----RDDDDRRNGHSP 233
            A  A         +L    I+V++A      D+D       P
Sbjct: 64  AAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 30/127 (23%), Positives = 46/127 (36%), Gaps = 25/127 (19%)

Query: 130 GIRRPGGGSSARRPSTNT----RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR- 184
           G     G S  R P  N     R ++T+F +       R RDLE  F   GK+  VRI  
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIIS 59

Query: 185 -------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNR 237
                  +  A+V++   +    A+      +L    I V+ +             ++NR
Sbjct: 60  DRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ-----------AEKNR 107

Query: 238 DRSPDRG 244
              P  G
Sbjct: 108 LSGPSSG 114

>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 = 55.0 bits (133), Expect = 1e-09
 Identities = 25/96 (26%), Positives = 37/96 (38%), Gaps = 12/96 (12%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAE 102
           E   R +FC       R  DLE  F   GKV  V + S        G A++   + +   
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 103 DAIRGLDRTEFGRKGRRLRVEWTKHER-GIRRPGGG 137
            AI GL        G  + V+ ++ E+  +  P  G
Sbjct: 82  LAI-GLTGQRL--LGVPIIVQASQAEKNRLSGPSSG 114

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDR 110
           +R +F   F      + L   F  +G V  V M   K  FA + M D   A +A+    +
Sbjct: 8   LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDV-GAREAVLSQSQ 66

Query: 111 TEFGRKGRRLRVEWTKHERGIRRPGGGS 138
                 G RLRV   + ++  + P   S
Sbjct: 67  HSL--GGHRLRVR-PREQKEFQSPASKS 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---FAFVQYEVQEDATR 200
           S+ +   +++FV  F P    +  L  +F  +G + SV + ++   FA V+         
Sbjct: 2   SSGSSGLRSVFVSGF-PRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREA 60

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
            L  +    L    + V    + +       SP
Sbjct: 61  VLSQSQ-HSLGGHRLRVRPREQKEFQSPASKSP 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 9/95 (9%)

Query: 134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------- 186
               ++A            LF+ +  P      DL   F P+G +IS ++  +       
Sbjct: 24  SAAAAAAAGKQIEGPEGCNLFIYHL-PQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSK 82

Query: 187 -FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            F FV ++  + A  A+ A N  ++  + + V+  
Sbjct: 83  CFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F  +   +   +DL   F  +G V       D+    S  F F+  D+   A+ AI+ +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  + G   +RL+V+  K
Sbjct: 103 NGFQVG--TKRLKVQLKK 118

>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 = 57.9 bits (140), Expect = 2e-10
 Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 14/100 (14%)

Query: 139 SARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------------R 185
           S  R      P+  ++V N    H + +DL+  F  Y    S   R             +
Sbjct: 34  SVFRSYEPGEPNCRIYVKNLA-KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMK 92

Query: 186 NFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
             AF+    ++ A +AL   N   L  + + V++A     
Sbjct: 93  GQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 132

>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 = 52.1 bits (125), Expect = 2e-08
 Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 15/94 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV---------DRVDMKS----GFAFIYMDDERDAED 103
           I+  N     ++ DL+ +F RY            D   MK     G AFI + +E+ A  
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 104 AIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGG 137
           A++  +       G+ + V++ +  R  + P  G
Sbjct: 108 ALKEANGYVLF--GKPMVVQFARSARPKQDPKEG 139

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 29/116 (25%), Positives = 45/116 (38%), Gaps = 3/116 (2%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-FAFVQYE 193
           GG    R    + R    + V    P     +DL+ H    G +    + R+    V++ 
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFV 59

Query: 194 VQEDATRALDATNMSKLTDRVISVEYA-VRDDDDRRNGHSPDRNRDRSPDRGRRRS 248
            +ED T A+   + +K         Y  V+ D  R   +   R+R RS  R R RS
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSRS 115

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 3/96 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVD-MKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +            DL+   R  G V   D  + G   +    + D   A+R LD T+F  
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF-- 76

Query: 116 KGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSK 151
           +       + + +    R      +R  S +   S+
Sbjct: 77  RSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSR 112

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 24/102 (23%), Positives = 45/102 (44%), Gaps = 14/102 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F G+   +    D++  F  +G++       D    KS G+ F+   ++ DAE+AI+ +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPS 150
                G  GR++R  W       + P   S+    +  + PS
Sbjct: 78  GGQWLG--GRQIRTNWATR----KPPAPKSTYESNTKQSGPS 113

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 53.9 bits (130), Expect = 3e-09
 Identities = 25/123 (20%), Positives = 43/123 (34%), Gaps = 18/123 (14%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNF 187
           G S +     +T     +FV +       T D++  F P+G+I   R+         + +
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDL-SPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRR 247
            FV +  + DA  A+       L  R I   +A R          P   +       ++ 
Sbjct: 60  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK---------PPAPKSTYESNTKQS 110

Query: 248 SPS 250
            PS
Sbjct: 111 GPS 113

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 8/88 (9%)

Query: 140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQY 192
           A+      +    L++ N  P     ++LE   +P+G++IS RI R+         F + 
Sbjct: 15  AQMAKQQEQDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARM 73

Query: 193 EVQEDATRALDATNMSKLTDRVISVEYA 220
           E  E     +   N   +          
Sbjct: 74  ESTEKCEAVIGHFNGKFIKTPPGVSAPT 101

>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 = 47.6 bits (114), Expect = 3e-07
 Identities = 11/73 (15%), Positives = 21/73 (28%), Gaps = 9/73 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV------DMKS-GFAFIYMDDERDAEDAIRGLD 109
           ++  N      + +LE + + +G+V            S G  F  M+     E  I   +
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87

Query: 110 RTEFGRKGRRLRV 122
                        
Sbjct: 88  GKFIK--TPPGVS 98

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 55.6 bits (135), Expect = 3e-10
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +F G+   +   + +   F  +G++       D    KS G+ F+   ++ DAE+AI+ +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 109 DRTEFGRKGRRLRVEW 124
                G  GR++R  W
Sbjct: 69  GGQWLG--GRQIRTNW 82

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATR 200
               +FV +  P    T  +   F P+G+I   R+         + + FV +  + DA  
Sbjct: 5   SHFHVFVGDLSP-EITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

Query: 201 ALDATNMSKLTDRVISVEYAVRD 223
           A+       L  R I   +A R 
Sbjct: 64  AIQQMGGQWLGGRQIRTNWATRK 86

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 7/102 (6%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFV 190
           G S +  P+  ++PSKTLFV       T    L+  F+   +   V  R     + F FV
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGL-SEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFV 59

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            +  +EDA  A +A    ++    +++++A +   +  +G S
Sbjct: 60  DFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KPKGEGGSGPS 100

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV----DRVDMKS-GFAFIYMDDERDAEDAIRGLDRT 111
           +F      D  +  L+  F    +     DR    S GF F+  + E DA+ A   ++  
Sbjct: 18  LFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDG 77

Query: 112 EFGRKGRRLRVEWTKHERGIRRPGGGS 138
           E    G ++ ++W K  +G    G  S
Sbjct: 78  EID--GNKVTLDWAK-PKGEGGSGPSS 101

>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 = 55.6 bits (134), Expect = 5e-10
 Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-FAFVQYEV 194
           G S +     + R    + V    P     +DL+ H    G +    + R+    V++  
Sbjct: 1   GSSGSSGGPPSRRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVR 59

Query: 195 QEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           +ED T A+   + +K         Y +R   D     S  R+R   P  G
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAY-IRVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 53.6 bits (129), Expect = 2e-09
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 3/89 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVD-MKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +            DL+   R  G V   D  + G   +    + D   A+R LD T+F  
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF-- 75

Query: 116 KGRRLRVEWTKHERGIRRPGGGSSARRPS 144
           +       + + +    R      +R   
Sbjct: 76  RSHEGETAYIRVKVDGPRSPSYGRSRSSG 104

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.9 bits (135), Expect = 5e-10
 Identities = 23/100 (23%), Positives = 34/100 (34%), Gaps = 19/100 (19%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV---------------DRVDMKS-GFAFIYMDDERD 100
           IF      +     +   F++ G +               DR   K  G A +  DD   
Sbjct: 10  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69

Query: 101 AEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSA 140
           A+ AI   D  EF   G  ++V +    R     GGG+  
Sbjct: 70  AKAAIDWFDGKEF--SGNPIKVSFAT-RRADFNRGGGNGR 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 17/108 (15%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS------VRIR----------RNFAFVQ 191
             + T+FV      +     +  +F+  G I +        I           +  A V 
Sbjct: 5   SDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 192 YEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDR 239
           ++    A  A+D  +  + +   I V +A R  D  R G +     + 
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEH 111

>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 = 55.7 bits (134), Expect = 5e-10
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 145 TNTRPSKTLFVINFDPYHTRTRD-LERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRA 201
           T +  +++L V N    +  +R+ L    E  G + ++ +   + ++F +Y   E++ RA
Sbjct: 20  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRA 79

Query: 202 LDATN 206
               N
Sbjct: 80  YVTLN 84

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEF 113
           +  G       ++ L  +  + G VD + M     ++F       +++ A   L+  E 
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 88

>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 = 55.5 bits (134), Expect = 7e-10
 Identities = 18/104 (17%), Positives = 31/104 (29%), Gaps = 20/104 (19%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS----------------GFAFIY 94
           ++    I+           DL   F++ G V                       G A + 
Sbjct: 12  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71

Query: 95  MDDERDAEDAIRGLDRTEFGRKGRRLRVEW--TKHERGIRRPGG 136
            +D   A+ A+   D  +F  +G +L+V     K         G
Sbjct: 72  YEDPPTAKAAVEWFDGKDF--QGSKLKVSLARKKPPMNSGPSSG 113

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 19/113 (16%), Positives = 31/113 (27%), Gaps = 18/113 (15%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS------VRIR----- 184
           G S +         +  ++V           DL   F+  G +          I      
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK 59

Query: 185 -----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
                +  A V YE    A  A++  +        + V  A R      +G S
Sbjct: 60  ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA-RKKPPMNSGPS 111

>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 = 55.0 bits (133), Expect = 8e-10
 Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 8/91 (8%)

Query: 138 SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFV 190
            S             L V N D +     D++  F  +G +    +           A V
Sbjct: 17  DSGFGGGAGVETGGKLLVSNLD-FGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADV 75

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYAV 221
            +E + DA +A+   N   L  R ++++   
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 53.1 bits (128), Expect = 4e-09
 Identities = 13/74 (17%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM------KS-GFAFIYMDDERDAEDAIRGLD 109
           +   N ++    +D++ LF  +G + +  +      +S G A ++ + + DA  A++  +
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 91

Query: 110 RTEFGRKGRRLRVE 123
                  GR + ++
Sbjct: 92  GVPLD--GRPMNIQ 103

>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 = 55.1 bits (133), Expect = 1e-09
 Identities = 18/101 (17%), Positives = 32/101 (31%), Gaps = 8/101 (7%)

Query: 138 SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFV 190
            S             L V N D +     D++  F  +G +    +           A V
Sbjct: 23  DSGCGGGEGVETGAKLLVSNLD-FGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 81

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGH 231
            +E + DA +A+       L  R + ++      D   + H
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 49.3 bits (118), Expect = 1e-07
 Identities = 12/74 (16%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------GFAFIYMDDERDAEDAIRGLD 109
           +   N ++    +D++ LF  +G + +  +         G A ++ +   DA  A++   
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97

Query: 110 RTEFGRKGRRLRVE 123
                  GR + ++
Sbjct: 98  GVPLD--GRPMDIQ 109

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 13/78 (16%)

Query: 57  IFCGNF------EYDARQSDLERLFRRYGKVDRVDM-----KS-GFAFIYMDDERDAEDA 104
           I   N         +  ++ + ++F ++GK+          K+ G+ F+       A DA
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 63

Query: 105 IRGLDRTEFGRKGRRLRV 122
           ++  D  +   K    RV
Sbjct: 64  VKNADGYKLD-KQHTFRV 80

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 168 LERHFEPYGKIISVRIRRN------FAFVQYEVQEDATRALDATNMSKL 210
           + + F  +GKI +            + F++Y     A  A+   +  KL
Sbjct: 24  IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 25/118 (21%), Positives = 42/118 (35%), Gaps = 23/118 (19%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------- 186
           G S +        P  T F+ N  PY      ++  F     I +VR+ R          
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKG 58

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           F + ++E  +    AL + N   L ++ I V+ A              +++D  P  G
Sbjct: 59  FGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA-----------DQAQDKDSGPSSG 104

>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 = 44.9 bits (107), Expect = 3e-06
 Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 13/92 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG-------KVDRVDMKS-GFAFIYMDDERDAEDAIRGL 108
            F GN  YD  +  ++  FR          +      +  GF +   +D      A+  L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 76

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSA 140
           +    G   +R+RV+     +   +  G SS 
Sbjct: 77  NEESLG--NKRIRVDVADQAQ--DKDSGPSSG 104

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 19/101 (18%), Positives = 33/101 (32%), Gaps = 11/101 (10%)

Query: 136 GGSSARRPS--TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RN 186
           G      P   + +     LF+ N    +    +L+           + +        R 
Sbjct: 1   GSHMLEDPVEGSESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 59

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDR 227
           F +V +E  ED  +AL+     K+    I +E     D  R
Sbjct: 60  FGYVDFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDGTR 99

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 13/77 (16%), Positives = 27/77 (35%), Gaps = 10/77 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV------DRVDMKS-GFAFIYMDDERDAEDAIRGLD 109
           +F GN   +   ++L+               D     +  F ++  +   D E A+  L 
Sbjct: 20  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELT 78

Query: 110 RTEFGRKGRRLRVEWTK 126
             +    G  +++E  K
Sbjct: 79  GLKVF--GNEIKLEKPK 93

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 9/71 (12%)

Query: 60  GNFEYDARQSDLERLFRRYGKVDRVDM-------KS-GFAFIYMDDERDAEDAIRGLDRT 111
            + +    +  L  LF + GKV  ++        K+ GF F+      DA+  I+     
Sbjct: 18  PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77

Query: 112 EFGRKGRRLRV 122
               K  RL +
Sbjct: 78  RLDLK-HRLFL 87

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 8/64 (12%)

Query: 155 VINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATN 206
           VI         + L   F   GK++++    +        F FV+     DA + + + +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 207 MSKL 210
             +L
Sbjct: 76  GKRL 79

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 54.2 bits (130), Expect = 5e-09
 Identities = 15/106 (14%), Positives = 33/106 (31%), Gaps = 13/106 (12%)

Query: 49  AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS----------GFAFIYMDDE 98
                   ++ G+F +      L ++ R  G  D V++K           G+A + +  E
Sbjct: 50  GLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASE 109

Query: 99  RDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPS 144
                 +  L        G ++ V      + + +    +  R   
Sbjct: 110 NSVHKLLELLPGKVLN--GEKVDVRPAT-RQNLSQFEAQARKRECV 152

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.0 bits (114), Expect = 5e-07
 Identities = 18/128 (14%), Positives = 40/128 (31%), Gaps = 12/128 (9%)

Query: 125 TKHERGIRRPGGGSSARRPSTNTRP-SKTLFVINFDPYHTRTRDLERHFEPYG--KIISV 181
            + E   +      +     +  R     ++V +F  + T  + L +     G   ++ +
Sbjct: 29  VRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSF-SWWTTDQQLIQVIRSIGVYDVVEL 87

Query: 182 RIRRN--------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           +   N        +A V    +    + L+      L    + V  A R +  +    + 
Sbjct: 88  KFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQAR 147

Query: 234 DRNRDRSP 241
            R   R P
Sbjct: 148 KRECVRVP 155

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.4 bits (126), Expect = 5e-09
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 13/78 (16%)

Query: 57  IFCGNF------EYDARQSDLERLFRRYGKVDRVDM-----KS-GFAFIYMDDERDAEDA 104
           I   N         +  ++ + ++F ++GK+          K+ G+ F+       A DA
Sbjct: 18  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 77

Query: 105 IRGLDRTEFGRKGRRLRV 122
           ++  D  +  ++    RV
Sbjct: 78  VKNADGYKLDKQ-HTFRV 94

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 16/81 (19%), Positives = 26/81 (32%), Gaps = 13/81 (16%)

Query: 142 RPSTNTRPSKTLFVINFDPYHTRTR------DLERHFEPYGKIISVRIRRN------FAF 189
           RP         + V N  P     R       + + F  +GKI +            + F
Sbjct: 7   RPQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIF 65

Query: 190 VQYEVQEDATRALDATNMSKL 210
           ++Y     A  A+   +  KL
Sbjct: 66  LEYASPAHAVDAVKNADGYKL 86

>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 = 55.5 bits (133), Expect = 5e-09
 Identities = 30/169 (17%), Positives = 50/169 (29%), Gaps = 14/169 (8%)

Query: 133 RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG--KIISVRIRRN---- 186
             G G++     T T     L++ N   + T   DL       G   I+ ++   N    
Sbjct: 51  DVGKGAAPNVVYTYTGKRIALYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANG 109

Query: 187 ----FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPD 242
               FA V    +  + + +D     +L  +   V    +    +    S    +     
Sbjct: 110 QSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS 169

Query: 243 RGRRRSPSPYRRERGSPDYGRGSSRSP---YRRERGSPDYGRVRSPSPY 288
              +  P         P  GRG  R P      +R     G    P P+
Sbjct: 170 GEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPF 218

>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 = 46.6 bits (110), Expect = 4e-06
 Identities = 18/130 (13%), Positives = 37/130 (28%), Gaps = 18/130 (13%)

Query: 39  RRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------S 88
            +  +   +  +      ++ GN  +     DL       G  D +++K           
Sbjct: 53  GKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSK 112

Query: 89  GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK------HERGIRRPGGGSSARR 142
           GFA + +  E  ++  +  L + E    G+   V           E   R+         
Sbjct: 113 GFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSG 170

Query: 143 PSTNTRPSKT 152
                 P  +
Sbjct: 171 EGKAGPPGGS 180

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 10/88 (11%)

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVR--IR-------RNFAFVQYEVQED 197
           +  S  +F+ N DP     + L   F  +G I+     +R       + +AF+ +   + 
Sbjct: 2   SSGSSGIFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 198 ATRALDATNMSKLTDRVISVEYAVRDDD 225
           +  A++A N   L +R I+V YA + D 
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAFKKDS 88

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 20/91 (21%), Positives = 33/91 (36%), Gaps = 12/91 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------DRVDMKS-GFAFIYMDDERDAEDAIRG 107
           IF GN + +  +  L   F  +G +        D     S G+AFI       ++ AI  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 108 LDRTEFGRKGRRLRVEW-TKHERGIRRPGGG 137
           ++        R + V +  K +     P  G
Sbjct: 68  MNGQYLC--NRPITVSYAFKKDSKGSGPSSG 96

>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 = 51.9 bits (125), Expect = 6e-09
 Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN-------F 187
           G S +   S+       + V N  P+     ++   F  Y  I  SV ++ N        
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           A V +E +++AT A+   N   +  R + +   
Sbjct: 60  AMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 51.9 bits (125), Expect = 7e-09
 Identities = 13/74 (17%), Positives = 28/74 (37%), Gaps = 10/74 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-DRVDMK-------SGFAFIYMDDERDAEDAIRGL 108
           I   N  +     ++   F  Y  +   V +K       +G A +  +   +A  A+  L
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 109 DRTEFGRKGRRLRV 122
           +    G   R++++
Sbjct: 78  NDRPIG--SRKVKL 89

>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 = 51.9 bits (125), Expect = 8e-09
 Identities = 20/93 (21%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN-------F 187
           G S +   S+       + V N  P+     ++   F  Y  I  SV ++ N        
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           A V +E +++AT A+   N   +  R + +   
Sbjct: 60  AMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92

>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 = 51.5 bits (124), Expect = 9e-09
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 10/75 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-DRVDMK-------SGFAFIYMDDERDAEDAIRGL 108
           I   N  +     ++   F  Y  +   V +K       +G A +  +   +A  A+  L
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 109 DRTEFGRKGRRLRVE 123
           +    G   R++++ 
Sbjct: 78  NDRPIG--SRKVKLV 90

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 10/91 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRAL 202
             T+FV           ++   F  YG +  V+I        + + FV +    D  + +
Sbjct: 9   PNTVFVGGI-DVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRRNGHSP 233
           +  +      + + +  A+R  +       P
Sbjct: 68  E--SQINFHGKKLKLGPAIRKQNLSTYHVQP 96

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 11/73 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           +F G  +    ++++   F RYG V       DR  +  G+ F+   ++ D +  +    
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69

Query: 110 RTEFGRKGRRLRV 122
           +  F   G++L++
Sbjct: 70  QINF--HGKKLKL 80

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.0 bits (125), Expect = 9e-09
 Identities = 20/117 (17%), Positives = 39/117 (33%), Gaps = 11/117 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN-------F 187
           G S +              + N  P+     D+ +  E       +V +  +        
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
           A VQ++ ++DA ++    +  KL  R   V     +D      + P + +   P  G
Sbjct: 60  ALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGK-SGPSSG 114

>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 = 42.8 bits (101), Expect = 2e-05
 Identities = 18/98 (18%), Positives = 26/98 (26%), Gaps = 15/98 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGL 108
               N  +   + D+ +                D      G A +   +E DA  + R L
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 76

Query: 109 DRTEFGRKGRRLRVEWT----KHERGIRRPGGGSSARR 142
            R +    GR   V         E     P  G S   
Sbjct: 77  HRKKLN--GREAFVHVVTLEDMREIEKNPPAQGKSGPS 112

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 53.3 bits (128), Expect = 1e-08
 Identities = 21/134 (15%), Positives = 38/134 (28%), Gaps = 8/134 (5%)

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRT 165
           R       G + R       K      +     S             L V N   +    
Sbjct: 44  RNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNL-DFGVSD 102

Query: 166 RDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVE 218
            D++  F  +G +    +  +        A V +E + DA +A+       L  R + ++
Sbjct: 103 ADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162

Query: 219 YAVRDDDDRRNGHS 232
                 D   + H 
Sbjct: 163 LVASQIDLEHHHHH 176

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 12/84 (14%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLD 109
           +   N ++    +D++ LF  +G + +  +         G A ++ +   DA  A++   
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150

Query: 110 RTEFGRKGRRLRVEWTKHERGIRR 133
                  GR + ++    +  +  
Sbjct: 151 GVPLD--GRPMDIQLVASQIDLEH 172

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 11/105 (10%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNF 187
           G S +      T P  T +V N  P++T   D++  F+    I SVR+         + F
Sbjct: 1   GSSGSSGKELPTEPPYTAYVGNL-PFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGF 58

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            +V+++  +    AL   + + L DR + V+ A     D+    S
Sbjct: 59  CYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSS 102

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV------DRVDMKS-GFAFIYMDDERDAEDAIRGLD 109
            + GN  ++  Q D++ +F+           D+   K  GF ++  D+    ++A+   D
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYD 76

Query: 110 RTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
               G   R LRV+  +  R   + G  S
Sbjct: 77  GALLG--DRSLRVDIAE-GRKQDKSGPSS 102

>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 = 53.3 bits (127), Expect = 2e-08
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRR-------NFAFVQYEVQEDATRALDATNMSKLTD 212
           P      D++   E  G+++++++RR          FV ++  E A + ++     K  +
Sbjct: 118 PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ-KYKE 176

Query: 213 RVISVEYAVRDDDDRRN 229
             + + +   D   ++N
Sbjct: 177 TDLLILFK-DDYFAKKN 192

>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 = 46.4 bits (109), Expect = 4e-06
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 10/81 (12%)

Query: 53  MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAI 105
             R ++   F  DA   D++      G+V  + M+        G  F+  D    A+  +
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167

Query: 106 RGLDRTEFGRKGRRLRVEWTK 126
                 ++  K   L + +  
Sbjct: 168 E-TPGQKY--KETDLLILFKD 185

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 16/112 (14%), Positives = 43/112 (38%), Gaps = 9/112 (8%)

Query: 134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRD-LERHFEPYGKIISVRI----RRNFA 188
               ++          S  L +I  + ++  T D L + F  +G ++ +       +  A
Sbjct: 10  AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA 69

Query: 189 FVQYEVQEDATRALDATNMSKLTDR--VISVEYAVRDDDDRRNGHSPDRNRD 238
            +QY     A  A  + +   + +    + ++++     + +   + D++RD
Sbjct: 70  LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY--NNDKSRD 119

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 60  GNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
            N  Y      L ++F ++G V ++          A +   D   A+ A   LD      
Sbjct: 34  ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN 93

Query: 116 KGRRLRVEWTKHER 129
               LR++++K   
Sbjct: 94  ACCTLRIDFSKLTS 107

>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 = 48.2 bits (115), Expect = 2e-07
 Identities = 18/104 (17%), Positives = 32/104 (30%), Gaps = 10/104 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FA 188
           G S +   S  +     + +    PY     D+   F P    + V I           A
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGL-PYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEA 58

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            V++   EDA  A+   + + +  R + +              S
Sbjct: 59  DVEFATHEDAVAAMAK-DKANMQHRYVELFLNSTAGTSGSGPSS 101

>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 = 48.3 bits (115), Expect = 2e-07
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEV 194
           GSS ++        + + +++F         L +  EP+G I +  I  + N AF++   
Sbjct: 4   GSSGQKGRVE--TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMAT 61

Query: 195 QEDATRALD--ATNMSKLTDRVISVEYAVR 222
            EDA  A+D   T  + +  + + V  + +
Sbjct: 62  TEDAQAAVDYYTTTPALVFGKPVRVHLSQK 91

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 18/105 (17%), Positives = 34/105 (32%), Gaps = 10/105 (9%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------F 187
           G   S+ +P         + V    P+     D+   F    ++ +V + ++        
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGM-PFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGN 58

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
             V++   +D   AL   N   +  R + V  A         GH 
Sbjct: 59  GLVKFLSPQDTFEALKR-NRMLMIQRYVEVSPATERQWVAAGGHI 102

>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 = 40.1 bits (94), Expect = 1e-04
 Identities = 14/91 (15%), Positives = 32/91 (35%), Gaps = 11/91 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLD 109
           +      + A ++D+   F    +VD V +        +G   +     +D  +A++  +
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RN 76

Query: 110 RTEFGRKGRRLRVEWTKHERGIRRPGGGSSA 140
           R       R + V      + +   G  +S 
Sbjct: 77  RMLMI--QRYVEVSPATERQWVAAGGHITSG 105

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 22/97 (22%), Positives = 35/97 (36%), Gaps = 12/97 (12%)

Query: 133 RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------- 183
           R        R      P  T F+ N  PY      ++  F     I +VR+         
Sbjct: 2   RGSHHHHHHRSRLPKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPER 59

Query: 184 RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            + F + ++E  +    AL + N   L +R I V+ A
Sbjct: 60  LKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVA 95

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 28/75 (37%), Gaps = 11/75 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG-------KVDRVDMKS-GFAFIYMDDERDAEDAIRGL 108
            F GN  YD  +  ++  FR          +      +  GF +   +D      A+  L
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 80

Query: 109 DRTEFGRKGRRLRVE 123
           +    G   RR+RV+
Sbjct: 81  NEESLG--NRRIRVD 93

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 48.9 bits (116), Expect = 3e-07
 Identities = 16/112 (14%), Positives = 43/112 (38%), Gaps = 9/112 (8%)

Query: 134 PGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRD-LERHFEPYGKIISVRI----RRNFA 188
               ++          S  L +I  + ++  T D L + F  +G ++ +       +  A
Sbjct: 28  AASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA 87

Query: 189 FVQYEVQEDATRALDATNMSKLTDR--VISVEYAVRDDDDRRNGHSPDRNRD 238
            +QY     A  A  + +   + +    + ++++     + +   + D++RD
Sbjct: 88  LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY--NNDKSRD 137

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 45.5 bits (107), Expect = 6e-06
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 60  GNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
            N  Y      L ++F ++G V ++          A +   D   A+ A   LD      
Sbjct: 52  ENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN 111

Query: 116 KGRRLRVEWTKHER 129
               LR++++K   
Sbjct: 112 ACCTLRIDFSKLTS 125

>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 = 47.0 bits (112), Expect = 5e-07
 Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 10/105 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN-------F 187
           G S +   S +T     + +    P+     ++ + F     +   + +  +        
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGE 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           AFVQ+  QE A +AL   +  ++  R I +  + R +       S
Sbjct: 60  AFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPSS 103

>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 = 40.1 bits (94), Expect = 1e-04
 Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 12/90 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------DRVDMKSGFAFIYMDDERDAEDAIRGL 108
           +      +   + ++ + F     V        D     +G AF+    +  AE A++  
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-K 76

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
            +   G   R + +  +     +R  G  S
Sbjct: 77  HKERIG--HRYIEIFKSSRAE-VRTSGPSS 103

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 216
                  +L   F  YG ++ V I    R FAFV +   + A           +    + 
Sbjct: 14  TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVH 71

Query: 217 VEYAV-RDDDDRRNGH 231
           +  A  + + +     
Sbjct: 72  ISNAEPKHNSNSGPSS 87

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIR 106
           +F G    D  + +L   F +YG V  V +      FAF+   D++ A+    
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

>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 = 46.9 bits (111), Expect = 6e-07
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEV 194
           G   ++        + + + N          + +  EPYGKI +  +   ++ AF++ E 
Sbjct: 12  GKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMET 71

Query: 195 QEDATRALD--ATNMSKLTDRVISVEYA 220
           +EDA   +D           R + V+ +
Sbjct: 72  REDAMAMVDHCLKKALWFQGRCVKVDLS 99

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 55  RPIFCGNFEYDA-RQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRT 111
           R I   N  +     S + +L   YGK+    +      AFI M+   DA   +    + 
Sbjct: 26  RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK 85

Query: 112 EFGRKGRRLRVEWTKHERGIR 132
               +GR ++V+ ++  + + 
Sbjct: 86  ALWFQGRCVKVDLSEKYKKLV 106

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 47.0 bits (111), Expect = 8e-07
 Identities = 29/123 (23%), Positives = 48/123 (39%), Gaps = 15/123 (12%)

Query: 137 GSSARRPSTNTR------PSKTLFVINFDPYHTRTRD-LERHFEPYGKIISVRI---RRN 186
           GSS +R +           +K L +   +P +  T D L     P GK+  + I      
Sbjct: 4   GSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI 63

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDR--VISVEYAVRDDDDRRNGHSPDRNRD-RSPDR 243
            A V++E    A +A  A N + +      + +EYA     +     + + + D   P  
Sbjct: 64  QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIR--NDNDSWDYTKPYL 121

Query: 244 GRR 246
           GRR
Sbjct: 122 GRR 124

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 3/72 (4%)

Query: 61  NFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKG 117
           N  Y      L  +    GKV R+ +       A +  +    A+ A   L+  +     
Sbjct: 32  NPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGC 91

Query: 118 RRLRVEWTKHER 129
             L++E+ +  R
Sbjct: 92  CTLKIEYARPTR 103

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.0 bits (116), Expect = 8e-07
 Identities = 18/93 (19%), Positives = 32/93 (34%), Gaps = 10/93 (10%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTR--------DLERHFEPYGKIISVRI--RRNFAFVQY 192
             +  + +KTL+V   D                +   F   G I  +R    +N  FV++
Sbjct: 127 IGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKF 186

Query: 193 EVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
           + Q +A  A +A +   L           R+  
Sbjct: 187 KYQANAEFAKEAMSNQTLLLPSDKEWDDRREGT 219

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 17/98 (17%), Positives = 32/98 (32%), Gaps = 21/98 (21%)

Query: 50  FEAMMRPIFCGNFEYD---------ARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDE 98
           F    + ++ G  +             +S +  +F R G +DR+         F+    +
Sbjct: 130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQ 189

Query: 99  RDAEDAIRGLDRTEFG----------RKGRRLRVEWTK 126
            +AE A   +                R+G  L V+W  
Sbjct: 190 ANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWAN 227

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 11/79 (13%)

Query: 57  IFCGNFEYDARQSDLER----LFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRG 107
           +   N +Y   + +L++     F R+GKV  V++         A + M++ +DA  A+  
Sbjct: 12  VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS 71

Query: 108 LDRTEFGRKGRRLRVEWTK 126
           L R + G   +++ V    
Sbjct: 72  LHRYKIG--SKKILVSLAT 88

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 144 STNTRPSKTLFVINFDPYHTRT---RDLERHFEPYGKIISVRIR-----RNFAFVQYEVQ 195
           S ++     + V N D   +R    + L+  F  +GK+ SV +      +  A VQ E  
Sbjct: 3   SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENL 62

Query: 196 EDATRALDATNMSKLTDRVISVEYA 220
           +DA  A+++ +  K+  + I V  A
Sbjct: 63  QDAIGAVNSLHRYKIGSKKILVSLA 87

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 18/102 (17%), Positives = 35/102 (34%), Gaps = 12/102 (11%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------- 186
             G   R     +   K +F+     + T    L  +F  +G++    + R+        
Sbjct: 11  SSGLVPRGSHMGSSGCK-MFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV-RDDDDR 227
           F FV +  Q    + L  +   +L  + I  + A  R    +
Sbjct: 69  FGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAFPRRAQPK 109

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS 216
                  +L++ F  YG+++ V I    R FAFV +   + A           +    + 
Sbjct: 20  TEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLIIKGISVH 77

Query: 217 VEYAV-RDDD 225
           +  A  + + 
Sbjct: 78  ISNAEPKHNK 87

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 7/69 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-DRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEF 113
           +F G    D    +L++ F +YG+V D    K    FAF+   D++ A+      +    
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLII 71

Query: 114 GRKGRRLRV 122
             KG  + +
Sbjct: 72  --KGISVHI 78

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 21/104 (20%), Positives = 45/104 (43%), Gaps = 15/104 (14%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFA 188
           GSS    S+ ++ +K +FV    P++    +L  +F+ +G +  V +         R F 
Sbjct: 1   GSS---GSSGSKSNK-IFVGGI-PHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFG 55

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAV-RDDDDRRNGH 231
           F+ +E ++   +A+   +   +  + + V+ A  RD        
Sbjct: 56  FITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 8/57 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAI 105
           IF G   ++  +++L   F+++G V       D    +  GF FI  +DE+  + A+
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

>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 = 43.8 bits (104), Expect = 6e-06
 Identities = 19/106 (17%), Positives = 43/106 (40%), Gaps = 13/106 (12%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------- 186
           G   S+       + S  L V+   P+ T  +DL+ +F  +G+++ V+++++        
Sbjct: 1   GSSGSSGVKRAVQKTSD-LIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 58

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV-RDDDDRRNGH 231
           F FV++   E   + +   +M  +  R    +    +   D     
Sbjct: 59  FGFVRFTEYETQVKVMSQRHM--IDGRWCDCKLPNSKQSQDSGPSS 102

>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 = 44.2 bits (105), Expect = 6e-06
 Identities = 25/95 (26%), Positives = 37/95 (38%), Gaps = 11/95 (11%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------R-RN 186
            G S       +T  +K +FV    PYHT    L ++FE +G I    +       + R 
Sbjct: 3   SGSSGMHGSQKDTTFTK-IFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 187 FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV 221
           + FV    +  A RA    N   +  R  +V  A 
Sbjct: 61  YGFVTMADRAAAERACKDPN-PIIDGRKANVNLAY 94

>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 = 43.1 bits (102), Expect = 7e-06
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 142 RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEV 194
              ++     T+ +    P++   +++     P  K +++RI RN       + FV +  
Sbjct: 2   SSGSSGTTCHTVKLRGA-PFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 195 QEDATRALDATNMSKLTDRVISV 217
           +E+  +AL   N   +  R I V
Sbjct: 60  EEEVKQALKC-NREYMGGRYIEV 81

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 9/72 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV------DRVDMKSGFAFIYMDDERDAEDAIRGLDR 110
           +      ++  + ++         V      +    K+G+ F+   +E + + A++  +R
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNR 71

Query: 111 TEFGRKGRRLRV 122
              G  GR + V
Sbjct: 72  EYMG--GRYIEV 81

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 14/97 (14%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRN--------FAFVQYE 193
            S ++  + +L++ + +PY      + R F   G  ++SV+I RN        + FV++ 
Sbjct: 2   SSGSSGMAASLWMGDLEPYMD-ENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 194 VQEDATRALDATN----MSKLTDRVISVEYAVRDDDD 226
               A + L   N          +   + YA      
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 14/88 (15%), Positives = 33/88 (37%), Gaps = 11/88 (12%)

Query: 51  EAMMRPIFCGNFEYDARQSDLERLFRRYG------KV--DRVDMKS-GFAFIYMDDERDA 101
             M   ++ G+ E    ++ + R F   G      K+  +R+     G+ F+   D   A
Sbjct: 6   SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65

Query: 102 EDAIRGLDRTEFG--RKGRRLRVEWTKH 127
           E  +  ++          +R ++ +  +
Sbjct: 66  EKCLHKINGKPLPGATPAKRFKLNYATY 93

>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 = 42.6 bits (101), Expect = 2e-05
 Identities = 22/104 (21%), Positives = 34/104 (32%), Gaps = 11/104 (10%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FA 188
           GSS    S      K LFV     + T    L  +F  YG+++   I ++        F 
Sbjct: 4   GSSGMNNSGADEIGK-LFVGGL-DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           FV+++        L +     L  R I  +             S
Sbjct: 62  FVKFKDPNCVGTVLASRP-HTLDGRNIDPKPCTPRGMQPSGPSS 104

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 17/108 (15%), Positives = 33/108 (30%), Gaps = 14/108 (12%)

Query: 136 GGSSARRPSTNTRPSKTLFVIN-FDPYHTRT---------RDLERHFEPYGKIISVRIRR 185
           G S +    +  R  + + + N F P               DL      +G+I  + +  
Sbjct: 1   GSSGSSGGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD 60

Query: 186 N----FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
                 A V +   E+A   +   +      R I+ +      D +  
Sbjct: 61  RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSG 108

>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 = 42.9 bits (101), Expect = 3e-05
 Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 10/96 (10%)

Query: 129 RGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-- 186
            G ++ G GS     +  +     + +    PY     D+   F P    + V I     
Sbjct: 25  TGGQQMGRGSGDSEFTVQSTTGHCVHMRGL-PYKATENDIYNFFSPLN-PVRVHIEIGPD 82

Query: 187 -----FAFVQYEVQEDATRALDATNMSKLTDRVISV 217
                 A V++   E+A  A+   + + +  R I +
Sbjct: 83  GRVTGEADVEFATHEEAVAAMSK-DRANMQHRYIEL 117

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 17/119 (14%), Positives = 34/119 (28%), Gaps = 13/119 (10%)

Query: 133 RPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII----SVRIRRN-- 186
             GG S+      +      + +    P+     ++   F  +  I      +       
Sbjct: 6   SGGGTSNEVAQFLSKENQVIVRMRGL-PFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64

Query: 187 -----FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRS 240
                 AFV +  +E A  AL   +   L  R I +  +   +  +        +   S
Sbjct: 65  GRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSS 122

>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 = 42.2 bits (99), Expect = 3e-05
 Identities = 23/120 (19%), Positives = 36/120 (30%), Gaps = 13/120 (10%)

Query: 135 GGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPY---GKIISVRIRRN----- 186
             GSS             + +    P+     D++           +  V          
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGL-PWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60

Query: 187 --FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRG 244
              AFV+ E ++D   AL   +   +  R I V  + R + D    HS   N    P  G
Sbjct: 61  SGEAFVELESEDDVKLALKK-DRESMGHRYIEVFKSHRTEMDWVLKHSG-PNSASGPSSG 118

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 40.9 bits (97), Expect = 3e-05
 Identities = 12/69 (17%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLT 211
             +T   D++ +FE +GK+    +         R F FV +E ++   +  +     ++ 
Sbjct: 8   SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFH-EIN 66

Query: 212 DRVISVEYA 220
           ++++  + A
Sbjct: 67  NKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 37.1 bits (87), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIR 106
           IF G    +    D++  F ++GKV       D+   +  GF F+  + E   E    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 9/69 (13%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLT 211
            + T    L  +F  +G++    + R+        F FV +  Q    + L  +   +L 
Sbjct: 9   SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELD 67

Query: 212 DRVISVEYA 220
            + I  + A
Sbjct: 68  SKTIDPKVA 76

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 9/55 (16%), Positives = 23/55 (41%), Gaps = 8/55 (14%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATN 206
              T    +  +F  +G++ S+ +        RR F F+ ++ +E   + ++   
Sbjct: 8   SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 38.6 bits (91), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIR 106
           IF G    D  +  +   F  +G+V+ +++          GF FI   +E   +  + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 41.7 bits (98), Expect = 5e-05
 Identities = 15/114 (13%), Positives = 34/114 (29%), Gaps = 10/114 (8%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIRRN-------FA 188
           G    R  +       +++    P+    + +   F+    +  S+ I            
Sbjct: 12  GQKRSRSRSPHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPD 242
           FV++  + D   AL   +   + +R I V    +     +      R +     
Sbjct: 71  FVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSS 123

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.4 bits (97), Expect = 6e-05
 Identities = 18/108 (16%), Positives = 30/108 (27%), Gaps = 6/108 (5%)

Query: 126 KHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV---- 181
            H       G        S        + + N  P     +DL+          +     
Sbjct: 4   SHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNL-PEGCSWQDLKDLARENSLETTFSSVN 62

Query: 182 -RIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRR 228
            R       +++  +E    AL+  N  +    VI+VE        RR
Sbjct: 63  TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPIRR 110

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV-----DMKSGFAFIYMDDERDAEDAIRGLDRT 111
           I   N        DL+ L R                 G   +    E    +A+  L+  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 112 EFGRKGRRLRVEWTKHERGIRR 133
           EF  +G  + VE   +   IRR
Sbjct: 91  EF--RGSVITVERDDNPPPIRR 110

>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 = 43.3 bits (101), Expect = 9e-05
 Identities = 59/332 (17%), Positives = 93/332 (28%), Gaps = 15/332 (4%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           +F     YD  +S L R F  YG + R+ M          G+AFI  + ERD   A +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL 168
           D  +   +   + VE  +  +G R    G                     D      R  
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224

Query: 169 ERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRR 228
                   +       R     + + + +  R       S+  DR        +++  R 
Sbjct: 225 PSPLPHRDRDRDRERERRERSRERDKERERRR-------SRSRDRRRRSRSRDKEERRRS 277

Query: 229 NGHSPDRNRDRSPDRGRRRSPSPYRRERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPY 288
              S D++RDR     R R  +   RER     G G   +       +P           
Sbjct: 278 RERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGP 337

Query: 289 RRDRGSPDYGRNSSRSPYKKERAAIGHGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPS 348
               G  + GR+  R   +  R+     R   R   R                  +G   
Sbjct: 338 DGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGG 397

Query: 349 PNNGRGPSRSPYERERPSPENGRGGSRSPYRR 380
             +          R+      G  G  +P   
Sbjct: 398 GQDNGLEGLGNDSRDMYMESEGGDGYLAPENG 429

>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 = 42.9 bits (100), Expect = 1e-04
 Identities = 47/286 (16%), Positives = 75/286 (26%), Gaps = 9/286 (3%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEV 194
           P+      KTLFV     Y T    L R FE YG I  + +  +        +AF++YE 
Sbjct: 95  PNAQGDAFKTLFVARV-NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153

Query: 195 QEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRR 254
           + D   A    +  K+  R + V+                     +   G   +     R
Sbjct: 154 ERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR 213

Query: 255 ERGSPDYGRGSSRSPYRRERGSPDYGRVRSPSPYRRDRGSPDYGRNSSRSPYKKERAAIG 314
           +  S    R        R+R        R  S  R         R+  R    + R    
Sbjct: 214 DDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEE 273

Query: 315 HGRGPSRSPYRRDRGSPENGHGSSPSPYRKGKPSPNNGRGPSRSPYERERPSPENGRGGS 374
             R   RS  +       +      +   + +     G G   +       +P +     
Sbjct: 274 RRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPG 333

Query: 375 RSPYRRERPSPDNGRVPSPNSMPEPRDSPGYDGADSPINERYRSRS 420
                      + GR          R             +R R   
Sbjct: 334 ELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHK 379

>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 = 39.9 bits (94), Expect = 1e-04
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLT 211
            + T  +DL+ +F  +G+++   I+ +        F F+ ++      + LD     +L 
Sbjct: 20  SWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLD 78

Query: 212 DRVISVEYA 220
            RVI  + A
Sbjct: 79  GRVIDPKKA 87

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 25/93 (26%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------------GFAFIYMDDERDA 101
           R ++ GN  +   +  +   F    ++  +                  FAF+      + 
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 102 EDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRP 134
             A+   D   F  +G+ L++         RRP
Sbjct: 67  TQAMA-FDGIIF--QGQSLKI---------RRP 87

>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 = 39.9 bits (93), Expect = 2e-04
 Identities = 17/118 (14%), Positives = 39/118 (33%), Gaps = 21/118 (17%)

Query: 126 KHERGIRRPGGGSSARRPS-----------TNTRPSKTLFVINFDPYHTRTRDLERHFEP 174
            H         GS     +            ++     + +    P+     ++ + F  
Sbjct: 7   HHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGL-PFGCTKEEIVQFFSG 65

Query: 175 YGKII-SVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD 224
              +   + +  +        AFVQ+  QE A +AL   +  ++  R I V  + +++
Sbjct: 66  LEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQEE 122

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 19/100 (19%)

Query: 149 PSKTLFVIN-FDP--------YHTRTRDLERHFEPYGKIISVRIRRN----------FAF 189
           P++ L ++N   P        Y     D+      YG + S+ I R             F
Sbjct: 4   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 63

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
           V++    D  +A+      K  +RV+  +Y   D   RR+
Sbjct: 64  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRD 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 10/100 (10%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHF-EPYGKIISVRI-------RRNFAFVQYEVQ 195
           S ++ P  +LFV +  P       L   F + Y      ++        + + FV++  +
Sbjct: 3   SGSSGPEYSLFVGDLTP-DVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 196 EDATRALDATN-MSKLTDRVISVEYAVRDDDDRRNGHSPD 234
            +  RAL        L  + + +  A+      +   S  
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGP 101

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 21/95 (22%), Positives = 34/95 (35%), Gaps = 13/95 (13%)

Query: 57  IFCGNFEYDARQSDLERLF-RRYG-----KV--DRVDMKSGFAFIYMDDERDAEDAIRGL 108
           +F G+   D     L   F + Y      KV  D+  +  G+ F+   DE + + A+   
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71

Query: 109 D-RTEFGRKGRRLRVEW--TKHERGIRRPGGGSSA 140
                 G   + +R+     K  R      G SS 
Sbjct: 72  QGAVGLG--SKPVRLSVAIPKASRVKPVESGPSSG 104

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 7/52 (13%)

Query: 175 YGKIISVRIRRN-------FAFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
           YG++  + +  N         +V++  +EDA +A+   N      + I  E 
Sbjct: 51  YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 167 DLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD 224
            L      +G ++S     N   A  +Y  +E+A +A  A N   L +  I  E    ++
Sbjct: 23  TLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSENE 82

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 16/89 (17%), Positives = 29/89 (32%), Gaps = 7/89 (7%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPY-----GKIISVRIRRNFAFVQYEVQEDA 198
           S+ +     + V    P       L  +FE       G ++S +       + +    DA
Sbjct: 2   SSGSSGGVAVEVRGLPP-AVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADA 60

Query: 199 TRALDATNMSKLTDRVISVEYAVRDDDDR 227
            R L   +  +L    +S+  A      R
Sbjct: 61  ERVLAQAD-HELHGAQLSLRPAPPRAPAR 88

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 16/112 (14%), Positives = 35/112 (31%), Gaps = 16/112 (14%)

Query: 149 PSKTLFVIN-FDPYHTRTRDLERHF--------EPYGKIISVRIRRN----FAFVQYEVQ 195
            ++   + N F+P        +             +G +I + + +N      +V+    
Sbjct: 6   ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSI 65

Query: 196 EDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRR 247
             A  A++A +      ++I+  Y         +   PD           RR
Sbjct: 66  AAAIAAVNALHGRWFAGKMITAAY---VPLPTYHNLFPDSMTATQLLVPSRR 114

>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 = 38.0 bits (89), Expect = 9e-04
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 160 PYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDATNMSKLT 211
            + T    L  ++E +GK+    + R+        F FV +    +   A+ A     + 
Sbjct: 36  SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP-HSID 94

Query: 212 DRVISVEYAVRDDDDRRNGHS 232
            RV+  + AV  ++      S
Sbjct: 95  GRVVEPKRAVAREESGSGPSS 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	425
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.94
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.8
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.75
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.75
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.74
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.74
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.74
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.74
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.72
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.72
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.72
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.72
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.72
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.71
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.71
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.71
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.7
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.7
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.7
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.7
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.7
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.7
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.7
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.69
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.69
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.69
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.69
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.68
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.68
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.68
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.68
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.68
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.67
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.67
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.67
2div_A	99	TRNA selenocysteine associated protein; structural	99.67
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.67
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.67
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.67
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.67
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.67
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.66
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.66
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.66
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.66
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.66
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.66
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.66
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.65
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.65
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.65
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.65
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.65
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.65
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.64
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.64
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.64
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.64
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.64
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.63
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.63
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.63
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.63
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.63
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.63
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.63
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.63
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.62
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.62
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.62
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.62
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.62
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.62
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.62
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.62
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.62
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.61
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.61
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.61
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.61
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.61
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.61
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.6
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.6
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.6
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.6
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.6
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.6
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.6
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.6
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.59
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.59
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.59
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.59
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.59
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.59
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.59
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.59
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.59
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.59
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.59
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.59
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.59
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.59
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.59
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.58
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.58
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.36
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.58
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.58
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.58
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.58
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.58
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.58
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.58
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.58
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.58
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.57
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.57
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.57
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.57
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.57
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.56
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.56
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.56
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.56
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.56
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.56
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.56
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.56
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.56
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.56
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.56
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.56
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.55
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.55
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.55
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.55
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.55
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.55
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.55
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.54
1x5p_A	97	Negative elongation factor E; structure genomics,	99.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.54
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.54
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.54
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.54
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.54
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.54
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.54
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.53
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.53
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.53
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.53
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.53
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.53
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.53
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.53
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.52
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.52
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.52
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.52
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.51
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.51
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.51
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.51
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.5
2div_A	99	TRNA selenocysteine associated protein; structural	99.49
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.49
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.49
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.49
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.48
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.48
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.48
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.48
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.48
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.48
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.48
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.48
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.47
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.47
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.47
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.47
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.47
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.47
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.47
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.47
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.47
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.47
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.47
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.47
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.47
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.47
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.47
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.46
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.46
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.46
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.46
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.46
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.45
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.44
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.44
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.43
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.43
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.43
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.43
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.43
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.43
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.43
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.42
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.42
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.41
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.13
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.41
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.41
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.4
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.4
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.4
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.4
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.4
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.39
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.38
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.38
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.37
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.37
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.35
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.34
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.34
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.34
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.32
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.31
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.31
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.3
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.3
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.29
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.26
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.22
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.19
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.16
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.15
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.13
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.12
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.12
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.1
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.08
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.06
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.05
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.86
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.76
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.57
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.52
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.42
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.18
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.07
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.06
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.87
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.74
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.49
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.47
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.46
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.09
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.01
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.89
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.75
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.67
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.21
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.13
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.44
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.35
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.22
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.75
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.22
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	87.78
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	84.16
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	83.55
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	82.47
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	81.9

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=1.2e-31  Score=244.88  Aligned_cols=157  Identities=23%  Similarity=0.436  Sum_probs=138.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ...++++|||+|||+++|+++|.++|++||+|..|.|.        +|||||+|.+.++|.+||..||+..+  .|+.|.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~--~g~~i~   88 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI--KGKPVR   88 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhc--CCcccc
Confidence            34567899999999999999999999999999999983        68999999999999999999999999  899999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCH
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQ  195 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~  195 (425)
                      |.++......              ......+|||+|| +..+++++|+++|.+||.|..|.|+      +|||||+|.+.
T Consensus        89 ~~~~~~~~~~--------------~~~~~~~l~v~nl-~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~  153 (213)
T 4f02_A           89 IMWSQRDPSL--------------RKSGVGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQ  153 (213)
T ss_dssp             EEECCCCTHH--------------HHHCTTEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSH
T ss_pred             cccccccccc--------------cccccccceECCc-ccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCH
Confidence            9998654311              1123468999999 8899999999999999999999985      68999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          196 EDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ++|.+|++.|||..|+|+.|.|.+|..+
T Consensus       154 ~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          154 EAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             HHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            9999999999999999999999999764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.5e-30  Score=226.93  Aligned_cols=150  Identities=20%  Similarity=0.444  Sum_probs=138.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      ++|||+|||+++|+++|.++|++||+|..|.|.       +|||||+|.+.++|.+|+..|||..|  .|+.|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQI--ENNIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCcc--CCCeeEEEEcCC
Confidence            589999999999999999999999999999983       68999999999999999999999999  899999999875


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHH
Q 014384          128 ERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDAT  199 (425)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~  199 (425)
                      ...              ....+..+|||+|| |..+++++|+++|++||.|..+.+.        +|+|||+|.+.++|.
T Consensus        79 ~~~--------------~~~~~~~~l~v~nl-~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  143 (166)
T 3md3_A           79 SQQ--------------SSSDDTFNLFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ  143 (166)
T ss_dssp             CCC--------------CCCTTCEEEEEESC-CTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             CCC--------------CCCCCCceEEECCC-CCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHH
Confidence            431              23445789999999 8899999999999999999999985        569999999999999


Q ss_pred             HHHHHcCCCccCCeEEEEEEee
Q 014384          200 RALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       200 ~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      +|+..|||..|+|+.|.|.||.
T Consensus       144 ~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          144 NAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHHHTTCEETTEECEEEESC
T ss_pred             HHHHHhCCCccCCcEEEEEecC
Confidence            9999999999999999999985

>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=99.97  E-value=5.5e-30  Score=224.12  Aligned_cols=149  Identities=27%  Similarity=0.460  Sum_probs=136.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++|||+|||+++|+++|.++|+.||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~   79 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSY   79 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEe--CCcEEEEEe
Confidence            46899999999999999999999999999999982        58999999999999999999999999  899999999


Q ss_pred             eccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHH
Q 014384          125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQE  196 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~  196 (425)
                      +....                ...+..+|||+|| |..+++++|+++|++||.|..+.+.        +|+|||+|.+.+
T Consensus        80 ~~~~~----------------~~~~~~~l~v~nl-~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  142 (168)
T 1b7f_A           80 ARPGG----------------ESIKDTNLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE  142 (168)
T ss_dssp             CCCCS----------------STTTTCEEEEESC-CTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             cCCCc----------------ccCCCCCEEEeCC-CCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHH
Confidence            87543                1245689999999 7899999999999999999999885        479999999999


Q ss_pred             HHHHHHHHcCCCccCC--eEEEEEEe
Q 014384          197 DATRALDATNMSKLTD--RVISVEYA  220 (425)
Q Consensus       197 ~A~~A~~~l~g~~~~g--~~i~v~~a  220 (425)
                      +|.+|+..|||..|.|  +.|.|.||
T Consensus       143 ~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          143 EAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999988  99999986

>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=99.97  E-value=7.1e-30  Score=229.26  Aligned_cols=162  Identities=20%  Similarity=0.375  Sum_probs=135.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .+...++|||+|||+++|+++|.++|+.||.|..|.|.        +|||||+|.+.++|.+||.. ++..|  .|+.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~--~g~~l~   85 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKV--DGRVVE   85 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEE--TTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEE--CCEEee
Confidence            45567999999999999999999999999999999883        68999999999999999955 88999  899999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEc
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYE  193 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~  193 (425)
                      |.++........          .....+..+|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.
T Consensus        86 v~~~~~~~~~~~----------~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~  154 (196)
T 1l3k_A           86 PKRAVSREDSQR----------PGAHLTVKKIFVGGI-KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD  154 (196)
T ss_dssp             EEECCC---------------------CCSEEEEECC-TTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             eecccCcccccc----------cccCCCcceEEEeCC-CCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEEC
Confidence            999876542211          122445689999999 8899999999999999999999985        579999999


Q ss_pred             CHHHHHHHHHHcCCCccCCeEEEEEEeeeCCCC
Q 014384          194 VQEDATRALDATNMSKLTDRVISVEYAVRDDDD  226 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~~  226 (425)
                      +.++|.+|+.. ++..|+|+.|.|.++..+...
T Consensus       155 ~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             SHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            99999999986 799999999999999886543

>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=99.97  E-value=1.2e-29  Score=221.38  Aligned_cols=148  Identities=24%  Similarity=0.489  Sum_probs=134.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.|.++
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~--~g~~l~v~~~   79 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYA   79 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCcc--CCceEEEEec
Confidence            5799999999999999999999999999999983        48999999999999999999999999  8999999998


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHH
Q 014384          126 KHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQED  197 (425)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~  197 (425)
                      ....                ......+|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.++
T Consensus        80 ~~~~----------------~~~~~~~l~v~nl-~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~  142 (167)
T 1fxl_A           80 RPSS----------------ASIRDANLYVSGL-PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE  142 (167)
T ss_dssp             CCCC----------------GGGTTCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             CCCc----------------ccCCCCcEEECCC-CCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHH
Confidence            7543                1234578999999 7889999999999999999999985        5799999999999


Q ss_pred             HHHHHHHcCCCccCCeE--EEEEEe
Q 014384          198 ATRALDATNMSKLTDRV--ISVEYA  220 (425)
Q Consensus       198 A~~A~~~l~g~~~~g~~--i~v~~a  220 (425)
                      |.+|++.|||..|.|+.  |.|.||
T Consensus       143 A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          143 AEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999999999964  888875

>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=99.97  E-value=1.1e-29  Score=230.17  Aligned_cols=166  Identities=19%  Similarity=0.279  Sum_probs=137.1

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           52 AMMRPIFCGNFE-YDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        52 ~~~~~l~V~nL~-~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .+.++|||+||+ ..+|+++|.++|++||.|..|.|.   +|||||+|.+.++|++||+.|||..|  .|+.|.|.+++.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~s~~   79 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFM--FGQKMNVCVSKQ   79 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEE--CCceEEEEEccC
Confidence            356899999999 899999999999999999999984   79999999999999999999999999  899999999975


Q ss_pred             ccCCCCCC----CCC----------CCC-------CCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcE--EEEEEe
Q 014384          128 ERGIRRPG----GGS----------SAR-------RPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI--ISVRIR  184 (425)
Q Consensus       128 ~~~~~~~~----~~~----------~~~-------~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v--~~v~~~  184 (425)
                      ........    ...          ...       .......+..+|||+|| |..+++++|+++|++||.|  ..+.+.
T Consensus        80 ~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NL-p~~~t~~~L~~~F~~~G~v~~~~v~~~  158 (205)
T 3tyt_A           80 PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNA-PLEVTEENFFEICDELGVKRPTSVKVF  158 (205)
T ss_dssp             SCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEE-CTTCCHHHHHHHHHHHTCCCCSEEEEC
T ss_pred             CccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEEE
Confidence            43211100    000          000       00112356789999999 8899999999999999998  888875


Q ss_pred             ------ccEEEEEEcCHHHHHHHHHHcCCCccCCe----EEEEEEe
Q 014384          185 ------RNFAFVQYEVQEDATRALDATNMSKLTDR----VISVEYA  220 (425)
Q Consensus       185 ------~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~i~v~~a  220 (425)
                            +|+|||+|.+.++|.+|+..|||..|.|.    ++.|.++
T Consensus       159 ~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          159 SGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             cCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence                  37999999999999999999999999986    5777665

>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=99.97  E-value=2.8e-29  Score=231.64  Aligned_cols=171  Identities=23%  Similarity=0.322  Sum_probs=144.7

Q ss_pred             hhcCCCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           49 AFEAMMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ....+.++|||+|||+ ++|+++|.++|++||.|..|.|.   +|||||+|.+.++|.+|+..|||..|  .|+.|.|.+
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~--~g~~l~v~~  106 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITL  106 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBC--SSSBCEEEC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEE
Confidence            3456789999999999 99999999999999999999995   79999999999999999999999999  899999999


Q ss_pred             eccccCCCCCCC----------------C---CCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEE-
Q 014384          125 TKHERGIRRPGG----------------G---SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRI-  183 (425)
Q Consensus       125 a~~~~~~~~~~~----------------~---~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~-  183 (425)
                      +...........                .   ...........+..+|||+|| |..+++++|+++|.+|| .|..|.+ 
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~~i~~v~i~  185 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFF  185 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECC-CTTCCHHHHHHHHHTTSCCEEEEEEC
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCC-CccCCHHHHHHHHHHcCCCeeEEEEE
Confidence            975421110000                0   000000122456799999999 78899999999999999 9999999 


Q ss_pred             --eccEEEEEEcCHHHHHHHHHHcCCCccC-CeEEEEEEeee
Q 014384          184 --RRNFAFVQYEVQEDATRALDATNMSKLT-DRVISVEYAVR  222 (425)
Q Consensus       184 --~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a~~  222 (425)
                        .+|||||+|.+.++|.+|+..|||..|+ |+.|.|.|++.
T Consensus       186 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          186 QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             ECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence              3789999999999999999999999999 99999999875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=3.7e-29  Score=228.04  Aligned_cols=167  Identities=21%  Similarity=0.411  Sum_probs=141.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||.++|+++|.++|+.||+|..|.|        .+|||||+|.+.++|.+|+..|||..|  .|+.|.
T Consensus        24 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~l~  101 (216)
T 2qfj_A           24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML--GGRNIK  101 (216)
T ss_dssp             HHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCC--C-CCCE
T ss_pred             ccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCee--CCeeEE
Confidence            3445789999999999999999999999999999998        379999999999999999999999999  899999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEc
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYE  193 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~  193 (425)
                      |.++..........     ...........+|||+|| +..+++++|+++|++||.|..|.+.        +|||||+|.
T Consensus       102 v~~~~~~~~~~~~~-----~~~~~~~~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~  175 (216)
T 2qfj_A          102 VGRPSNIGQAQPII-----DQLAEEARAFNRIYVASV-HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE  175 (216)
T ss_dssp             EECCSCCGGGHHHH-----HHHHHHHTTSCEEEEECC-CTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEES
T ss_pred             EecCCCccccchhh-----hhhhcccCCCcEEEEeCC-CCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEec
Confidence            98876543110000     000011245689999999 7889999999999999999999985        579999999


Q ss_pred             CHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          194 VQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       194 ~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      +.++|.+|+..|||..|+|+.|.|.++....
T Consensus       176 ~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             SHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             CHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999999999999998764

>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=99.96  E-value=5.8e-29  Score=236.58  Aligned_cols=169  Identities=22%  Similarity=0.419  Sum_probs=141.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLE----RLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~----~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ...+.++|||+|||+++|+++|+    ++|.+||.|..|.|.     +|||||+|.+.++|.+|+..|||..|  .|+.|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l   82 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPM   82 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCee--CCcEE
Confidence            44678999999999999999966    999999999999984     69999999999999999999999999  89999


Q ss_pred             EEEEeccccCCCCCCCCC-------------------------------------CC-----------------------
Q 014384          121 RVEWTKHERGIRRPGGGS-------------------------------------SA-----------------------  140 (425)
Q Consensus       121 ~V~~a~~~~~~~~~~~~~-------------------------------------~~-----------------------  140 (425)
                      .|.|+...........+.                                     ..                       
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            999997644210000000                                     00                       


Q ss_pred             -----------------------------------CCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-
Q 014384          141 -----------------------------------RRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-  184 (425)
Q Consensus       141 -----------------------------------~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-  184 (425)
                                                         ........+.++|||+|| +..+++++|+++|++||.|..|.+. 
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNL-PEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCC-CCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                               000123345689999999 7899999999999999999999996 


Q ss_pred             --ccEEEEEEcCHHHHHHHHHHcCCCccC-CeEEEEEEee
Q 014384          185 --RNFAFVQYEVQEDATRALDATNMSKLT-DRVISVEYAV  221 (425)
Q Consensus       185 --~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a~  221 (425)
                        +|||||+|.+.++|.+|++.|||..|. |+.|.|.|++
T Consensus       242 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence              489999999999999999999999999 9999999986

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.96  E-value=5.8e-29  Score=223.66  Aligned_cols=168  Identities=17%  Similarity=0.338  Sum_probs=141.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRY----G-------KVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~----G-------~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ..++|||+|||+++|+++|.++|+.|    |       .|..+.+  .+|||||+|.+.++|.+|| .|||..|  .|+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~--~g~~   79 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQS   79 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEE--TTEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEE--cCce
Confidence            46899999999999999999999999    5       6777777  4899999999999999999 9999999  8999


Q ss_pred             EEEEEeccccCCCCCCCC----CCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccE
Q 014384          120 LRVEWTKHERGIRRPGGG----SSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNF  187 (425)
Q Consensus       120 l~V~~a~~~~~~~~~~~~----~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~  187 (425)
                      |.|.++............    ...........+..+|||+|| |..+++++|+++|.+||.|..|.+.        +||
T Consensus        80 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl-~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~  158 (198)
T 2yh0_A           80 LKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  158 (198)
T ss_dssp             EEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECC-CTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEE
T ss_pred             EEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceE
Confidence            999998765422111110    011122233467799999999 7899999999999999999999985        579


Q ss_pred             EEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       188 afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      |||+|.+.++|.+|++.|||..|+|+.|.|.++....
T Consensus       159 afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          159 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             EEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999999999998753

>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=99.96  E-value=2.9e-29  Score=220.45  Aligned_cols=148  Identities=19%  Similarity=0.384  Sum_probs=134.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRY----G-------KVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~----G-------~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      +.++|||+|||+++|+++|.++|++|    |       .|..+.+  .+|||||+|.++++|.+|+ .|||..|  .|+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~--~g~~   79 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQS   79 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEE--TTEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEe--cCce
Confidence            46899999999999999999999999    7       7888877  4899999999999999999 9999999  8999


Q ss_pred             EEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEE
Q 014384          120 LRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQ  191 (425)
Q Consensus       120 l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~  191 (425)
                      |.|.++....                ......+|||+|| |..+++++|+++|++||.|..|.+.        +|||||+
T Consensus        80 i~v~~~~~~~----------------~~~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~  142 (172)
T 2g4b_A           80 LKIRRPHDYQ----------------PLPGAHKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE  142 (172)
T ss_dssp             CEEECCSSCC----------------CCTTTTCEEEECC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEE
T ss_pred             eeecCCcccC----------------CCCCCCEEEEEcC-CCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEE
Confidence            9999876533                1233689999999 8899999999999999999999985        5699999


Q ss_pred             EcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          192 YEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       192 f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      |.+.++|.+|++.|||..|+|+.|.|.||
T Consensus       143 f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             ESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             eCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999999999999999999999987

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=8.7e-29  Score=217.82  Aligned_cols=153  Identities=22%  Similarity=0.351  Sum_probs=134.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCCeec-CCCcEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRTEFG-RKGRRLR  121 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~~ig-~~gr~l~  121 (425)
                      +.++|||+|||+++|+++|.++|++||+|..|.|.          +|||||+|.+.++|.+|++.|||..+. ..++.|.
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            46899999999999999999999999999999872          579999999999999999999998762 2378888


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcC
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEV  194 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~  194 (425)
                      |.++.....               ...+..+|||+|| |..+++++|+++|++||.|..|.+.       +|||||+|.+
T Consensus        82 ~~~~~~~~~---------------~~~~~~~l~v~nl-~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~  145 (175)
T 3nmr_A           82 MKPADSEKN---------------NAVEDRKLFIGMI-SKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT  145 (175)
T ss_dssp             EEECGGGCC---------------SCGGGSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESS
T ss_pred             Ecccccccc---------------ccCCCCeEEEcCC-CCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECC
Confidence            888765441               1235679999999 8889999999999999999999985       5699999999


Q ss_pred             HHHHHHHHHHcCCCccC---CeEEEEEEee
Q 014384          195 QEDATRALDATNMSKLT---DRVISVEYAV  221 (425)
Q Consensus       195 ~~~A~~A~~~l~g~~~~---g~~i~v~~a~  221 (425)
                      .++|.+|++.|||..+.   |+.|.|.||.
T Consensus       146 ~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          146 RAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999999999998776   4899999973

>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=99.96  E-value=7.3e-29  Score=237.05  Aligned_cols=193  Identities=20%  Similarity=0.259  Sum_probs=158.3

Q ss_pred             eeeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEE--
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDM--   86 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i--   86 (425)
                      ..||||.|.+...+..+............        +.......++|||+|||+.+|+++|.++|..|| .|..|.|  
T Consensus        81 ~g~afV~f~~~~~A~~A~~~~~~~~~g~~--------i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  152 (292)
T 2ghp_A           81 FRFARIEFARYDGALAAITKTHKVVGQNE--------IIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS  152 (292)
T ss_dssp             SEEEEEEESSHHHHHHHHTTTTCEETTEE--------CEEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-
T ss_pred             cEEEEEEECCHHHHHHHHHhCCcEeCCcE--------EEEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe
Confidence            47999999988776666543332221111        112335689999999999999999999999999 9999998  


Q ss_pred             -----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCC
Q 014384           87 -----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPY  161 (425)
Q Consensus        87 -----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~  161 (425)
                           .+|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+.........         .....+..+|||+|| |.
T Consensus       153 ~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~~~~~---------~~~~~~~~~l~v~nl-p~  220 (292)
T 2ghp_A          153 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSNPLEKSKRT---------DSATLEGREIMIRNL-ST  220 (292)
T ss_dssp             ------CCEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCCC------------------CCTTTEEEEEEE-CT
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCcccccc---------cccCCCCceEEEECC-Cc
Confidence                 379999999999999999999999999  8999999998765422111         123566789999999 78


Q ss_pred             C-CCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          162 H-TRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       162 ~-~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      . +++++|+++|.+||.|..|.++         +|||||+|.+.++|.+|+ .|||..|+|+.|.|.|+..+
T Consensus       221 ~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          221 ELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             ccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            8 9999999999999999999885         469999999999999999 99999999999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=5.3e-29  Score=224.32  Aligned_cols=167  Identities=23%  Similarity=0.327  Sum_probs=142.1

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           53 MMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        53 ~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..++|||+|||+ .+|+++|.++|++||.|..|.|.   +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+...
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~l~v~~a~~~   79 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCC--SSCCCEEEECCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCee--cCeEEEEEEecCC
Confidence            358999999999 99999999999999999999995   79999999999999999999999999  8999999999754


Q ss_pred             cCCCCCCC-------------------CCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEe---c
Q 014384          129 RGIRRPGG-------------------GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIR---R  185 (425)
Q Consensus       129 ~~~~~~~~-------------------~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~---~  185 (425)
                      ........                   ............+..+|||+|| |..+++++|+++|.+|| .|..|.+.   +
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl-~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~  158 (198)
T 1qm9_A           80 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDR  158 (198)
T ss_dssp             SCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCC-CTTCCHHHHHHHHHHTTSCCCEEEESSTTS
T ss_pred             CcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCC-CCCCCHHHHHHHHHHcCCCceEEEEEeCCC
Confidence            31110000                   0000011122456899999999 78899999999999999 99999993   6


Q ss_pred             cEEEEEEcCHHHHHHHHHHcCCCccC-CeEEEEEEeee
Q 014384          186 NFAFVQYEVQEDATRALDATNMSKLT-DRVISVEYAVR  222 (425)
Q Consensus       186 g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a~~  222 (425)
                      |+|||+|.+.++|.+|+..|||..|+ |+.|.|.|+..
T Consensus       159 g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             SCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            89999999999999999999999999 99999999875

>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=99.96  E-value=9.1e-29  Score=235.47  Aligned_cols=191  Identities=17%  Similarity=0.188  Sum_probs=157.4

Q ss_pred             eeEEEEeCCCCccccccc-CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--
Q 014384           11 HYLLIVYSHSVWPVQKKY-LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--   87 (425)
                      .||||.|.+...+..+.. ++...... ....      .......++|||+|||+.+|+++|.++|+.||.|..|.|.  
T Consensus        58 g~afV~f~~~~~A~~A~~~l~~~~~~g-~~i~------v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~  130 (284)
T 3smz_A           58 GTAFVTLLNGEQAEAAINAFHQSRLRE-RELS------VQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYS  130 (284)
T ss_dssp             TEEEEEESSHHHHHHHHHHHTTCEETT-EECE------EEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC
T ss_pred             CEEEEEeCCHHHHHHHHHHcCCCeeCC-eEEE------EEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEee
Confidence            499999998776555542 22222111 1111      1123456899999999999999999999999999999872  


Q ss_pred             ------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCC
Q 014384           88 ------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPY  161 (425)
Q Consensus        88 ------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~  161 (425)
                            +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+......             ....+..+|||+|| |.
T Consensus       131 ~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~--~g~~i~v~~a~~~~~~-------------~~~~~~~~l~v~nl-p~  194 (284)
T 3smz_A          131 ERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTDAGQLT-------------PALLHSRCLCVDRL-PP  194 (284)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCGGGCC-------------TTTTSCSEEEEECC-CT
T ss_pred             CCCCccceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEEECCCCCCC-------------cccCCccEEEEecC-Cc
Confidence                  68999999999999999999999999  8999999999765421             12356789999999 67


Q ss_pred             C-CCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          162 H-TRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       162 ~-~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      . +++++|+++|+.||.|..|.+.       +|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+..+.
T Consensus       195 ~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          195 GFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             TCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             ccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            7 5899999999999999999885       5799999999999999999999999999999999997754

>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=99.96  E-value=3.8e-29  Score=220.57  Aligned_cols=157  Identities=18%  Similarity=0.333  Sum_probs=136.5

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ..+...++|||+|||..+|+++|.++|..||.|..+.|       ++|||||+|.+.++|.+|+ .|||..|  .|+.|.
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~   84 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKV--FGNEIK   84 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEE--TTEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEe--CCeEEE
Confidence            35567899999999999999999999999986544222       3799999999999999999 6999999  799999


Q ss_pred             EEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE---eccEEEEEEcCHHHH
Q 014384          122 VEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDA  198 (425)
Q Consensus       122 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~---~~g~afV~f~~~~~A  198 (425)
                      |.++.....              ....+..+|||+|| |..+++++|+++|++||.|..+..   .+|||||+|.+.++|
T Consensus        85 v~~~~~~~~--------------~~~~~~~~l~v~nl-p~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A  149 (175)
T 1fje_B           85 LEKPKGRDS--------------KKVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA  149 (175)
T ss_dssp             EECCCCSSC--------------STTGGGGEEEEESC-CSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHH
T ss_pred             EecCCCccc--------------cccccCCEEEEeCC-CCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHHH
Confidence            999876431              12345789999999 888999999999999999988811   268999999999999


Q ss_pred             HHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          199 TRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       199 ~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .+|+..|||..|+|+.|.|.|+.++
T Consensus       150 ~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          150 EKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999999999999999999764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=3.4e-29  Score=218.95  Aligned_cols=149  Identities=20%  Similarity=0.469  Sum_probs=133.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      +.++|||+|||+++|+++|.++|+.||+|..|.|.        +|||||+|.+.++|.+|+..  +..|  +|+.|.|.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~--~g~~i~v~~   77 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHIL--DGKVIDPKR   77 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEE--TTEECCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--cccc--CCeEccccc
Confidence            46899999999999999999999999999999983        68999999999999999974  5677  799999998


Q ss_pred             eccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHH
Q 014384          125 TKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQE  196 (425)
Q Consensus       125 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~  196 (425)
                      +.....                ..+..+|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.+
T Consensus        78 ~~~~~~----------------~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~  140 (167)
T 2cjk_A           78 AIPRDE----------------QDKTGKIFVGGI-GPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD  140 (167)
T ss_dssp             CCCHHH----------------HHHCEEEEEEEE-CTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHH
T ss_pred             ccchhh----------------ccCCCeEEECCC-CCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHH
Confidence            765431                223579999999 8899999999999999999999985        469999999999


Q ss_pred             HHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          197 DATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       197 ~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +|.+|++ +++..|+|+.|.|.+|.++
T Consensus       141 ~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          141 AVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999998 8999999999999999764

>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=99.95  E-value=1.8e-27  Score=223.90  Aligned_cols=149  Identities=29%  Similarity=0.408  Sum_probs=135.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....++|||+|||+++|+++|.++|+.||.|..|.|.  +|||||+|.+.++|..|+..|||..|  .|+.|.|.|+..
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i--~g~~l~v~~a~~   95 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL--KSRPLRIRFATH   95 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEE--CCceeEeeeccc
Confidence            34566899999999999999999999999999999995  89999999999999999999999999  899999999753


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHH
Q 014384          128 ERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATR  200 (425)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~  200 (425)
                                            ..+|||+|| |..+++++|+++|..||.|..|.+.       +|||||+|.+.++|.+
T Consensus        96 ----------------------~~~l~v~nl-~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~  152 (261)
T 3sde_A           96 ----------------------GAALTVKNL-SPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARK  152 (261)
T ss_dssp             ----------------------SSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHH
T ss_pred             ----------------------CCcccccCC-CCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHH
Confidence                                  468999999 7889999999999999999999985       6899999999999999


Q ss_pred             HHHHcCC-CccC---CeEEEEEEeeeC
Q 014384          201 ALDATNM-SKLT---DRVISVEYAVRD  223 (425)
Q Consensus       201 A~~~l~g-~~~~---g~~i~v~~a~~~  223 (425)
                      |+..||+ ..+.   |++|.|.++...
T Consensus       153 A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          153 ALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHhcCCeEEecCCCceEEEeecccc
Confidence            9999955 4444   899999998765

>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=99.95  E-value=8.9e-27  Score=221.68  Aligned_cols=149  Identities=20%  Similarity=0.316  Sum_probs=137.4

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ......++|||+|||+++|+++|.++|+.|| |..|.+  .+|||||+|.+.++|.+|+..|||..|  .|+.|.|.++.
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v~~~~   93 (284)
T 3smz_A           17 RQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRL--RERELSVQLQP   93 (284)
T ss_dssp             HHHHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCee--CCeEEEEEecC
Confidence            3445679999999999999999999999999 999988  489999999999999999999999999  89999999853


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHH
Q 014384          127 HERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDA  198 (425)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A  198 (425)
                                            +..+|||+|| |..+++++|+++|..||.|..+.+.        +|||||+|.+.++|
T Consensus        94 ----------------------~~~~l~v~nl-p~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a  150 (284)
T 3smz_A           94 ----------------------TDALLCVANL-PPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA  150 (284)
T ss_dssp             ----------------------CSCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             ----------------------CCCEEEEcCC-CCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHH
Confidence                                  2469999999 8899999999999999999999885        56999999999999


Q ss_pred             HHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          199 TRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       199 ~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..|+..|+|..|+|+.|.|.++...
T Consensus       151 ~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          151 ARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCGG
T ss_pred             HHHHHHhCCCEeCCcEEEEEECCCC
Confidence            9999999999999999999999765

>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=99.94  E-value=1.7e-26  Score=220.53  Aligned_cols=148  Identities=20%  Similarity=0.264  Sum_probs=133.6

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ......++|||+|||+++|+++|.++|+.||+|..|.|.      +|||||+|.+.++|.+|+ .|||..|  .|+.|.|
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~--~g~~i~v  112 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVV--GQNEIIV  112 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEE--TTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHH-HhCCcEe--CCcEEEE
Confidence            345678999999999999999999999999999999983      699999999999999999 6999999  8999999


Q ss_pred             EEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEe-------ccEEEEEEcC
Q 014384          123 EWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIR-------RNFAFVQYEV  194 (425)
Q Consensus       123 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~-------~g~afV~f~~  194 (425)
                      .++.                       ..+|||+|| |..+++++|.++|..|| .|..|.++       +|||||+|.+
T Consensus       113 ~~~~-----------------------~~~l~v~nl-p~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~  168 (292)
T 2ghp_A          113 SHLT-----------------------ECTLWMTNF-PPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS  168 (292)
T ss_dssp             EECC-----------------------SCEEEEECC-CTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSS
T ss_pred             EECC-----------------------CCEEEEECC-CCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECC
Confidence            9863                       478999999 88899999999999999 99999884       6899999999


Q ss_pred             HHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          195 QEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       195 ~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .++|..|+..|||..|.|+.|.|.++...
T Consensus       169 ~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  197 (292)
T 2ghp_A          169 KEDARYCVEKLNGLKIEGYTLVTKVSNPL  197 (292)
T ss_dssp             HHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            99999999999999999999999998764

>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=99.86  E-value=2.4e-21  Score=194.38  Aligned_cols=78  Identities=31%  Similarity=0.500  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| +..+++++|+++|.+||.|+.|.|+        +|||||+|.+.++|.+||..|||..|+|+.|.|
T Consensus        98 ~~~~~~~lfV~nL-~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V  176 (437)
T 3pgw_S           98 QGDAFKTLFVARV-NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  176 (437)
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEE
Confidence            3456789999999 8899999999999999999999985        689999999999999999999999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .|+....
T Consensus       177 ~~a~~~~  183 (437)
T 3pgw_S          177 DVERGRT  183 (437)
T ss_pred             EEeCCCC
Confidence            9998653

>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=99.84  E-value=4.8e-21  Score=156.99  Aligned_cols=103  Identities=17%  Similarity=0.286  Sum_probs=69.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|.      +|||||+|.+.++|++||..|||..|  +|+.|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~--~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECC
Confidence            46789999999999999999999999999999983      78999999999999999999999999  89999999987


Q ss_pred             cccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHH
Q 014384          127 HERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTR  166 (425)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~  166 (425)
                      .......        ..........+|||+|| +..+|++
T Consensus        82 ~~~~~~~--------~~~~~~~~~~~lyv~Nl-~~~~T~~  112 (115)
T 4f25_A           82 SRKEREA--------ELGARAKEFTNVYIKNF-GPGSTRA  112 (115)
T ss_dssp             CCCC------------------------------------
T ss_pred             Ccccccc--------ccccccCCCCceEeCCC-CCCcccc
Confidence            6442111        11122334567999999 5566554

>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=99.84  E-value=7.3e-21  Score=163.49  Aligned_cols=132  Identities=20%  Similarity=0.235  Sum_probs=111.0

Q ss_pred             CCEEEEEEcCHHHHHHHHHhc-CCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHH
Q 014384           88 SGFAFIYMDDERDAEDAIRGL-DRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTR  166 (425)
Q Consensus        88 kg~aFV~F~~~~~A~~A~~~l-ng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~  166 (425)
                      +|+++|+|.+.++|++|+..| ||..|  +| .|.|.++.......................+.++|||+|| |..++++
T Consensus        13 ~G~~~ve~~~~~~A~~a~~~~~ng~~~--~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl-~~~~t~~   88 (150)
T 2i2y_A           13 KGETTTEAVDAATAEKVFKQYANDNGV--DG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNL-GNNGNKT   88 (150)
T ss_dssp             CEEEEEECSSHHHHTTTHHHHHHHHTC--CC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESC-CSCCSCH
T ss_pred             cccceeeecCHHHHHHHHHHHhcCCCC--CC-ceecccccCccccccccccccccccccCCCCCCEEEEeCC-CCCCCHH
Confidence            799999999999999999999 99999  89 9999988654321111111111233445567799999999 7889999


Q ss_pred             HHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          167 DLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       167 ~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +|+++|.+||.|..|.++   +|||||+|.+.++|..|+..|||..|+|+.|.|.++..+
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999996   789999999999999999999999999999999999774

>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=99.80  E-value=2.9e-19  Score=154.74  Aligned_cols=132  Identities=24%  Similarity=0.279  Sum_probs=100.3

Q ss_pred             eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHH
Q 014384           87 KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTR  166 (425)
Q Consensus        87 ~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~  166 (425)
                      .+|||||+|.+.++|++|+..+++...  .+..+.+............   ...........+..+|||+|| |..++++
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~~~--~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~l~v~nl-~~~~~~~   85 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYANDNG--VDGEWTYDDATKTFTVTEG---SHHHHHHMDVEGMTSLKVDNL-TYRTSPD   85 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHHHT--CCCEEEEETTTTEEEEECC---CCCSSCCCCCCBCCEEEEESC-CTTCCHH
T ss_pred             ccchhHHHHHHHHhHHHHHHhhcccCC--CCCcccccCcccccccccc---ccccccccCCCCCCEEEEeCC-CCCCCHH
Confidence            379999999999999999988886433  2333333221111000000   001122233456789999999 8899999


Q ss_pred             HHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          167 DLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       167 ~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      +|+++|++||.|..|.|+        +|||||+|.+.++|..|++.|||..|+|+.|.|.++....
T Consensus        86 ~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           86 TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             HHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             HHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            999999999999999985        5799999999999999999999999999999999998753

>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=99.78  E-value=7.8e-19  Score=139.71  Aligned_cols=75  Identities=20%  Similarity=0.396  Sum_probs=69.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+++|+++|.++|++||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~V   93 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL--QSKTIKV   93 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            3456899999999999999999999999999999883        68999999999999999999999999  8999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .||++
T Consensus        94 ~~AkP   98 (99)
T 4fxv_A           94 SYARP   98 (99)
T ss_dssp             EECCB
T ss_pred             EEeeC
Confidence            99964

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=7e-19  Score=140.48  Aligned_cols=97  Identities=36%  Similarity=0.571  Sum_probs=81.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCC
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGI  131 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~  131 (425)
                      ++|||+|||+.+|+++|.++|++||+|..|.|   ++|||||+|.+.++|++|+..|||..|  +|+.|.|.|+......
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI--CGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCS--SSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeE--CCcEEEEEEccCCCCc
Confidence            58999999999999999999999999999999   479999999999999999999999999  8999999999876532


Q ss_pred             CCCCCCCCCCCCCCCCCCCcEEEEEcCC
Q 014384          132 RRPGGGSSARRPSTNTRPSKTLFVINFD  159 (425)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~l~V~nl~  159 (425)
                      ....      ..........+|||+||+
T Consensus        79 ~~~~------~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           79 SRFD------RPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SCCC------SCCCSCCCCSCCCSCCCC
T ss_pred             ccCC------CCCccccCCCceecCCCC
Confidence            2211      111223446789999993

>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=99.76  E-value=3.4e-17  Score=164.19  Aligned_cols=76  Identities=32%  Similarity=0.611  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .+.++|||+|||+.||+++|.++|++||+|+.|.|.        +|||||+|.+.++|.+||..|||+.|  +|+.|.|+
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~  177 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI--DGRRVLVD  177 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            345799999999999999999999999999999883        79999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus       178 ~a~~~~  183 (437)
T 3pgw_S          178 VERGRT  183 (437)
T ss_pred             EeCCCC
Confidence            998644

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.75  E-value=2.7e-18  Score=135.59  Aligned_cols=80  Identities=13%  Similarity=0.147  Sum_probs=71.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      ...+.++|||+|||..+|+++|.++|++||+|..|.|.  +|||||+|++.++|.+|+..||+..+.+.|++|.|+|++.
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            44678999999999999999999999999999999984  8999999999999999999999986322799999999986


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      +.
T Consensus        97 k~   98 (100)
T 3r27_A           97 QK   98 (100)
T ss_dssp             SC
T ss_pred             cc
Confidence            43

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.75  E-value=2.2e-18  Score=131.44  Aligned_cols=72  Identities=14%  Similarity=0.116  Sum_probs=68.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ...-|||+||++.+|+++|.+||.+||+|..|.|  ++|||||+|.+.++|++|+..||+..|  .|++|.|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l--~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVL--ANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEE--CCcEEEEEECC
Confidence            4678999999999999999999999999999998  599999999999999999999999999  89999999873

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=6.2e-18  Score=131.98  Aligned_cols=77  Identities=32%  Similarity=0.599  Sum_probs=73.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ....++|||+|||.++|+++|.++|++||+|..|.|.+|||||+|.+.++|++|+..|||..|  +|+.|.|+|+....
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~~~   81 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKL--HGVNINVEASKNKS   81 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEETTEEEEEESSHHHHHHHHHHHTTCBC--SSCBCEEECSSCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCEEEEEECCHHHHHHHHHHhcCCcc--CCcEEEEEECCCCC
Confidence            457899999999999999999999999999999999999999999999999999999999999  89999999998765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.6e-18  Score=136.26  Aligned_cols=78  Identities=21%  Similarity=0.307  Sum_probs=71.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCC--CeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDR--TEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng--~~ig~~gr~l~V~~a  125 (425)
                      .+.+.++|||+|||+.+|+++|+++|++||+|.+|.|.  +|||||+|++.++|++|+..|++  ..|  .|++|.|.|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l--~Gr~l~V~~A   89 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIYIQFS   89 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEE--TTEECCBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceE--CCEEEEEEEc
Confidence            45678999999999999999999999999999999996  79999999999999999998864  678  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      +...
T Consensus        90 ~~~~   93 (105)
T 1sjq_A           90 NHKE   93 (105)
T ss_dssp             SSSS
T ss_pred             CCCC
Confidence            8754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=7.9e-18  Score=131.38  Aligned_cols=78  Identities=33%  Similarity=0.536  Sum_probs=73.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .....++|||+|||+.+|+++|.++|++||.|..|.|.++||||+|.+.++|++|+..|||..|  +|+.|.|.|+....
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV--KGKRINVELSTKGQ   82 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEESCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEECCCCC
Confidence            3467899999999999999999999999999999999999999999999999999999999999  89999999998754

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=131.20  Aligned_cols=78  Identities=32%  Similarity=0.557  Sum_probs=73.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .....++|||+|||+.+|+++|+++|++||.|..|.|.++||||+|.+.++|.+|+..|||..|  +|+.|.|.|+....
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF--QGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSSEEEEEESCHHHHHHHHHHHTTEEE--TTEEEEEEESSCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECCEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEEEccCCC
Confidence            4567899999999999999999999999999999999999999999999999999999999999  89999999998754

>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=99.74  E-value=1.5e-17  Score=133.25  Aligned_cols=77  Identities=23%  Similarity=0.494  Sum_probs=73.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccC
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERG  130 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~  130 (425)
                      .+.++|||+|||+.+|+++|+++|.+||.|..|.|.++||||+|.+.++|++||..|||..|  +|+.|.|.|+.....
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDL--EGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEeCCHHHHHHHHHHHCCCcc--CCCEEEEEEcCCCcc
Confidence            45789999999999999999999999999999999999999999999999999999999999  899999999987653

>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=99.74  E-value=1.4e-18  Score=142.12  Aligned_cols=100  Identities=21%  Similarity=0.392  Sum_probs=87.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +...++|||+|||+.+|+++|.++|+.||.|..|.|.     +|||||+|.+.++|.+|+..|||..|  +|+.|.|.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a   82 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNV--SNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBS--SSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEe
Confidence            4567899999999999999999999999999999993     79999999999999999999999999  8999999999


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc
Q 014384          126 KHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK  177 (425)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~  177 (425)
                      ......                        .++ ....++++|+++|++||.
T Consensus        83 ~~~~~~------------------------~~~-~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRAF------------------------QKM-DTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHHT------------------------TTS-CHHHHHHHHHHHHHHHCC
T ss_pred             cCChhh------------------------hhh-hHhHhHHHHHHHHHHhCC
Confidence            865422                        124 456668999999999984

>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=99.74  E-value=9.6e-18  Score=132.88  Aligned_cols=78  Identities=27%  Similarity=0.490  Sum_probs=72.4

Q ss_pred             hhcCCCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           49 AFEAMMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      ......++|||+|||. .+|+++|.++|++||.|..|.|++|||||+|.+.++|.+|+..|||..|  +|+.|.|+|++.
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~   94 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMN--FGKKLILEVSSS   94 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEECSSEEEEEESSHHHHHHHHHHHTTSEE--TTEECEEEECCC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEecCC
Confidence            3556789999999998 9999999999999999999999999999999999999999999999999  899999999875


Q ss_pred             c
Q 014384          128 E  128 (425)
Q Consensus       128 ~  128 (425)
                      .
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=4.8e-18  Score=134.35  Aligned_cols=78  Identities=26%  Similarity=0.457  Sum_probs=72.0

Q ss_pred             hcCCCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           50 FEAMMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ...+.++|||+|||+ .+|+++|.++|++||.|..|.|++|||||+|.+.++|.+|+..|||..|  .|+.|.|+|+...
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 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMN--FGKKLILEVSSSN   83 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEETTEEEEEESCHHHHHHHHHHHTCSSC--BTTTBCEEEEECC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCee--CCcEEEEEEcCcC
Confidence            446789999999998 9999999999999999999999999999999999999999999999999  7999999999865


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        84 ~   84 (96)
T 2kvi_A           84 A   84 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=7.5e-18  Score=136.65  Aligned_cols=76  Identities=18%  Similarity=0.417  Sum_probs=70.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +.+.++|||+||++.+|+++|.++|++||+|..|.|        ++|||||+|.+.++|++|++.|||..|  +|+.|.|
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~--~gr~i~V   80 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSV--MGNIIHA   80 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEE
Confidence            356789999999999999999999999999999988        379999999999999999999999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      +++...
T Consensus        81 ~~a~~~   86 (110)
T 3s8s_A           81 QLDIKG   86 (110)
T ss_dssp             EECSTT
T ss_pred             EECCCC
Confidence            998654

>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=99.73  E-value=3.9e-18  Score=135.85  Aligned_cols=77  Identities=21%  Similarity=0.247  Sum_probs=70.4

Q ss_pred             cCCCceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCC--eecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRT--EFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~--~ig~~gr~l~V~~a  125 (425)
                      ..+.++|||+|||+ .+|+++|.++|.+||+|..|.|.  +|||||+|++.++|.+|+..||+.  .|  .|++|.|+|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~--~Gr~l~V~~a   89 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALV--FGKPVRVHLS   89 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceE--CCcEEEEEEC
Confidence            35688999999999 99999999999999999999995  699999999999999999999875  47  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        90 ~~~~   93 (102)
T 1x4d_A           90 QKYK   93 (102)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            8655

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=4.7e-18  Score=133.88  Aligned_cols=76  Identities=20%  Similarity=0.390  Sum_probs=68.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCe----ecC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGK--VDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTE----FGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~--V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~----ig~  115 (425)
                      ....+.||||+|||+.+|+++|.++|++||.  |.+|.|        ++|||||+|.+.++|.+|++.|||..    |  
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i--   82 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKI--   82 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEE--
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceE--
Confidence            3467899999999999999999999999995  567877        37999999999999999999999974    6  


Q ss_pred             CCcEEEEEEecc
Q 014384          116 KGRRLRVEWTKH  127 (425)
Q Consensus       116 ~gr~l~V~~a~~  127 (425)
                      +|+.|.|+||+.
T Consensus        83 ~Gr~i~V~~Aks   94 (95)
T 2lkz_A           83 DGKTIGVDFAKS   94 (95)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEccC
Confidence            899999999974

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.8e-17  Score=130.63  Aligned_cols=78  Identities=21%  Similarity=0.396  Sum_probs=73.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRY--GKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~--G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....++|||+|||+.+|+++|+++|.+|  |.|..|.+.+|||||+|.+.++|.+|+..|||..|  +|+.|.|.|+..
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~a~~   88 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAKP   88 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEE--TTEEEEEECCCC
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeCCeEEEEeCCHHHHHHHHHHhCCCEe--CCcEEEEEECCC
Confidence            34567899999999999999999999999  99999999999999999999999999999999999  899999999987


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        89 ~~   90 (99)
T 2cpd_A           89 VD   90 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=2.2e-17  Score=127.22  Aligned_cols=74  Identities=26%  Similarity=0.528  Sum_probs=69.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|.++|++||.|..|.|        .+|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v   81 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRV   81 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEE
Confidence            456799999999999999999999999999999998        489999999999999999999999999  8999999


Q ss_pred             EEec
Q 014384          123 EWTK  126 (425)
Q Consensus       123 ~~a~  126 (425)
                      +|++
T Consensus        82 ~~ak   85 (85)
T 3mdf_A           82 NLAK   85 (85)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9974

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.72  E-value=1.7e-17  Score=134.21  Aligned_cols=79  Identities=25%  Similarity=0.477  Sum_probs=73.2

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ......++|||+|||..+|+++|.++|++||.|..|.|.+|||||+|.+.++|++|+..|||..|  +|+.|.|.|+...
T Consensus        26 ~~~~~~~~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           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSF--ANQPLEVVYSKLP  103 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEETTEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEESCSCC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEecCC
Confidence            34567799999999999999999999999999999999999999999999999999999999999  8999999999865


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus       104 ~  104 (108)
T 2jvo_A          104 A  104 (108)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.72  E-value=4.1e-17  Score=130.61  Aligned_cols=78  Identities=21%  Similarity=0.466  Sum_probs=72.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||+.+|+++|.++|++||.|..|.|.      +|||||+|.+.++|.+|+..|||..|  .|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKI--LGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCc--CCCeEEEE
Confidence            44667999999999999999999999999999999994      59999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            998755

>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=99.72  E-value=1.8e-17  Score=144.48  Aligned_cols=131  Identities=19%  Similarity=0.312  Sum_probs=72.5

Q ss_pred             EEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCC-CCC---CCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHH
Q 014384           93 IYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIR-RPG---GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL  168 (425)
Q Consensus        93 V~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~-~~~---~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L  168 (425)
                      .+|++.++|..|+..|++......|+.+.+.++....... ...   .............+.++|||+|| |..+++++|
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nL-p~~~t~~~L   89 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSI-HEEAQEDEI   89 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESC-CTTCCHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCC-CCCCCHHHH
Confidence            7899999999999999998774457777777643322100 000   00001223344566789999999 789999999


Q ss_pred             HhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          169 ERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       169 ~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      +++|.+||.|..|.|+        +|||||+|.+.++|..||..|||..|.|+.|.|.|+..+.
T Consensus        90 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  153 (165)
T 1rk8_A           90 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  153 (165)
T ss_dssp             HHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC
T ss_pred             HHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            9999999999999996        5799999999999999999999999999999999998864

>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=99.72  E-value=3.1e-17  Score=127.24  Aligned_cols=74  Identities=19%  Similarity=0.473  Sum_probs=69.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ..++|||+|||.++|+++|.++|++||.|..|.|         .+|||||+|.+.++|.+|+..|||..|  +|+.|.|+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~   80 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQI--DGQEITAT   80 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeE--CCeEEEEE
Confidence            4689999999999999999999999999999998         589999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      ++...
T Consensus        81 ~a~~~   85 (88)
T 4a8x_A           81 AVLAP   85 (88)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            99754

>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=99.72  E-value=3e-17  Score=132.89  Aligned_cols=78  Identities=40%  Similarity=0.698  Sum_probs=72.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.     +|||||+|.+.++|++||+.||+..|  +|+.|.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~   95 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEF   95 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEE
Confidence            44567899999999999999999999999999999993     78999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      ++...
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            98765

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=132.97  Aligned_cols=76  Identities=21%  Similarity=0.271  Sum_probs=71.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeC-CEEEEEEcCHHHHHHHHHhcCCCeecCCC-----cEEEEEEe
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRKG-----RRLRVEWT  125 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~k-g~aFV~F~~~~~A~~A~~~lng~~ig~~g-----r~l~V~~a  125 (425)
                      ...++|||+|||+++|+++|+++|.+||+|..|.|.. |||||+|.+.++|++||+.|||..|  +|     +.|.|+++
T Consensus        13 ~~~~~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           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKVD   90 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETTTEEEEEESSHHHHHHHHHHSSSEEE--ECTTSCEEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecCCEEEEEECCHHHHHHHHHHHCcCCc--cCCcCcceEEEEEeC
Confidence            4578999999999999999999999999999999976 9999999999999999999999999  78     99999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        91 ~~~~   94 (108)
T 1x4c_A           91 GPRS   94 (108)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            8754

>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=99.72  E-value=3.9e-17  Score=129.70  Aligned_cols=78  Identities=28%  Similarity=0.460  Sum_probs=72.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|.++|.+||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V   82 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHV   82 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEES--SSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEE
Confidence            4567899999999999999999999999999999993        69999999999999999999999999  8999999


Q ss_pred             EEeccccC
Q 014384          123 EWTKHERG  130 (425)
Q Consensus       123 ~~a~~~~~  130 (425)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (99)
T 1whw_A           83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EEcCCCcc
Confidence            99987653

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.72  E-value=7.9e-18  Score=131.72  Aligned_cols=74  Identities=15%  Similarity=0.306  Sum_probs=66.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcC-CCeecCCCcEEEEE
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDM--------KSGFAFIYMDDERDAEDAIRGLD-RTEFGRKGRRLRVE  123 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~ln-g~~ig~~gr~l~V~  123 (425)
                      +++|||+|||+++|+++|.++|++|| +|.+|.|        ++|||||+|.+.++|++||+.|+ +..|  +|+.|.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~--~gr~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNI--LGQKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEE--TTEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEE--CCEEEEEE
Confidence            36899999999999999999999999 8999987        37999999999999999998875 5678  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+.+..
T Consensus        79 ~a~~~~   84 (91)
T 2lxi_A           79 YSDPKP   84 (91)
T ss_dssp             CCCSCC
T ss_pred             EcCCCC
Confidence            998654

>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=99.72  E-value=3.3e-17  Score=130.52  Aligned_cols=78  Identities=15%  Similarity=0.241  Sum_probs=70.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcC--CCeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLD--RTEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~ln--g~~ig~~gr~l~V~~a  125 (425)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|.  +|||||+|.+.++|.+|+..|+  +..|  .|+.|.|.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~--~Gr~l~V~~a   88 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHL--RNQPIYIQYS   88 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceE--CCcEEEEEEc
Confidence            34567899999999999999999999999999999985  7999999999999999999775  5678  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        89 ~~~~   92 (101)
T 2cq1_A           89 NHKE   92 (101)
T ss_dssp             SCSS
T ss_pred             Cccc
Confidence            8655

>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=99.72  E-value=2.5e-17  Score=132.00  Aligned_cols=79  Identities=11%  Similarity=0.169  Sum_probs=70.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|.  +|||||+|.+.++|.+|+..||+..+.+.|+.|.|+|+...
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            4567899999999999999999999999999999985  79999999999999999998977542228999999999875


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        92 ~   92 (104)
T 1wex_A           92 R   92 (104)
T ss_dssp             S
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=99.71  E-value=4.5e-17  Score=130.39  Aligned_cols=78  Identities=24%  Similarity=0.488  Sum_probs=73.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|.      +|||||+|.+.++|++|+..|||..|  +|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~   88 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEE
Confidence            45667999999999999999999999999999999995      78999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        89 ~a~~~~   94 (103)
T 2cq3_A           89 NATARV   94 (103)
T ss_dssp             ECCSSC
T ss_pred             EcccCC
Confidence            998765

>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=99.71  E-value=2.6e-17  Score=127.43  Aligned_cols=75  Identities=20%  Similarity=0.505  Sum_probs=67.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~   81 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL--GGRQIRTN   81 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEE
Confidence            456899999999999999999999999999999983        68999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      |+...
T Consensus        82 ~a~~k   86 (87)
T 3bs9_A           82 WATRK   86 (87)
T ss_dssp             EEC--
T ss_pred             ecCCC
Confidence            99753

>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=99.71  E-value=2.3e-17  Score=134.82  Aligned_cols=78  Identities=21%  Similarity=0.310  Sum_probs=71.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCC--CeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDR--TEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng--~~ig~~gr~l~V~~a  125 (425)
                      ...+.++|||+|||+++|+++|+++|++||+|..|.|.  +|||||+|++.++|.+|+..|++  ..|  .|+.|.|.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l--~Gr~l~V~~a  104 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIYIQFS  104 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCB--TTBCCEEEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceE--CCeEEEEEEc
Confidence            34567899999999999999999999999999999995  79999999999999999998985  567  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      +...
T Consensus       105 ~~k~  108 (119)
T 2ad9_A          105 NHKE  108 (119)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8755

>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=2.8e-17  Score=129.92  Aligned_cols=76  Identities=22%  Similarity=0.354  Sum_probs=71.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLE----RLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~----~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ...++|||+|||+.+|+++|+    ++|++||+|..|.|.     +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~--~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKI--GSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEE
Confidence            456899999999999999999    999999999999996     89999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.71  E-value=3e-17  Score=133.10  Aligned_cols=77  Identities=26%  Similarity=0.576  Sum_probs=72.3

Q ss_pred             cCCCceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           51 EAMMRPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~-~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ....++|||+|||+. +|+++|+++|.+||.|..|.|++|||||+|.+.++|++|+..|||..|  +|+.|.|+|+....
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVL--AGQTLDINMAGEPK  101 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEETTEEEEECSSSHHHHHHHHHHTTCEE--TTEECCEEESCCCC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEeCCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEECCCCC
Confidence            345689999999999 999999999999999999999999999999999999999999999999  89999999997544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.71  E-value=8.2e-17  Score=131.55  Aligned_cols=80  Identities=20%  Similarity=0.462  Sum_probs=73.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|+++|.+||.|..|.|.        +|||||+|.+.++|++||..|||..|  +|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~   88 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL--GGRQIR   88 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEE
Confidence            44677999999999999999999999999999999983        58999999999999999999999999  899999


Q ss_pred             EEEeccccCC
Q 014384          122 VEWTKHERGI  131 (425)
Q Consensus       122 V~~a~~~~~~  131 (425)
                      |.|+......
T Consensus        89 V~~a~~~~~~   98 (115)
T 2dgo_A           89 TNWATRKPPA   98 (115)
T ss_dssp             EEESSCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999876533

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=2.2e-17  Score=133.73  Aligned_cols=77  Identities=21%  Similarity=0.242  Sum_probs=70.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      .+....+|||+|||+++|+++|+++|.+|| +|..|.|.    +|||||+|.+.++|++||..|||..|  +|+.|.|++
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l--~Gr~i~V~~  101 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEF--RGSVITVER  101 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEE--TTEEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEE
Confidence            456678999999999999999999999999 89999983    89999999999999999999999999  899999999


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8754

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.3e-17  Score=131.20  Aligned_cols=78  Identities=14%  Similarity=0.345  Sum_probs=72.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|.      +|||||+|.+.++|.+|+..|||..|  +|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIV--ATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBS--SSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEEE
Confidence            44578999999999999999999999999999999985      78999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        89 ~a~~~~   94 (103)
T 2d9p_A           89 LAQRKE   94 (103)
T ss_dssp             ECSSCC
T ss_pred             Eecccc
Confidence            998765

>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=7e-17  Score=127.20  Aligned_cols=76  Identities=24%  Similarity=0.502  Sum_probs=71.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.|.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~   80 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL--AGRPMRVG   80 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCS--SSSCCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEE
Confidence            467899999999999999999999999999999983        68999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        81 ~a~~~~   86 (95)
T 2dnz_A           81 HVTERL   86 (95)
T ss_dssp             ESSCCC
T ss_pred             Eccccc
Confidence            998754

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.6e-17  Score=126.08  Aligned_cols=75  Identities=23%  Similarity=0.471  Sum_probs=69.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhc-CCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGL-DRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~l-ng~~ig~~gr~l~V~~a~  126 (425)
                      .....++|||+|||..+|+++|.++|.+||.|..|.|.  +|||||+|.+.++|.+|+..| ||..|  +|+.|.|+|++
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~--~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIV--NGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEE--TTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeE--CCCEEEEEecC
Confidence            34567899999999999999999999999999999995  699999999999999999988 99999  89999999974

>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=99.70  E-value=5.6e-17  Score=130.26  Aligned_cols=78  Identities=23%  Similarity=0.359  Sum_probs=72.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|++||.|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~   88 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL--YGKPIR   88 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC--SSCBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeE--CCeEEE
Confidence            44667999999999999999999999999999999983        68999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        89 v~~a~~~~   96 (105)
T 1x5u_A           89 VNKASAHN   96 (105)
T ss_dssp             EEETTTTS
T ss_pred             EEECCCCC
Confidence            99998765

>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=99.70  E-value=4.8e-17  Score=124.71  Aligned_cols=73  Identities=19%  Similarity=0.505  Sum_probs=68.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +.+|||+|||+.+|+++|.++|.+||.|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.|.|+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~a   78 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWA   78 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEEC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCee--CCcEEEEEec
Confidence            3689999999999999999999999999999883        78999999999999999999999999  8999999999


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        79 ~~~   81 (83)
T 3md1_A           79 AKL   81 (83)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            764

>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=3.8e-17  Score=130.85  Aligned_cols=78  Identities=33%  Similarity=0.549  Sum_probs=72.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   88 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY--DHLILN   88 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCee--CCcEEE
Confidence            34667999999999999999999999999999999983        57999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        89 v~~a~~~~   96 (103)
T 2cq0_A           89 VEWAKPST   96 (103)
T ss_dssp             EEESSCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=4.4e-17  Score=128.06  Aligned_cols=75  Identities=25%  Similarity=0.535  Sum_probs=69.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.+.++|++|+..|||..|  .|+.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   89 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQL--FGRVIK   89 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEE--TTEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCee--CCcEEE
Confidence            34567899999999999999999999999999999993        68999999999999999999999999  899999


Q ss_pred             EEEec
Q 014384          122 VEWTK  126 (425)
Q Consensus       122 V~~a~  126 (425)
                      |+||+
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99984

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=4.1e-17  Score=129.17  Aligned_cols=77  Identities=23%  Similarity=0.415  Sum_probs=71.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCC--CcEEEEEEec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRK--GRRLRVEWTK  126 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~--gr~l~V~~a~  126 (425)
                      ..+.++|||+|||+.+|+++|.++|++||+|..|.|.  +|||||+|.+.++|++|+..|||..|  .  |+.|.|+|+.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~~~g~~l~V~~a~   91 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPL--GGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBC--SSSSCBCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEe--CCCCcEEEEEECC
Confidence            4567899999999999999999999999999999996  67999999999999999999999999  7  9999999998


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        92 ~~~   94 (97)
T 1why_A           92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.4e-17  Score=130.19  Aligned_cols=78  Identities=26%  Similarity=0.598  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   85 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV--DGRQIR   85 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT--TSCCCE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCeEEE
Confidence            34567999999999999999999999999999999993        68999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        86 v~~a~~~~   93 (102)
T 1x5s_A           86 VDQAGKSS   93 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEECCCCC
Confidence            99998765

>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=99.70  E-value=5.4e-17  Score=128.20  Aligned_cols=75  Identities=24%  Similarity=0.450  Sum_probs=70.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      +.++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.|.|
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~~   78 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL--GSRFLKCGY   78 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEE
Confidence            36799999999999999999999999999999983        79999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus        79 a~~~~   83 (96)
T 2x1f_A           79 SSNSD   83 (96)
T ss_dssp             CSCSS
T ss_pred             cCCCC
Confidence            98754

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.7e-17  Score=130.87  Aligned_cols=78  Identities=36%  Similarity=0.597  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   86 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL--DGRELR   86 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCB--TTBCCE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEE--CCcEEE
Confidence            34667999999999999999999999999999999983        68999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        87 V~~a~~~~   94 (103)
T 2dnm_A           87 VQVARYGR   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEECCcCC
Confidence            99998654

>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=4.3e-17  Score=128.67  Aligned_cols=76  Identities=20%  Similarity=0.350  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV-DMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v-~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ...++|||+|||+.+|+++|.++|++||.|..| .|.        +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v   80 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL--CNRPITV   80 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE--TTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEE
Confidence            467899999999999999999999999999988 772        68999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus        81 ~~a~~~~   87 (96)
T 1x5t_A           81 SYAFKKD   87 (96)
T ss_dssp             EESCCCC
T ss_pred             EEecccC
Confidence            9998755

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.70  E-value=9.7e-18  Score=141.19  Aligned_cols=118  Identities=29%  Similarity=0.333  Sum_probs=73.1

Q ss_pred             eeeeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-
Q 014384            9 QCHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-   87 (425)
Q Consensus         9 ~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-   87 (425)
                      -|+|.|+.|....++..+...-..-....- ...............++|||+|||+.+|+++|.++|++||.|..|.|. 
T Consensus         3 ~~~~~~~~~~~~~~~~~a~~~~~g~~~~g~-~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~   81 (135)
T 2lea_A            3 SSHHHHHHSSGLVPRGSHMASMTGGQQMGR-GSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR   81 (135)
T ss_dssp             ---------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCC
T ss_pred             ccccccccccCCCchhhhhhhccCCCCCCC-CCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence            388889988887776555432211110000 000011112344557899999999999999999999999999999983 


Q ss_pred             -------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           88 -------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        88 -------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                             +|||||+|.+.++|++||..|||..|  .|+.|.|.|++...
T Consensus        82 ~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i--~g~~l~V~~a~~~~  128 (135)
T 2lea_A           82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRVQMARYGR  128 (135)
T ss_dssp             CSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCS--SSSCCEEEECCCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCC
Confidence                   68999999999999999999999999  89999999998754

>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=99.70  E-value=7.9e-17  Score=131.95  Aligned_cols=78  Identities=23%  Similarity=0.458  Sum_probs=72.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +....++|||+|||..+|+++|.++|++||.|..|.|.       +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~--~g~~l~V   80 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSL--HGKAIKV   80 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBC--SSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            34667899999999999999999999999999999994       49999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      +|++...
T Consensus        81 ~~a~~~~   87 (116)
T 2fy1_A           81 EQAKKPS   87 (116)
T ss_dssp             EECCCSS
T ss_pred             EECCCCC
Confidence            9998765

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.3e-17  Score=128.37  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=70.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .+.+.++|||+|||+.+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   88 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR   88 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE--CCEEEE
Confidence            44567899999999999999999999999999999983        68999999999999999999999999  899999


Q ss_pred             EEEecc
Q 014384          122 VEWTKH  127 (425)
Q Consensus       122 V~~a~~  127 (425)
                      |+|++.
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999864

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.5e-17  Score=130.10  Aligned_cols=78  Identities=26%  Similarity=0.515  Sum_probs=72.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|        .+|||||+|.+.++|++|+..|||..|  +|+.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~   85 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIR   85 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE--TTEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCcEEE
Confidence            3456799999999999999999999999999999998        379999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        86 V~~a~~~~   93 (102)
T 2cqb_A           86 VNLAKPMR   93 (102)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99998765

>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=99.70  E-value=2e-16  Score=127.79  Aligned_cols=77  Identities=21%  Similarity=0.289  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec-cEEEEEEcCHHHHHHHHHHcCCCccCC-----eEEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR-NFAFVQYEVQEDATRALDATNMSKLTD-----RVISVEY  219 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~-g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~i~v~~  219 (425)
                      .....++|||+|| |..+++++|+++|.+||.|..|.|.. |||||+|.+.++|++||+.||+..|.|     +.|.|.+
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~   89 (108)
T 1x4c_A           11 SRRSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   89 (108)
T ss_dssp             CCSCCCEEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEETTTEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEecCCEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEe
Confidence            3456789999999 89999999999999999999999987 999999999999999999999999999     9999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      +...
T Consensus        90 a~~~   93 (108)
T 1x4c_A           90 DGPR   93 (108)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9873

>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=99.70  E-value=6.7e-17  Score=129.82  Aligned_cols=77  Identities=23%  Similarity=0.454  Sum_probs=71.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCC---cEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKG---RRL  120 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~g---r~l  120 (425)
                      ....++|||+|||+.+|+++|.++|++||.|..|.|.       +|||||+|.+.++|++||..|||..|  .|   +.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~gg~~~~l   89 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQT--MPGASSSL   89 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCC--CTTCSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCcc--CCCCCccE
Confidence            3567999999999999999999999999999999994       68999999999999999999999998  66   999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      .|.|+....
T Consensus        90 ~V~~a~~~~   98 (105)
T 2dnh_A           90 VVKFADTDK   98 (105)
T ss_dssp             EEEESCSSC
T ss_pred             EEEECccCc
Confidence            999998765

>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=99.70  E-value=4.5e-17  Score=127.85  Aligned_cols=77  Identities=26%  Similarity=0.426  Sum_probs=70.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEE-eCCEEEEEEcCHHHHHHHHHhcCC-CeecCCCcEEEEEEecc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGK-VDRVDM-KSGFAFIYMDDERDAEDAIRGLDR-TEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~-V~~v~i-~kg~aFV~F~~~~~A~~A~~~lng-~~ig~~gr~l~V~~a~~  127 (425)
                      ....++|||+|||+++|+++|+++|++||. |..+.+ ++|||||+|.+.++|++|+..||| ..|  +|+.|.|+|+..
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--~g~~l~v~~a~~   82 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL--HGKIMEVDYSVS   82 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEE--TTEECEEEECCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEcCCCEEEEEECCHHHHHHHHHHccCCeeE--CCEEEEEEEccC
Confidence            456789999999999999999999999999 666555 699999999999999999999999 899  899999999987


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        83 ~~   84 (93)
T 2cqh_A           83 KK   84 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.1e-16  Score=129.52  Aligned_cols=79  Identities=16%  Similarity=0.424  Sum_probs=73.7

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ......++|||+|||..+|+++|.++|.+||.|..|.|.  +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+.
T Consensus        20 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~   97 (109)
T 1x4g_A           20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTI--EGHVVKCYWGK   97 (109)
T ss_dssp             HSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEECCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEEEecC
Confidence            355677899999999999999999999999999999996  79999999999999999999999999  89999999998


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        98 ~~~  100 (109)
T 1x4g_A           98 ESP  100 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.70  E-value=1.6e-17  Score=134.21  Aligned_cols=77  Identities=23%  Similarity=0.336  Sum_probs=69.9

Q ss_pred             cCCCceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCC--eecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRT--EFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~-~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~--~ig~~gr~l~V~~a  125 (425)
                      ..+.++|||+|||++ +|+++|.++|.+||+|..|.|.  +|||||+|++.++|.+|+..||+.  .|  .|+.|.|+|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l--~Gr~l~V~~a   99 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF--QGRCVKVDLS   99 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS--SSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceE--CCEEEEEEEC
Confidence            456899999999998 9999999999999999999995  799999999999999999988754  46  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus       100 ~~~~  103 (112)
T 1x4f_A          100 EKYK  103 (112)
T ss_dssp             CSCS
T ss_pred             cccc
Confidence            7654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=9.3e-17  Score=127.29  Aligned_cols=76  Identities=18%  Similarity=0.439  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      .+.++|||+|||+.+|+++|.++|++||+|..|.|.           +|||||+|.+.++|++|+..|||..|  +|+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l   80 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV--DGHKL   80 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE--TTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCee--CCeEE
Confidence            467899999999999999999999999999999884           37999999999999999999999999  89999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      .|.|+....
T Consensus        81 ~V~~a~~~~   89 (98)
T 2cpf_A           81 EVRISERAT   89 (98)
T ss_dssp             EEECSSCSS
T ss_pred             EEEEccCCC
Confidence            999998755

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=7.5e-17  Score=128.34  Aligned_cols=78  Identities=17%  Similarity=0.360  Sum_probs=71.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.       +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v   90 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTI--KENIIKV   90 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEES--SSCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            34567899999999999999999999999999999984       59999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9998654

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=4.6e-17  Score=129.35  Aligned_cols=77  Identities=31%  Similarity=0.553  Sum_probs=72.1

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..+.++|||+|||+.+|+++|+++|.+||+|..|.|.  +|||||+|.+.++|++|+..|||..|  +|+.|.|.|+...
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 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFACHS   89 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCB--TTBCCEEEESSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEe--CCceEEEEEcCCC
Confidence            4567899999999999999999999999999999995  69999999999999999999999999  8999999999875


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        90 ~   90 (99)
T 2cpj_A           90 A   90 (99)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.69  E-value=5.2e-17  Score=127.91  Aligned_cols=76  Identities=26%  Similarity=0.393  Sum_probs=70.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+.+|+++|.++|++||+|..|.|.       +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V   89 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRL--YGRPINV   89 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEE--CCCEEEE
Confidence            34567899999999999999999999999999999984       68999999999999999999999999  8999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .|++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99863

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=9.8e-17  Score=127.41  Aligned_cols=77  Identities=23%  Similarity=0.523  Sum_probs=71.1

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|+++|.+||.|..|.|        .+|||||+|.+.++|++||. ||+..|  +|+.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~--~g~~l~   82 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDI--MGKKVE   82 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBS--SSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEE--CCeEEE
Confidence            3456799999999999999999999999999999999        37999999999999999997 999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.++....
T Consensus        83 V~~a~~~~   90 (99)
T 2dgs_A           83 VKRAEPRD   90 (99)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCc
Confidence            99998755

>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=99.69  E-value=4.9e-17  Score=132.12  Aligned_cols=76  Identities=21%  Similarity=0.319  Sum_probs=70.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ...++|||+|||+.+|+++|.++|++||.|..|.|  .+|||||+|.+.++|++|+..|||..|  +|+.|.|+|+....
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~~~   85 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF--HHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBS--SSSBCEEEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEE--CCeEEEEEECCCCc
Confidence            34689999999999999999999999999999999  489999999999999999999999999  89999999997643

>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=99.69  E-value=6.3e-17  Score=132.33  Aligned_cols=74  Identities=22%  Similarity=0.300  Sum_probs=65.1

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec-cEEEEEEcCHHHHHHHHHHcCCCccCCeE-----EEEEEee
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR-NFAFVQYEVQEDATRALDATNMSKLTDRV-----ISVEYAV  221 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~-g~afV~f~~~~~A~~A~~~l~g~~~~g~~-----i~v~~a~  221 (425)
                      ...++|||+|| |..+++++|+++|.+||.|..|.|.. |||||+|.+.++|.+||+.||+..|+|+.     |.|..+.
T Consensus        14 r~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~   92 (115)
T 3beg_B           14 RSENRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   92 (115)
T ss_dssp             ---CCEEEEEC-CSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEecCCEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCC
Confidence            45689999999 89999999999999999999999987 99999999999999999999999999998     5555544


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus        93 ~   93 (115)
T 3beg_B           93 P   93 (115)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.69  E-value=7.6e-17  Score=131.79  Aligned_cols=78  Identities=19%  Similarity=0.319  Sum_probs=71.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|+++|.+||.|..|.|.        +|||||+|.+.++|++||..|||..|  +|+.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~   98 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI--GMKRLK   98 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEE--CCEEEE
Confidence            33566899999999999999999999999999999883        58999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+|+....
T Consensus        99 V~~a~~~~  106 (115)
T 2cpz_A           99 VQLKRSKN  106 (115)
T ss_dssp             EECCCCSC
T ss_pred             EEEcCCCC
Confidence            99998754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.69  E-value=9.4e-17  Score=129.39  Aligned_cols=75  Identities=16%  Similarity=0.380  Sum_probs=70.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.       +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V  102 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPL--DGRPMNI  102 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEE
Confidence            44667999999999999999999999999999999984       78999999999999999999999999  8999999


Q ss_pred             EEec
Q 014384          123 EWTK  126 (425)
Q Consensus       123 ~~a~  126 (425)
                      +|+.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=4.1e-17  Score=130.14  Aligned_cols=76  Identities=29%  Similarity=0.463  Sum_probs=70.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....++|||+|||..+|+++|.++|++||.|..|.|  .+|||||+|.+.++|.+|+..|||..|  +|+.|.|.|++.
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~a~~  100 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPF--QGRNLRTGWGKE  100 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEE--TTEECCCCBCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEeccC
Confidence            3455789999999999999999999999999999999  489999999999999999999999999  899999999864

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6e-17  Score=131.16  Aligned_cols=77  Identities=25%  Similarity=0.500  Sum_probs=71.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||..+|+++|+++|++||+|..|.|.      +|||||+|.+.++|++|+..|||..|  +|+.|.|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            44567999999999999999999999999999999994      79999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      ++...
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.7e-17  Score=129.68  Aligned_cols=77  Identities=18%  Similarity=0.482  Sum_probs=71.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||..+|+++|.++|++||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V   97 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL--MGQPISV   97 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBS--SSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEE--CCcEEEE
Confidence            3556899999999999999999999999999999983        68999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=128.33  Aligned_cols=78  Identities=19%  Similarity=0.308  Sum_probs=71.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+.+|+++|+++|.+||.|..|.|.       +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v   88 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLL--FDRPMHV   88 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe--CCCEEEE
Confidence            34567899999999999999999999999999999983       68999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus        89 ~~a~~~~   95 (114)
T 2do0_A           89 KMDERAL   95 (114)
T ss_dssp             EECSCCC
T ss_pred             EEcccCC
Confidence            9987644

>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=99.68  E-value=1.5e-16  Score=129.02  Aligned_cols=78  Identities=18%  Similarity=0.385  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcC------CCeecC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLD------RTEFGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~ln------g~~ig~  115 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|.        +|||||+|.+.++|.+||..||      |..|  
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~--   88 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--   88 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE--
Confidence            44668999999999999999999999999999999983        7899999999999999999999      9999  


Q ss_pred             CCcEEEEEEecccc
Q 014384          116 KGRRLRVEWTKHER  129 (425)
Q Consensus       116 ~gr~l~V~~a~~~~  129 (425)
                      +|+.|.|.|+....
T Consensus        89 ~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           89 DGRQLKVDLAVTRD  102 (111)
T ss_dssp             SSCEEEEECCCCCC
T ss_pred             cCEEEEEEECCCCc
Confidence            89999999998754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.68  E-value=8.9e-17  Score=125.80  Aligned_cols=77  Identities=23%  Similarity=0.352  Sum_probs=71.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ....++|||+|||..+|+++|+++|.+||+|..|.|.      +|||||+|.+.++|++|+..|||..|  +|+.|.|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKL--SGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCB--TTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEE
Confidence            3567899999999999999999999999999999984      69999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98754

>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=129.37  Aligned_cols=78  Identities=18%  Similarity=0.431  Sum_probs=71.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~   99 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQ   99 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEE--TTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE--CCcEEE
Confidence            34567899999999999999999999999999999983        69999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus       100 V~~a~~~~  107 (110)
T 1oo0_B          100 VDWCFVKG  107 (110)
T ss_dssp             EEESEESS
T ss_pred             EEEcccCC
Confidence            99998654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.8e-16  Score=128.60  Aligned_cols=77  Identities=22%  Similarity=0.465  Sum_probs=70.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+||+|..|.|.        +|||||+|.+.++|++||..||+ .|  +|+.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~--~g~~l~   89 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKAN   89 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cC--CCEEEE
Confidence            45678999999999999999999999999999999993        68999999999999999999998 78  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+|+....
T Consensus        90 V~~a~~~~   97 (116)
T 2cqd_A           90 VNLAYLGA   97 (116)
T ss_dssp             EEESTTTC
T ss_pred             EEEcccCC
Confidence            99997654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.68  E-value=3.7e-17  Score=130.23  Aligned_cols=75  Identities=21%  Similarity=0.274  Sum_probs=69.7

Q ss_pred             CCCceEEEcCCCC------CCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCC
Q 014384           52 AMMRPIFCGNFEY------DARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKG  117 (425)
Q Consensus        52 ~~~~~l~V~nL~~------~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~g  117 (425)
                      ...++|||+|||.      .+++++|.++|++||.|..|.|        ++|||||+|.+.++|.+|+..|||..|  .|
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~--~g   81 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL--DL   81 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBS--SS
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCccc--CC
Confidence            3468999999999      9999999999999999999998        379999999999999999999999999  78


Q ss_pred             -cEEEEEEeccc
Q 014384          118 -RRLRVEWTKHE  128 (425)
Q Consensus       118 -r~l~V~~a~~~  128 (425)
                       +.|.|.++.+.
T Consensus        82 ~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 KHRLFLYTMKDV   93 (100)
T ss_dssp             SCBCEEEESHHH
T ss_pred             CeEEEEEECchh
Confidence             99999998754

>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=1.4e-16  Score=125.98  Aligned_cols=78  Identities=19%  Similarity=0.452  Sum_probs=71.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLE----RLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~----~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ...+.++|||+|||..+|+++|.    ++|++||.|..|.|.     +|||||+|.+.++|.+|+..|||..|  .|+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l   81 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPM   81 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEE--TTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEE--CCcEE
Confidence            45678999999999999999999    999999999999984     79999999999999999999999999  89999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      .|.|+....
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=127.88  Aligned_cols=78  Identities=29%  Similarity=0.578  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhc-CCCeecCCCcE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGL-DRTEFGRKGRR  119 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~l-ng~~ig~~gr~  119 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.         +|||||+|.+.++|.+||..| ||..|  .|+.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--~g~~   88 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL--YGRR   88 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS--SSCB
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE--CCCE
Confidence            45667999999999999999999999999999999982         689999999999999999999 99999  8999


Q ss_pred             EEEEEecccc
Q 014384          120 LRVEWTKHER  129 (425)
Q Consensus       120 l~V~~a~~~~  129 (425)
                      |.|.|+....
T Consensus        89 l~v~~a~~~~   98 (107)
T 2cph_A           89 LVLEWADSEV   98 (107)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEeCCCCC
Confidence            9999998765

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=9.7e-17  Score=133.24  Aligned_cols=77  Identities=16%  Similarity=0.303  Sum_probs=70.1

Q ss_pred             cCCCceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLE----RLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~----~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ..+.++|||+||++.+++++|+    ++|++||.|..|.+.     +|||||+|.+.++|..|+..|||..|  .|+.|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l--~gr~l~  103 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPF--QGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCC--TTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEe--CCCEEE
Confidence            3557899999999999999876    799999999999883     79999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99998654

>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=7.2e-17  Score=129.16  Aligned_cols=74  Identities=19%  Similarity=0.349  Sum_probs=68.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...++|||+|||+++|+++|.++|++||+|..|.|.       +|||||+|.+.++|.+||. +||..|  +|+.|.|.|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~--~gr~l~V~~   85 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKY--KETDLLILF   85 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCC--TTTTCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEE--CCEEEEEEE
Confidence            456899999999999999999999999999999994       7999999999999999996 999999  899999999


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      +...
T Consensus        86 ~~~~   89 (103)
T 1s79_A           86 KDDY   89 (103)
T ss_dssp             HHHH
T ss_pred             chHH
Confidence            8653

>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=99.67  E-value=8.2e-17  Score=130.10  Aligned_cols=78  Identities=21%  Similarity=0.475  Sum_probs=71.8

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ......++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i--~g~~l   98 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL--AGRPM   98 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCS--SSSCC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEE--CCEEE
Confidence            345667999999999999999999999999999999983        68999999999999999999999999  89999


Q ss_pred             EEEEeccc
Q 014384          121 RVEWTKHE  128 (425)
Q Consensus       121 ~V~~a~~~  128 (425)
                      .|.++...
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99998764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.67  E-value=1.1e-16  Score=127.25  Aligned_cols=75  Identities=21%  Similarity=0.380  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEe--------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--------VDMK--------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--------v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      .+...++|||+|||.++|+++|.++|++||.|..        |.|.        +|||||+|.+.++|.+|+..|||..|
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            4567899999999999999999999999999998        8772        68999999999999999999999999


Q ss_pred             cCCCcEEEEEEec
Q 014384          114 GRKGRRLRVEWTK  126 (425)
Q Consensus       114 g~~gr~l~V~~a~  126 (425)
                        .|+.|.|++|+
T Consensus        89 --~g~~l~V~~A~   99 (99)
T 2la6_A           89 --SGNPIKVSFAT   99 (99)
T ss_dssp             --SSSBCEEEECC
T ss_pred             --CCcEEEEEecC
Confidence              89999999974

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=7.7e-17  Score=127.59  Aligned_cols=77  Identities=29%  Similarity=0.442  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .....++|||+|||+.+|+++|+++|.+||.|. +.+    .+|||||+|.+.++|++|+..|||..|  +|+.|.|.++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~V~~a   91 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRL--GTDTLRVALA   91 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCS--SSSCCEEEEC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEc
Confidence            345678999999999999999999999999996 444    389999999999999999999999999  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.67  E-value=9.7e-17  Score=133.33  Aligned_cols=78  Identities=18%  Similarity=0.462  Sum_probs=72.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|..|.|.        +|||||+|.+.++|++||..|||..|  +|+.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~   95 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL--MGQPIS   95 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBS--SSSBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCee--CCeEEE
Confidence            34557899999999999999999999999999999983        79999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+|+....
T Consensus        96 v~~a~~~~  103 (126)
T 3ex7_B           96 VDWCFVRG  103 (126)
T ss_dssp             EEESEESS
T ss_pred             EEEecCCC
Confidence            99998755

>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=9.6e-17  Score=127.45  Aligned_cols=77  Identities=17%  Similarity=0.388  Sum_probs=70.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCee-EEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE--
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVD-RVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR--  119 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~-~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~--  119 (425)
                      ....++|||+|||+.+|+++|.++|++||.|. .|.|.        +|||||+|.+.++|++|++.|||..|  .|+.  
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~~~   83 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPL--PGATPA   83 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEE--SSCSSC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCcc--CCCCcc
Confidence            45689999999999999999999999999999 99883        58999999999999999999999999  7998  


Q ss_pred             --EEEEEecccc
Q 014384          120 --LRVEWTKHER  129 (425)
Q Consensus       120 --l~V~~a~~~~  129 (425)
                        |.|.|+....
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              9999987643

>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=99.67  E-value=2.8e-17  Score=128.27  Aligned_cols=73  Identities=18%  Similarity=0.343  Sum_probs=63.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYG--KVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G--~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      .+|||+|||+.+|+++|.++|++||  .|..|.|        ++|||||+|.+.++|++|++.|||..|  +|+.|.|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~--~gr~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL--HGQNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCS--SSCCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCee--CCEEEEEEE
Confidence            4799999999999999999999999  9999887        368999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus        80 ~~~~~   84 (90)
T 3p5t_L           80 SNKLE   84 (90)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            87654

>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=99.67  E-value=2.3e-16  Score=136.17  Aligned_cols=78  Identities=23%  Similarity=0.510  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|++||+|..|.|        ++|||||+|.+.++|++||..||+..|  +|+.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~  112 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL--DDRIIR  112 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEE--TTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEE
Confidence            4456799999999999999999999999999999999        368999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+|+....
T Consensus       113 V~~a~~~~  120 (156)
T 1h2v_Z          113 TDWDAGFK  120 (156)
T ss_dssp             EEEESCCC
T ss_pred             EEECCCCC
Confidence            99998755

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.7e-16  Score=129.27  Aligned_cols=78  Identities=21%  Similarity=0.383  Sum_probs=71.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVD--------RVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~--------~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      .....++|||+|||+.+|+++|.++|.+||.|.        .|.|.        +|||||+|.+.++|++||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            346779999999999999999999999999998        57772        78999999999999999999999999


Q ss_pred             cCCCcEEEEEEecccc
Q 014384          114 GRKGRRLRVEWTKHER  129 (425)
Q Consensus       114 g~~gr~l~V~~a~~~~  129 (425)
                        .|+.|.|.|+....
T Consensus        91 --~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 --QGSKLKVSLARKKP  104 (113)
T ss_dssp             --TTEECEEECSSCCC
T ss_pred             --CCCEEEEEECCCCC
Confidence              89999999998765

>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=99.67  E-value=1.2e-16  Score=138.09  Aligned_cols=77  Identities=36%  Similarity=0.653  Sum_probs=71.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|.++|+.||.|..|.|.        +|||||+|.+.++|.+||..|||..|  .|+.|.|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v  144 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL--DGRELRV  144 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEES--SSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEE
Confidence            3457899999999999999999999999999999983        68999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       145 ~~a~~~~  151 (158)
T 2kn4_A          145 QMARYGR  151 (158)
T ss_dssp             EEECCSS
T ss_pred             EECCCCC
Confidence            9998754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.1e-16  Score=131.42  Aligned_cols=75  Identities=21%  Similarity=0.327  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+++|+++|+++|++||+|..|.|.        +|||||+|.+.++|++|+..|||..|  +|+.|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~  113 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQV--GTKRLK  113 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEE--TTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEE--CCEEEE
Confidence            44567999999999999999999999999999999983        78999999999999999999999999  899999


Q ss_pred             EEEec
Q 014384          122 VEWTK  126 (425)
Q Consensus       122 V~~a~  126 (425)
                      |+|++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99974

>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=99.67  E-value=8e-17  Score=134.43  Aligned_cols=78  Identities=27%  Similarity=0.490  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .+.+.++|||+|||+.+|+++|+++|++||+|..|.|.        +|||||+|.+.++|++||..|||..|  +|+.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i--~g~~l~  119 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIR  119 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCS--SSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEE
Confidence            45677999999999999999999999999999999983        68999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+|+....
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99997654

>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=99.66  E-value=2.1e-16  Score=122.81  Aligned_cols=72  Identities=33%  Similarity=0.661  Sum_probs=67.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+.+|+++|.++|++||.|..|.|.        +|||||+|.+.++|++|+ .|||..|  +|+.|.|.++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~--~g~~l~V~~a   82 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLF--RGRQIKVIPK   82 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEE--TTEECEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEE--CCcEEEEEEc
Confidence            5799999999999999999999999999999883        789999999999999999 9999999  8999999998


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        83 ~~~   85 (89)
T 3ucg_A           83 RTN   85 (89)
T ss_dssp             TTT
T ss_pred             cCC
Confidence            764

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.5e-16  Score=127.56  Aligned_cols=79  Identities=15%  Similarity=0.287  Sum_probs=72.3

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCe-ecCCCcEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRR-YGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTE-FGRKGRRL  120 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~-~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~-ig~~gr~l  120 (425)
                      .....++|||+|||+.+|+++|.++|.+ ||.|..|.|       ++|||||+|.+.++|.+|+..|||.. |  +|+.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--~g~~l   82 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGL--GSKPV   82 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSS--SSSCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCccc--CCEeE
Confidence            3456789999999999999999999999 999999998       37899999999999999999999999 8  89999


Q ss_pred             EEEEeccccC
Q 014384          121 RVEWTKHERG  130 (425)
Q Consensus       121 ~V~~a~~~~~  130 (425)
                      .|.++.....
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9999976553

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.66  E-value=6.8e-16  Score=123.49  Aligned_cols=79  Identities=25%  Similarity=0.470  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.++++||||+|.+.++|.+|++.||+..|.|+.|.|.++.....
T Consensus         7 ~~~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~i~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A            7 GMAKVKVLFVRNL-ANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CCCCCCCEEEECC-CTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            3456789999999 788999999999999999999999999999999999999999999999999999999999987643

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.66  E-value=4.2e-16  Score=131.74  Aligned_cols=78  Identities=23%  Similarity=0.483  Sum_probs=72.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|.++|+.||+|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~  115 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI--LNKRLK  115 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEEC--SSCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEE
Confidence            45667999999999999999999999999999999883        78999999999999999999999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus       116 v~~a~~~~  123 (139)
T 1u6f_A          116 VALAASGH  123 (139)
T ss_dssp             EEESSCCC
T ss_pred             EEECCCCC
Confidence            99998765

>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=99.66  E-value=2.9e-16  Score=121.57  Aligned_cols=74  Identities=24%  Similarity=0.502  Sum_probs=67.0

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ......++|||+|||+.+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+ .+++..|  +|+.|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~~~~~~~--~g~~i   82 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL-DQKEHRL--DGRVI   82 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHH-HSSCEEE--TTEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHH-HhCCCEE--CCEEE
Confidence            345678999999999999999999999999999999983        789999999999999999 5688888  89999


Q ss_pred             EEEEe
Q 014384          121 RVEWT  125 (425)
Q Consensus       121 ~V~~a  125 (425)
                      .|.+|
T Consensus        83 ~v~~A   87 (87)
T 3s7r_A           83 DPKKA   87 (87)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99985

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=3.1e-16  Score=125.52  Aligned_cols=76  Identities=20%  Similarity=0.444  Sum_probs=69.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|.++|.+|| |..|.|.        +|||||+|.+.++|++|| .|||..|  .|+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~   86 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALL--GDRSLR   86 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEE--TTEECE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeE--CCeEEE
Confidence            345679999999999999999999999997 9999883        689999999999999999 9999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        87 V~~a~~~~   94 (103)
T 2dng_A           87 VDIAEGRK   94 (103)
T ss_dssp             EEECCCCC
T ss_pred             EEEecCCC
Confidence            99998754

>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=2.2e-16  Score=126.88  Aligned_cols=77  Identities=17%  Similarity=0.304  Sum_probs=70.4

Q ss_pred             cCCCceEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           51 EAMMRPIFCGNFEYDA------RQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~------t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      ....++|||+|||+.+      |+++|.++|++||.|..|.|.      +|||||+|.+.++|.+|+..|||..|  +|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~--~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL--DKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEEC--STT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCccc--CCC
Confidence            3456899999999999      889999999999999999984      79999999999999999999999999  898


Q ss_pred             -EEEEEEecccc
Q 014384          119 -RLRVEWTKHER  129 (425)
Q Consensus       119 -~l~V~~a~~~~  129 (425)
                       .|.|.++....
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             99999987543

>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=3e-16  Score=125.83  Aligned_cols=75  Identities=21%  Similarity=0.479  Sum_probs=69.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ....++|||+|||+.+|+++|.++|..|| |..|.|.         +|||||+|.+.++|++|| .|||..|  .|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~   87 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL--GNKRIR   87 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEE--TTEECE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEe--CCcEEE
Confidence            35679999999999999999999999999 9999983         689999999999999999 9999999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+++....
T Consensus        88 V~~a~~~~   95 (104)
T 1wi8_A           88 VDVADQAQ   95 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            99998765

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=6.8e-16  Score=120.30  Aligned_cols=78  Identities=27%  Similarity=0.433  Sum_probs=73.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDD  225 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~~  225 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.+.++||||+|.+.++|.+|++.||+..|+|+.|.|+++..+..
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESC-CSSCCHHHHHHHHHTSSCEEEEEEETTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEECCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            456789999999 889999999999999999999999999999999999999999999999999999999999987543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.66  E-value=4.3e-16  Score=128.92  Aligned_cols=77  Identities=22%  Similarity=0.344  Sum_probs=70.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCE-EEEEEcCHHHHHHHHHhcCCCeecCCC--cEEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGF-AFIYMDDERDAEDAIRGLDRTEFGRKG--RRLRVEW  124 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~-aFV~F~~~~~A~~A~~~lng~~ig~~g--r~l~V~~  124 (425)
                      +.....|||+||++.+|+++|.++|++||+|..|.|.   +|| |||+|.+.++|++|++.|||..|  .|  +.|+|+|
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i--~g~~~~LrI~~  102 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNI--YNACCTLRIDF  102 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEE--ETTEEEEEEEE
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCee--cCCCcEEEEEe
Confidence            4455678899999999999999999999999999883   677 99999999999999999999999  56  9999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      ++...
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98765

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.66  E-value=1.8e-16  Score=144.02  Aligned_cols=117  Identities=15%  Similarity=0.181  Sum_probs=87.1

Q ss_pred             eeeEEEEeCCCCccccccc-CCcceeecccc-cccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-
Q 014384           10 CHYLLIVYSHSVWPVQKKY-LPRRLYVLGFR-RSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-   86 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-   86 (425)
                      ..||||.|.+...+..+.. .+..+.....+ ................+|||+|||+.+|+++|.++|.+||.|..|.| 
T Consensus        57 ~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~  136 (213)
T 4f02_A           57 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV  136 (213)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE
T ss_pred             cccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEee
Confidence            3599999988766554431 12211111110 00111111223345679999999999999999999999999999998 


Q ss_pred             -----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           87 -----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        87 -----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                           ++|||||+|.+.++|.+||..|||..|  +|+.|.|.|+...
T Consensus       137 ~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~--~g~~i~V~~a~~~  181 (213)
T 4f02_A          137 CDENGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSR  181 (213)
T ss_dssp             EETTEEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECCCH
T ss_pred             ccCCCCceEEEEEeCCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCC
Confidence                 379999999999999999999999999  8999999999754

>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=99.65  E-value=1.2e-16  Score=129.88  Aligned_cols=77  Identities=18%  Similarity=0.303  Sum_probs=70.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCC
Q 014384           51 EAMMRPIFCGNFEYDARQSDLE---RLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRK  116 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~---~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~  116 (425)
                      ....++|||+|||+.+|+++|.   ++|.+||+|..|.|.           +|||||+|.+.++|++||..|||..|  +
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~--~   89 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV--D   89 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE--T
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE--C
Confidence            3456899999999999999999   999999999999984           27999999999999999999999999  8


Q ss_pred             CcEEEEEEecccc
Q 014384          117 GRRLRVEWTKHER  129 (425)
Q Consensus       117 gr~l~V~~a~~~~  129 (425)
                      |+.|.|.|+....
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999998754

>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=99.65  E-value=1.8e-16  Score=126.95  Aligned_cols=76  Identities=33%  Similarity=0.616  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.|.
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~   83 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF--SGRALRVD   83 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSC--SSSCBEEE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCee--CCcEEEEE
Confidence            345899999999999999999999999999999883        78999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        84 ~a~~~~   89 (104)
T 1p1t_A           84 NAASEK   89 (104)
T ss_dssp             ETTCTT
T ss_pred             eCCCcc
Confidence            997654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.8e-16  Score=122.09  Aligned_cols=76  Identities=17%  Similarity=0.295  Sum_probs=70.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....++|||+||  .+|+++|+++|.+||+|..|.|.  +|||||+|.+.++|.+||..|||..|  +|+.|.|.|+..
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~v~~a~~   86 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV--ESVQLKVNIARK   86 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEE--TTEEEEEECCSS
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEECCC
Confidence            3456789999996  89999999999999999999985  89999999999999999999999999  899999999976


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        87 ~~   88 (97)
T 1x5p_A           87 QP   88 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=5.6e-17  Score=136.51  Aligned_cols=116  Identities=27%  Similarity=0.374  Sum_probs=73.1

Q ss_pred             CEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHH
Q 014384           89 GFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDL  168 (425)
Q Consensus        89 g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L  168 (425)
                      .++|++|.+...|..|+..++|...  .|.. .+.+                ........+.++|||+|| |..+++++|
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~--~g~~-~~~~----------------~~~~~~~~~~~~l~V~nL-p~~~te~~L   64 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQ--MGRG-SMSY----------------GRPPPDVEGMTSLKVDNL-TYRTSPDTL   64 (135)
T ss_dssp             ---------------------------------CCS----------------CCSCSSGGGCCCEEEECC-CSSCHHHHH
T ss_pred             ccccccccCCCchhhhhhhccCCCC--CCCC-CCCc----------------CCCCCCCCCCCEEEEeCC-CCCCCHHHH
Confidence            3678888888888889988888765  2322 1111                112234456789999999 889999999


Q ss_pred             HhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          169 ERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       169 ~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      +++|++||.|..|.|+        +|||||+|.+.++|.+|++.||+..|+|+.|.|.++....
T Consensus        65 ~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           65 RRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             HHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             HHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999985        4699999999999999999999999999999999998753

>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=1e-16  Score=126.19  Aligned_cols=75  Identities=13%  Similarity=0.219  Sum_probs=65.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|+++|.+||.|..+.+        .+|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~gr~l~v   89 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKL   89 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeE--CCcEEEE
Confidence            345689999999999999999999999999876555        369999999999999999999999999  8999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      +++..
T Consensus        90 ~~a~s   94 (95)
T 2ek1_A           90 SGPSS   94 (95)
T ss_dssp             ECCC-
T ss_pred             EeccC
Confidence            98753

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.65  E-value=2.7e-16  Score=135.58  Aligned_cols=75  Identities=16%  Similarity=0.335  Sum_probs=68.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYG--KVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G--~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      ...++|||+|||+.+|+++|.++|+.||  .|..|.|        ++|||||+|.+.++|.+||..|||..|  +|+.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~--~Gr~l~  130 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL--NGEKVD  130 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEE--TTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE--CCeEeE
Confidence            3568999999999999999999999999  9999988        378999999999999999999999999  899999


Q ss_pred             EEEeccc
Q 014384          122 VEWTKHE  128 (425)
Q Consensus       122 V~~a~~~  128 (425)
                      |.++...
T Consensus       131 V~~a~~~  137 (156)
T 3n9u_C          131 VRPATRQ  137 (156)
T ss_dssp             EEECCHH
T ss_pred             EEEcCCC
Confidence            9998653

>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=1.4e-16  Score=126.30  Aligned_cols=76  Identities=13%  Similarity=0.205  Sum_probs=68.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|+++|.+||.|..+.+        ++|||||+|.+.++|++|+..|||..|  .|+.|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V   89 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKL   89 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE--TTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCee--CCeEEEE
Confidence            355689999999999999999999999999975544        379999999999999999999999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      +++...
T Consensus        90 ~~a~~~   95 (98)
T 2cqp_A           90 VLGSGP   95 (98)
T ss_dssp             EESSCS
T ss_pred             EEcCCC
Confidence            998753

>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=5.6e-16  Score=128.38  Aligned_cols=78  Identities=15%  Similarity=0.346  Sum_probs=72.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||..+|+++|+++|++||+|..|.|       .+|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V  108 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL--DGRPMDI  108 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEES--SSCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEE--CCcEEEE
Confidence            3456789999999999999999999999999999999       369999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      +|+....
T Consensus       109 ~~a~~~~  115 (124)
T 2kt5_A          109 QLVASQI  115 (124)
T ss_dssp             EEECCTT
T ss_pred             EEeCCCC
Confidence            9998754

>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=99.65  E-value=2.6e-16  Score=128.34  Aligned_cols=75  Identities=28%  Similarity=0.443  Sum_probs=69.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|..||.|..|.|.        +|||||+|.+.++|++|| .|||..|  +|+.|.|.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V~   99 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRL--LGVPIIVQ   99 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEE--TTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEe--CCeEEEEE
Confidence            346899999999999999999999999999999993        689999999999999999 9999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus       100 ~a~~~~  105 (114)
T 2cq4_A          100 ASQAEK  105 (114)
T ss_dssp             EHHHHH
T ss_pred             ecCCCc
Confidence            987654

>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=3.6e-16  Score=125.72  Aligned_cols=80  Identities=21%  Similarity=0.321  Sum_probs=71.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCee-cCCCcEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEF-GRKGRRL  120 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~i-g~~gr~l  120 (425)
                      .....++|||+|||..+|+++|+++|++||+|..|.|.        +|||||+|.+.++|.+|+..|||..| ...|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            44667999999999999999999999999999999983        69999999999999999999999765 2247999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      .|.|+....
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            999998755

>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=99.65  E-value=3.4e-16  Score=126.56  Aligned_cols=80  Identities=14%  Similarity=0.251  Sum_probs=70.7

Q ss_pred             hcCCCceEEE--cCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCee-c--CCCcEEEE
Q 014384           50 FEAMMRPIFC--GNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEF-G--RKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V--~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~i-g--~~gr~l~V  122 (425)
                      ...++++|||  +||++.+|+++|+++|++||+|..|.|.  +|||||+|.+.++|++|++.|||..| .  ..|++|.|
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v  100 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL  100 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEE
Confidence            4456789999  7799999999999999999999999985  78999999999999999999999977 1  14889999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       101 ~~a~~~p  107 (114)
T 2cq2_A          101 NFVEKVQ  107 (114)
T ss_dssp             EEESCCC
T ss_pred             EecccCc
Confidence            9987544

>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=99.65  E-value=4.5e-16  Score=123.64  Aligned_cols=74  Identities=27%  Similarity=0.445  Sum_probs=68.8

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..+++|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.|||..|+|+.|.|.|
T Consensus        17 ~~gt~lfV~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           17 FQGTNLIVNYL-PQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34578999999 8999999999999999999999985        57999999999999999999999999999999999


Q ss_pred             eee
Q 014384          220 AVR  222 (425)
Q Consensus       220 a~~  222 (425)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.3e-16  Score=124.80  Aligned_cols=78  Identities=22%  Similarity=0.431  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .....++|||+|||+.+|+++|+++|.+||.|.-+..    .+|||||+|.+.++|++||..|||..|  +|+.|.|+|+
T Consensus        11 ~~~~~~~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           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREI--EGRAIRLELQ   88 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEE--TTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEe--CCeEEEEEEc
Confidence            4466899999999999999999999999998843332    489999999999999999999999999  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        89 ~~~~   92 (101)
T 2fc9_A           89 GPRG   92 (101)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8754

>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=99.65  E-value=1.8e-16  Score=129.56  Aligned_cols=73  Identities=22%  Similarity=0.302  Sum_probs=64.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeC-CEEEEEEcCHHHHHHHHHhcCCCeecCCCcE-----EEEEEe
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGRKGRR-----LRVEWT  125 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~k-g~aFV~F~~~~~A~~A~~~lng~~ig~~gr~-----l~V~~a  125 (425)
                      ...++|||+|||+++|+++|+++|.+||+|..|.|.. |||||+|.+.++|++||+.|||..|  +|+.     |.|..+
T Consensus        14 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           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKVD   91 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBC--CCTTSCCCBCEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecCCEEEEEECCHHHHHHHHHHhCCCEE--CCcEeeeEEEEeccC
Confidence            3568999999999999999999999999999999976 9999999999999999999999999  8988     555554


Q ss_pred             c
Q 014384          126 K  126 (425)
Q Consensus       126 ~  126 (425)
                      .
T Consensus        92 ~   92 (115)
T 3beg_B           92 G   92 (115)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.5e-16  Score=126.48  Aligned_cols=77  Identities=18%  Similarity=0.364  Sum_probs=70.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|+++|.+||+|..|.|.        +|||||+|.+.++|.+||.. |+..|  +|+.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~--~g~~l~   88 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTL--DGRNID   88 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEE--TTEEEB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeE--CCEEEE
Confidence            45677999999999999999999999999999999983        58999999999999999987 99999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.++....
T Consensus        89 V~~a~~~~   96 (105)
T 2dh8_A           89 PKPCTPRG   96 (105)
T ss_dssp             CCCSCCSS
T ss_pred             EEEccCCC
Confidence            99998655

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.6e-16  Score=119.96  Aligned_cols=78  Identities=26%  Similarity=0.433  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.+.++||||+|.+.++|.+|++.||+..|.|+.|.|.++....
T Consensus         6 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~v~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A            6 SGKASTKLHVGNI-SPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             CCCSSEEEEEESC-CSSCCHHHHHHHHHTTSCCCEEEECSSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEECCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3566789999999 88999999999999999999999999999999999999999999999999999999999998754

>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=99.64  E-value=5.8e-16  Score=132.95  Aligned_cols=79  Identities=20%  Similarity=0.256  Sum_probs=70.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      +....+|||+||++.+|+++|+++|++||+|+.|.|.    +|||||+|.+.++|++|+..|||..|...++.|+|+|++
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            3445679999999999999999999999999999983    579999999999999999999999993123999999998


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.64  E-value=5.3e-16  Score=127.76  Aligned_cols=75  Identities=20%  Similarity=0.253  Sum_probs=67.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCE-EEEEEcCHHHHHHHHHhcCCCeecCCC--cEEEEEEecc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGF-AFIYMDDERDAEDAIRGLDRTEFGRKG--RRLRVEWTKH  127 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~-aFV~F~~~~~A~~A~~~lng~~ig~~g--r~l~V~~a~~  127 (425)
                      ....|||+||++.+|+++|.++|++||.|..|.|.  .|| |||+|.+.++|.+|++.|||..|  .|  +.|.|+||+.
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i--~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI--YAGCCTLKIEYARP  101 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCC--BTTBSEEEEECCSC
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEe--cCCCeEEEEEEecC
Confidence            34557899999999999999999999999999884  586 99999999999999999999999  55  6999999987


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus       102 ~~  103 (124)
T 2e5i_A          102 TR  103 (124)
T ss_dssp             SC
T ss_pred             Cc
Confidence            64

>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=99.64  E-value=9.1e-16  Score=124.00  Aligned_cols=76  Identities=24%  Similarity=0.354  Sum_probs=69.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEe---------CCEEEEEEcCHHHHHHHHHhcC--CCeecCCCcE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGK-VDRVDMK---------SGFAFIYMDDERDAEDAIRGLD--RTEFGRKGRR  119 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~-V~~v~i~---------kg~aFV~F~~~~~A~~A~~~ln--g~~ig~~gr~  119 (425)
                      ...++|||+|||+.+|+++|.++|.+||. |..|.|.         +|||||+|.+.++|.+|+..||  +..|  +|+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~--~g~~   83 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL--WGHQ   83 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCB--TTBC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCcee--cCCe
Confidence            45789999999999999999999999998 9999884         7899999999999999999996  5888  8999


Q ss_pred             EEEEEecccc
Q 014384          120 LRVEWTKHER  129 (425)
Q Consensus       120 l~V~~a~~~~  129 (425)
                      |.|.|+....
T Consensus        84 l~V~~a~~~~   93 (109)
T 2dis_A           84 IAVDWAEPEI   93 (109)
T ss_dssp             CEEEESCSSC
T ss_pred             EEEEEcCCCC
Confidence            9999998765

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.9e-15  Score=120.01  Aligned_cols=80  Identities=30%  Similarity=0.405  Sum_probs=74.3

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccC--CcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPY--GKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~--G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .....+.++|||+|| |..+++++|+++|.+|  |.|..|.+++|||||+|.+.++|.+|+..||+..|+|+.|.|.++.
T Consensus         9 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~g~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A            9 EDTMSSVKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             CSCSSCCCEEEEESC-CTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             ccccCCcCEEEEeCC-CCCCCHHHHHHHHHhcCCcceEEEEEeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            344567899999999 8889999999999999  9999999999999999999999999999999999999999999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      ...
T Consensus        88 ~~~   90 (99)
T 2cpd_A           88 PVD   90 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.64  E-value=6.5e-16  Score=125.02  Aligned_cols=78  Identities=18%  Similarity=0.378  Sum_probs=66.5

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ......++|||+|||..+|+++|.++|+.||+|..|.|.        +|||||+|.+.++|.+|+..+ +..|  +|+.|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l--~g~~l   96 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHEL--DSKTI   96 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEE--TTEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcC--CCEEE
Confidence            455677999999999999999999999999999999983        689999999999999999776 5888  89999


Q ss_pred             EEEEecccc
Q 014384          121 RVEWTKHER  129 (425)
Q Consensus       121 ~V~~a~~~~  129 (425)
                      .|.++....
T Consensus        97 ~V~~a~~~~  105 (109)
T 2rs2_A           97 DPKVAFPRR  105 (109)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCCC
Confidence            999998654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=1.9e-16  Score=118.90  Aligned_cols=67  Identities=22%  Similarity=0.475  Sum_probs=62.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.+.++|++|++ |||..|  +|+.|.|.+|
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-IHFHEI--NNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCS--SSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEE--CCEEEEEEeC
Confidence            59999999999999999999999999999983        6899999999999999995 999999  8999999875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.64  E-value=4.9e-16  Score=128.68  Aligned_cols=76  Identities=28%  Similarity=0.598  Sum_probs=70.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+ .|||..|  +|+.|.|
T Consensus        33 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~l~V  109 (124)
T 2jwn_A           33 EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVF--RGRTIKV  109 (124)
T ss_dssp             HHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEE--TTEECEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeE--CCeEEEE
Confidence            3456899999999999999999999999999999983        789999999999999999 8999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       110 ~~a~~~~  116 (124)
T 2jwn_A          110 LPKRTNM  116 (124)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9998644

>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=99.64  E-value=4.1e-16  Score=136.21  Aligned_cols=114  Identities=13%  Similarity=0.189  Sum_probs=86.5

Q ss_pred             eeeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--   87 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--   87 (425)
                      ..||||.|.+...+..+...+...... .................++|||+|||..+|+++|.++|++||.|..|.|.  
T Consensus        51 ~g~afV~f~~~~~A~~A~~~~~~~~~g-~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~  129 (172)
T 2g4b_A           51 KNFAFLEFRSVDETTQAMAFDGIIFQG-QSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD  129 (172)
T ss_dssp             TTEEEEEESSHHHHHHHGGGTTCEETT-EECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEEC
T ss_pred             CCEEEEEeCCHHHHHHHHHhCCcEecC-ceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEec
Confidence            359999999877665555333222211 11111011111223447899999999999999999999999999999982  


Q ss_pred             ------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           88 ------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        88 ------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                            +|||||+|.+.++|.+|+..|||..|  +|+.|.|.||.
T Consensus       130 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~As  172 (172)
T 2g4b_A          130 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRAS  172 (172)
T ss_dssp             TTTCSEEEEEEEEESSTTHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             CCCCCcceEEEEEeCCHHHHHHHHHHcCCCEE--CCeEEEEEeCC
Confidence                  68999999999999999999999999  89999999973

>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=99.64  E-value=4e-16  Score=121.12  Aligned_cols=75  Identities=19%  Similarity=0.339  Sum_probs=69.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ...++|||+|||+.+|+++|+++|.+| .|..|.|  .+|||||+|.+.++|++|+..|||..|  +|+.|.|+|+....
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF--RGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEE--TTEEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeE--CCcEEEEEEcCCCc
Confidence            356899999999999999999999999 9999888  489999999999999999999999999  89999999987644

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.64  E-value=9.2e-16  Score=121.03  Aligned_cols=78  Identities=18%  Similarity=0.230  Sum_probs=71.5

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCc--cCCeEEEEEEe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSK--LTDRVISVEYA  220 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~--~~g~~i~v~~a  220 (425)
                      ...+|+.+|||+|| |..+++++|.++|++||.|..|.+.  +|||||+|.+.++|..|++.|++..  |.|+.|.|+|+
T Consensus        16 ~~~~ps~~l~V~NL-p~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           16 HKTPASPVVHIRGL-IDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             -CCCCCSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             ccCCCCcEEEEeCC-CCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            34678899999999 8999999999999999999999996  7899999999999999999999876  78999999999


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      +.+
T Consensus        95 ~~k   97 (100)
T 3r27_A           95 TSQ   97 (100)
T ss_dssp             SCS
T ss_pred             ccc
Confidence            764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=119.24  Aligned_cols=77  Identities=25%  Similarity=0.428  Sum_probs=72.8

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.+.++||||+|.+.++|.+|++.|||..|+|+.|.|.++....
T Consensus         6 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~~~~~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A            6 SGNTWKIFVGNV-SAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SCCSCCEEEESC-CTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHcCCCEEEEEEECCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            456789999999 88999999999999999999999999999999999999999999999999999999999998753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.63  E-value=2.6e-16  Score=120.19  Aligned_cols=66  Identities=20%  Similarity=0.369  Sum_probs=61.9

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc-EEE
Q 014384           55 RPIFCGNFEYDA------RQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR-RLR  121 (425)
Q Consensus        55 ~~l~V~nL~~~~------t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr-~l~  121 (425)
                      ++|||+|||..+      |+++|.++|++||+|..|.|.      +|||||+|.+.++|.+|+..|||..|  +|+ .|.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~--~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL--DKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCC--SSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCccc--CCceeEE
Confidence            689999999999      789999999999999999984      79999999999999999999999999  788 877


Q ss_pred             E
Q 014384          122 V  122 (425)
Q Consensus       122 V  122 (425)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=7.5e-17  Score=124.31  Aligned_cols=73  Identities=16%  Similarity=0.322  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|+|.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~~~~~   80 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV--QAQMAKQS   80 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTC--CEESCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeE--eeEEEeec
Confidence            567899999999999999999999999999999983        78999999999999999999999999  79988877


Q ss_pred             Eec
Q 014384          124 WTK  126 (425)
Q Consensus       124 ~a~  126 (425)
                      ++.
T Consensus        81 ~~~   83 (85)
T 1x4e_A           81 GPS   83 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.63  E-value=1.5e-15  Score=120.85  Aligned_cols=77  Identities=21%  Similarity=0.309  Sum_probs=70.1

Q ss_pred             CCCCcEEEEEcCCCC-CCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCC--ccCCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPY-HTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMS--KLTDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~-~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~i~v~~a~  221 (425)
                      ..+.++|||+|| |. .+++++|+++|++||.|..|.|+  ++||||+|.+.++|..|++.||+.  .|.|+.|.|.++.
T Consensus        12 ~~p~~~l~V~nL-p~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   90 (102)
T 1x4d_A           12 VETRRVVHIMDF-QRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQ   90 (102)
T ss_dssp             CCCCCEEEEESC-CCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEEC
T ss_pred             CCCCCEEEEeCC-CCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECC
Confidence            457899999999 78 99999999999999999999997  489999999999999999999864  5999999999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      ...
T Consensus        91 ~~~   93 (102)
T 1x4d_A           91 KYK   93 (102)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.8e-16  Score=120.16  Aligned_cols=73  Identities=22%  Similarity=0.315  Sum_probs=65.7

Q ss_pred             CCce-EEEcCCCCCCCHHH----HHHHHhhc-CCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           53 MMRP-IFCGNFEYDARQSD----LERLFRRY-GKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        53 ~~~~-l~V~nL~~~~t~~~----L~~lF~~~-G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ++.| |||+|||..+++++    |.++|++| |+|.+|.  .|+|||+|.+.++|..|++.|||..|  .|++|+|.||+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt--gG~AfV~F~~~esA~~A~~~l~G~~l--~gr~i~v~~A~   82 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT--GCSAILRFINQDSAERAQKRMENEDV--FGNRIIVSFTP   82 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC--TTCEEEEESSHHHHHHHHHHHTTCCS--SSSCCEEESSC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe--cCEEEEEECCHHHHHHHHHHhcCCcc--CCceEEEEecC
Confidence            3445 99999999999988    56899999 5999884  49999999999999999999999999  79999999998


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        83 ~~s   85 (96)
T 2diu_A           83 KNR   85 (96)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            765

>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=99.63  E-value=5.4e-16  Score=126.63  Aligned_cols=77  Identities=22%  Similarity=0.329  Sum_probs=69.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCe----eEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKV----DRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V----~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ..+.++|||+|||..+|+++|.++|.+||.|    ..+.+.    +|||||+|.+.++|.+|+..|||..|  +|+.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~v   99 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL--YGKILVI   99 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC--SSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEe--CCcEEEE
Confidence            3567899999999999999999999999998    555553    79999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       100 ~~a~~~~  106 (115)
T 2cpx_A          100 EFGKNKK  106 (115)
T ss_dssp             EECCCCS
T ss_pred             EEccCCC
Confidence            9998755

>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=6.8e-16  Score=134.49  Aligned_cols=77  Identities=18%  Similarity=0.450  Sum_probs=70.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+.+|+++|.++|.+||.|..|.|.        +|||||+|.+.++|.+||..|||..|  .|+.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V  146 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQV  146 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            3456789999999999999999999999999999984        68999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       147 ~~a~~~~  153 (165)
T 1rk8_A          147 DWCFVKG  153 (165)
T ss_dssp             EESEECC
T ss_pred             EEecCCC
Confidence            9998754

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.63  E-value=7e-16  Score=121.79  Aligned_cols=78  Identities=26%  Similarity=0.538  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEEcCCCC-CCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          146 NTRPSKTLFVINFDPY-HTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~-~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ...+.++|||+|| |. .+++++|+++|.+||.|..|.+++|||||+|.+.++|..|++.|||..+.|+.|.|+++....
T Consensus         6 ~~~~~~~l~V~nl-p~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A            6 NIPPKSRLFIGNL-PLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             ---CCEEEEEESS-TTSCCCHHHHHHHHTTTCCCCEEEEETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             cCCCCCEEEEeCC-CcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            3567889999999 77 899999999999999999999999999999999999999999999999999999999998754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9.6e-16  Score=125.38  Aligned_cols=75  Identities=16%  Similarity=0.437  Sum_probs=69.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+.+|+++|.++|.+||+|..|.|.        +|||||+|.+.++|.+||.. |+..|  +|+.|.|.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~--~g~~l~V~  101 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSI--DGRVVEPK  101 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEE--TTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEE--CCEEEEEE
Confidence            345899999999999999999999999999999983        68999999999999999976 99999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ++....
T Consensus       102 ~a~~~~  107 (116)
T 1x4b_A          102 RAVARE  107 (116)
T ss_dssp             CCSSCC
T ss_pred             ECCCCc
Confidence            998765

>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=1.2e-16  Score=124.56  Aligned_cols=73  Identities=38%  Similarity=0.713  Sum_probs=65.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +++|||+|||..+|+++|.++|++||+|..|.|.        +|||||+|.+.+ |.+|+..|||..|  +|+.|.|++|
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~--~g~~l~V~~a   77 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDF--MGRTIRVTEA   77 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCC--SSSSCSEEEC
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEE--CCeEEEEEEc
Confidence            4789999999999999999999999999999983        789999999999 9999999999999  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        78 ~~~~   81 (90)
T 2ki2_A           78 NPKK   81 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            8654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=5.2e-16  Score=122.41  Aligned_cols=78  Identities=21%  Similarity=0.379  Sum_probs=70.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .....++|||+|||..+|+++|.++|..||.|..|..   ++|||||+|.+.++|.+|+..|||..|  +|+.|.|.|+.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~   89 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTG   89 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEE--TTEEEEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEEcC
Confidence            3456789999999999999999999999999987732   489999999999999999999999999  89999999997


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        90 ~~~   92 (96)
T 1fjc_A           90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=5.7e-16  Score=134.19  Aligned_cols=114  Identities=17%  Similarity=0.323  Sum_probs=85.8

Q ss_pred             eeEEEEeCCCCcccccc-cCCcceeecc-cccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-
Q 014384           11 HYLLIVYSHSVWPVQKK-YLPRRLYVLG-FRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-   87 (425)
                      .||||.|.+...+..+. .+........ ..................+|||+|||..+|+++|.++|+.||.|..|.+. 
T Consensus        42 g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~  121 (166)
T 3md3_A           42 NYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW  121 (166)
T ss_dssp             EEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEE
T ss_pred             CEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEe
Confidence            59999998877655444 2222211110 00000011111344567899999999999999999999999999999883 


Q ss_pred             -------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           88 -------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        88 -------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                             +|||||+|.+.++|.+|+..|||..|  .|+.|.|.||+
T Consensus       122 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~i~v~~a~  165 (166)
T 3md3_A          122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWAA  165 (166)
T ss_dssp             CTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEESC
T ss_pred             cCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc--CCcEEEEEecC
Confidence                   68999999999999999999999999  89999999985

>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=1.1e-15  Score=119.33  Aligned_cols=76  Identities=13%  Similarity=0.274  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+++|+++|+++|..| .|..|.|.       +|||||+|.+.++|.+||. |||..|  .|+.|.|
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~--~gr~i~v   81 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYM--GGRYIEV   81 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEE--TTEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCcee--CCcEEEE
Confidence            34567899999999999999999999999 89999883       7899999999999999998 999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        82 ~~a~~~~   88 (91)
T 2dgw_A           82 FREKSGP   88 (91)
T ss_dssp             EEESSCC
T ss_pred             EECCcCC
Confidence            9997653

>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=99.63  E-value=1.6e-15  Score=121.29  Aligned_cols=76  Identities=17%  Similarity=0.350  Sum_probs=68.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||+.+|+++|+++|.+||+|..|.|.        +|||||+|.+.++|++||.  ++..|  +|+.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~--~g~~l~   86 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMI--DGRWCD   86 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEE--TTEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCee--CCeEEE
Confidence            44667899999999999999999999999999999883        5799999999999999997  46788  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.|+....
T Consensus        87 v~~a~~~~   94 (103)
T 2cqg_A           87 CKLPNSKQ   94 (103)
T ss_dssp             EECCCTTC
T ss_pred             EEecCCCC
Confidence            99998765

>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=99.63  E-value=6e-16  Score=125.38  Aligned_cols=76  Identities=22%  Similarity=0.407  Sum_probs=71.4

Q ss_pred             CCCCcEEEEEcCCCCC-CCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          147 TRPSKTLFVINFDPYH-TRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~-~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..+.++|||+|| |.. +++++|+++|.+||.|..|.+.++||||+|.+.++|.+|++.||+..|+|+.|.|.++...
T Consensus        24 ~~~~~~l~V~nl-~~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           24 KSINSRVFIGNL-NTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             TTCSSEEEECSC-CCSSCCHHHHHHHHGGGSCCSEEEEETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCCCcEEEEeCC-CcccCCHHHHHHHHHhCCCeEEEEEeCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            445689999999 787 8999999999999999999999999999999999999999999999999999999999764

>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=99.63  E-value=6.4e-16  Score=132.44  Aligned_cols=77  Identities=36%  Similarity=0.605  Sum_probs=71.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .....++|||+|||+.+|+++|.++|++||.|..|.|.   +|||||+|.+.++|..|+..|||..|  .|+.|.|.|+.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~~a~  146 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL--CGCRVRVELSN  146 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCS--SSSCCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEEcC
Confidence            44567999999999999999999999999999999994   89999999999999999999999999  89999999987


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus       147 ~~  148 (150)
T 2i2y_A          147 GE  148 (150)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.62  E-value=4.6e-16  Score=130.21  Aligned_cols=77  Identities=21%  Similarity=0.348  Sum_probs=69.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--EEE--------eCCEEEEEEcCHHHHHHHHHhcCCC----eecC
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--VDM--------KSGFAFIYMDDERDAEDAIRGLDRT----EFGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--v~i--------~kg~aFV~F~~~~~A~~A~~~lng~----~ig~  115 (425)
                      .....++|||+|||+.+|+++|+++|.+||.|..  |.|        ++|||||+|.+. +|.+|+..|||.    .|  
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~--   95 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI--   95 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG--
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC--
Confidence            3456789999999999999999999999999966  777        379999999999 999999999999    88  


Q ss_pred             CCcEEEEEEecccc
Q 014384          116 KGRRLRVEWTKHER  129 (425)
Q Consensus       116 ~gr~l~V~~a~~~~  129 (425)
                      +|+.|.|.|+....
T Consensus        96 ~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           96 DGKTINVEFAKGSK  109 (131)
T ss_dssp             GGCCCCCEECCCSC
T ss_pred             CCEEEEEEECCCCC
Confidence            89999999998754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.62  E-value=9.8e-16  Score=129.47  Aligned_cols=74  Identities=24%  Similarity=0.501  Sum_probs=68.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .....++|||+|||..+|+++|+++|++||+|..|.|        .+|||||+|.+.++|++|+..|||..|  .|+.|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~  136 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIR  136 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEE--TTEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEE--CCEEEE
Confidence            4456799999999999999999999999999999998        279999999999999999999999999  899999


Q ss_pred             EEEe
Q 014384          122 VEWT  125 (425)
Q Consensus       122 V~~a  125 (425)
                      |.||
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9986

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=4.1e-15  Score=118.84  Aligned_cols=80  Identities=25%  Similarity=0.443  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        10 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           10 ITRYQVVNLYVKNL-DDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCCSSCCCEEEECC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             cCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34557889999999 8899999999999999999999997      6799999999999999999999999999999999


Q ss_pred             EeeeCCC
Q 014384          219 YAVRDDD  225 (425)
Q Consensus       219 ~a~~~~~  225 (425)
                      ++..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9988643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=3.2e-16  Score=118.25  Aligned_cols=68  Identities=18%  Similarity=0.424  Sum_probs=63.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ++|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.+.++|++|+..++ ..|  +|+.|.|.+|
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-HEL--DSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCC--SSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-Ccc--CCEEEEEEec
Confidence            589999999999999999999999999999883        6899999999999999999999 888  8999999987

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=121.73  Aligned_cols=78  Identities=21%  Similarity=0.416  Sum_probs=68.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      .....++|||+|||+.+|+++|+++|+.|+.|..+..     ++|||||+|.+.++|++||..|||..|  +|+.|.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~V~~   88 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEI--DGNKVTLDW   88 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeE--CCeEEEEEE
Confidence            4567899999999999999999999999976554443     268999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      ++...
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98765

>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=3.2e-16  Score=124.75  Aligned_cols=76  Identities=22%  Similarity=0.453  Sum_probs=66.4

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ......++|||+|||.++|+++|.++|+.|| |..|.|.         +|||||+|.+.++|.+|+ .|||..|  +|+.
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~--~g~~   89 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL--GNRR   89 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCB--TTBC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEE--CCeE
Confidence            3456679999999999999999999999999 9999982         689999999999999999 9999999  8999


Q ss_pred             EEEEEeccc
Q 014384          120 LRVEWTKHE  128 (425)
Q Consensus       120 l~V~~a~~~  128 (425)
                      |.|+++...
T Consensus        90 l~V~~a~~~   98 (100)
T 2j76_E           90 IRVDVADQA   98 (100)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEeccCC
Confidence            999998764

>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=99.62  E-value=5.8e-15  Score=117.44  Aligned_cols=79  Identities=19%  Similarity=0.362  Sum_probs=71.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc--CCCccCCeEEEEEEe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT--NMSKLTDRVISVEYA  220 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~a  220 (425)
                      ....+.++|||+|| |..+++++|+++|++||.|..|.+.  +|||||+|.+.++|..|++.|  ++..|.|+.|.|.|+
T Consensus        10 ~~~~p~~~l~V~nL-p~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           10 MDGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             CCSSCCSEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             ccCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            34567899999999 8899999999999999999999987  589999999999999999977  567899999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        89 ~~~~   92 (101)
T 2cq1_A           89 NHKE   92 (101)
T ss_dssp             SCSS
T ss_pred             Cccc
Confidence            8754

>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=99.62  E-value=2e-15  Score=119.41  Aligned_cols=78  Identities=23%  Similarity=0.492  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEEcCCCC-CCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          145 TNTRPSKTLFVINFDPY-HTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~-~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ....+.++|||+|| +. .+++++|+++|.+||.|..|.+.+|||||+|.+.++|.+|++.|||..|+|+.|.|+++...
T Consensus        17 ~~~~~~~~l~V~nL-p~~~~t~~~L~~~F~~~G~v~~v~i~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           17 RGSHMKSRLFIGNL-PLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             --CCTTCEEEEESC-CSSCCCHHHHHHHHGGGSCEEEEEECSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCCCEEEEeCC-CcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            44567899999999 77 89999999999999999999999999999999999999999999999999999999998764

>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=1.5e-15  Score=118.17  Aligned_cols=77  Identities=22%  Similarity=0.371  Sum_probs=62.1

Q ss_pred             hhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           49 AFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        49 ~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .......+|||+|||+++|+++|+++|++||+|.+|.|.   +|||||+|.+.++|++    |+|..+.+.|+.|.|.++
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            355678999999999999999999999999999999994   8999999999999983    566665337999999998


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7643

>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=99.62  E-value=5.3e-16  Score=126.59  Aligned_cols=77  Identities=18%  Similarity=0.217  Sum_probs=69.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKV-DRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V-~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      .+...++|||+|||+++|+++|.++|..||.| ..|.|       ++|||||+|.+.++|++||.. |+..|  +|+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~--~gr~i~   87 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKL--NGREAF   87 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEE--TTEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCcc--CCeEEE
Confidence            34567899999999999999999999999999 77887       489999999999999999965 99999  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |.++....
T Consensus        88 v~~a~~~~   95 (114)
T 2cpy_A           88 VHVVTLED   95 (114)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99987654

>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=99.62  E-value=7e-15  Score=117.51  Aligned_cols=80  Identities=34%  Similarity=0.514  Sum_probs=73.9

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|.      ++||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A            9 SESKSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             SCCSCCCCEEEEESC-CTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345567799999999 8899999999999999999999997      689999999999999999999999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++..+.
T Consensus        88 ~~a~~~~   94 (103)
T 2cq3_A           88 NNATARV   94 (103)
T ss_dssp             EECCSSC
T ss_pred             EEcccCC
Confidence            9998864

>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=99.62  E-value=2e-15  Score=125.39  Aligned_cols=80  Identities=23%  Similarity=0.434  Sum_probs=73.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.|||..|+|+.|.
T Consensus        17 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           17 QRSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             CCCSSSEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            44566789999999 8899999999999999999999995        67999999999999999999999999999999


Q ss_pred             EEEeeeCCC
Q 014384          217 VEYAVRDDD  225 (425)
Q Consensus       217 v~~a~~~~~  225 (425)
                      |.|+.....
T Consensus        96 v~~a~~~~~  104 (126)
T 3ex7_B           96 VDWCFVRGP  104 (126)
T ss_dssp             EEESEESSS
T ss_pred             EEEecCCCC
Confidence            999988643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.61  E-value=6.9e-16  Score=126.70  Aligned_cols=76  Identities=18%  Similarity=0.212  Sum_probs=68.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGK---VDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~---V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      .....++|||+|||+++|+++|.++|+.||.   |..|.|.       +|||||+|.+.++|++||. |||..|  .|+.
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~--~gr~   89 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESM--GHRY   89 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEE--TTEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeE--CCeE
Confidence            3456789999999999999999999999999   8888883       7899999999999999997 999999  8999


Q ss_pred             EEEEEeccc
Q 014384          120 LRVEWTKHE  128 (425)
Q Consensus       120 l~V~~a~~~  128 (425)
                      |.|.++...
T Consensus        90 i~V~~a~~~   98 (118)
T 2db1_A           90 IEVFKSHRT   98 (118)
T ss_dssp             EEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999998654

>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=99.61  E-value=4.3e-16  Score=130.85  Aligned_cols=75  Identities=17%  Similarity=0.189  Sum_probs=68.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGK---VDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~---V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      .....++|||+|||+++|+++|.++|+.||.   |..|.|.       +|||||+|.+.++|++||. |||..|  .|+.
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l--~gr~  116 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESM--GHRY  116 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEES--SSSE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEE--CCEE
Confidence            4456789999999999999999999999999   7888873       7899999999999999997 999999  8999


Q ss_pred             EEEEEecc
Q 014384          120 LRVEWTKH  127 (425)
Q Consensus       120 l~V~~a~~  127 (425)
                      |.|.++..
T Consensus       117 i~V~~a~~  124 (136)
T 2hgl_A          117 IEVFKSHR  124 (136)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCh
Confidence            99998754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.6e-15  Score=115.60  Aligned_cols=74  Identities=22%  Similarity=0.222  Sum_probs=68.8

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .....|||+|| +..+++++|+++|.+||+|..+.+.  +|||||+|.+.++|.+|++.||+..+.|++|.|.+|.+
T Consensus         5 ~~~~wL~VgNL-~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            5 WGSSWLLLKNL-TAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCCCEEEEECC-CTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             CccceEEEeCC-CccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            34678999999 7888899999999999999999985  89999999999999999999999999999999999853

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.3e-15  Score=120.20  Aligned_cols=75  Identities=17%  Similarity=0.293  Sum_probs=68.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEe----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV-DMK----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v-~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ...++|||+|||+.+|+++|.++|.+||.|..| .|.    .+.|||+|.+.++|.+|+..|||..|  +|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~--~g~~l~V~~a~   90 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQL--ENFTLKVAYIP   90 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBC--SSCBCEEEECC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEcC
Confidence            456899999999999999999999999999999 463    45699999999999999999999999  89999999998


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.61  E-value=3e-16  Score=125.07  Aligned_cols=76  Identities=16%  Similarity=0.285  Sum_probs=67.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....++|||+|||+.+|+++|+++|.+||.|..+.+       ++|||||+|.+.++|.+||+ |||..|  .|+.|.|.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~--~g~~l~V~   90 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKV--FGNEIKLE   90 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCB--TTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEE--CCcEEEEE
Confidence            456789999999999999999999999998765222       38999999999999999997 999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ++....
T Consensus        91 ~a~~~~   96 (101)
T 1fj7_A           91 KPKGRD   96 (101)
T ss_dssp             CCSCCC
T ss_pred             EcCCCC
Confidence            997654

>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=99.61  E-value=4.9e-15  Score=119.72  Aligned_cols=80  Identities=26%  Similarity=0.418  Sum_probs=73.1

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|.     ++||||+|.+.++|.+|++.||+..|+|+.|.|.
T Consensus        16 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCCCSSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344566789999999 8899999999999999999999995     5799999999999999999999999999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      ++....
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            998754

>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=99.61  E-value=1.4e-15  Score=122.01  Aligned_cols=75  Identities=13%  Similarity=0.227  Sum_probs=67.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....+|||+|||+.+|+++|.++|..||.|.. |.|       ++|||||+|.+.++|++||.. |+..|  .|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~--~gr~i~v   88 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERI--GHRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCS--SSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-Ccchh--CCcEEEE
Confidence            456789999999999999999999999999987 777       379999999999999999976 99999  7999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      .++...
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            998654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.9e-15  Score=118.77  Aligned_cols=75  Identities=27%  Similarity=0.465  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CC-EEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SG-FAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg-~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ...++|||+|||+.+|+++|.++|.+||.|..|.+.  .+ ||||+|.+.++|.+|+. |||..|  +|+.|.|.++...
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-QSQHSL--GGHRLRVRPREQK   82 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEE--TTEECCCBCSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEE--CCEEEEEEECCcC
Confidence            456899999999999999999999999999998553  12 99999999999999998 999999  8999999988654


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        83 ~   83 (94)
T 2e5g_A           83 E   83 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=5.8e-15  Score=116.08  Aligned_cols=77  Identities=27%  Similarity=0.413  Sum_probs=71.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .+.++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|.+|++.||+..|+|+.|.|.+
T Consensus         3 ~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            3 SGSSGLYVGSL-HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             SCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            46789999999 7889999999999999999999995        46999999999999999999999999999999999


Q ss_pred             eeeCCC
Q 014384          220 AVRDDD  225 (425)
Q Consensus       220 a~~~~~  225 (425)
                      +..+..
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            988643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.61  E-value=2.4e-15  Score=121.78  Aligned_cols=76  Identities=16%  Similarity=0.267  Sum_probs=70.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+..+|||+|| +..+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.|||..|+|+.|.|.
T Consensus         3 ~~p~~~lfV~nL-~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~   81 (110)
T 3s8s_A            3 QIPLKEVTFARL-NDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ   81 (110)
T ss_dssp             CSCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCcEEEEECC-CCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            356789999999 7899999999999999999999985        5799999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ++...
T Consensus        82 ~a~~~   86 (110)
T 3s8s_A           82 LDIKG   86 (110)
T ss_dssp             ECSTT
T ss_pred             ECCCC
Confidence            98653

>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=99.61  E-value=6.3e-15  Score=117.92  Aligned_cols=79  Identities=16%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCC--ccCCeEEEEEEe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMS--KLTDRVISVEYA  220 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~i~v~~a  220 (425)
                      ....+.++|||+|| |..+++++|+++|++||.|..|.|.  +|||||+|.+.++|.+|++.|++.  .|+|+.|.|.|+
T Consensus        10 ~~~~p~~~l~V~nL-p~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           10 HKVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCSEEEEESC-CSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CcCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            34567899999999 8899999999999999999999987  689999999999999999988654  599999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T 1wex_A           89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             cCcc
Confidence            8754

>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=99.61  E-value=9.2e-16  Score=133.33  Aligned_cols=112  Identities=17%  Similarity=0.257  Sum_probs=83.7

Q ss_pred             eeEEEEeCCCCccccccc-CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--
Q 014384           11 HYLLIVYSHSVWPVQKKY-LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--   87 (425)
                      .||||.|.+...+..+.. ++.... ...................++|||+|||..+|+++|.++|++||.|..|.|.  
T Consensus        46 g~afV~f~~~~~A~~a~~~l~~~~~-~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~  124 (168)
T 1b7f_A           46 GYAFVDFTSEMDSQRAIKVLNGITV-RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD  124 (168)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCEE-TTEECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEEC
T ss_pred             eEEEEEECCHHHHHHHHHhcCCCEe-CCcEEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEc
Confidence            499999998776555442 222111 1111100001111234567899999999999999999999999999999883  


Q ss_pred             ------CCEEEEEEcCHHHHHHHHHhcCCCeecCCC--cEEEEEEe
Q 014384           88 ------SGFAFIYMDDERDAEDAIRGLDRTEFGRKG--RRLRVEWT  125 (425)
Q Consensus        88 ------kg~aFV~F~~~~~A~~A~~~lng~~ig~~g--r~l~V~~a  125 (425)
                            +|||||+|.+.++|.+|+..|||..|  .|  +.|.|.||
T Consensus       125 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~~~l~V~~A  168 (168)
T 1b7f_A          125 KLTGRPRGVAFVRYNKREEAQEAISALNNVIP--EGGSQPLSVRLA  168 (168)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC--TTCSSCCEEEEC
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhcCCEe--cCCCeEEEEEeC
Confidence                  58999999999999999999999999  56  99999986

>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=99.60  E-value=5.5e-15  Score=116.80  Aligned_cols=80  Identities=26%  Similarity=0.399  Sum_probs=73.1

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccC--CeEEEEEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLT--DRVISVEY  219 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~  219 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.+.  ++||||+|.+.++|.+|++.||+..|.  |+.|.|.|
T Consensus        11 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           11 YGKANPTTRLWVGGL-GPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCCCCCSCEEEECC-CSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            344567789999999 8889999999999999999999997  569999999999999999999999999  99999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +..+.
T Consensus        90 a~~~~   94 (97)
T 1why_A           90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98753

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=8e-15  Score=117.17  Aligned_cols=79  Identities=28%  Similarity=0.491  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.||+..|+|+.|.
T Consensus        10 ~~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A           10 RRADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCSSSEEEEEESC-CTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            34567899999999 8899999999999999999999995        46999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++..+.
T Consensus        89 v~~a~~~~   96 (103)
T 2cq0_A           89 VEWAKPST   96 (103)
T ss_dssp             EEESSCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=99.60  E-value=7.9e-15  Score=117.18  Aligned_cols=80  Identities=23%  Similarity=0.335  Sum_probs=73.3

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|.      +|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        10 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           10 EDDGQPRTLYVGNL-SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CCSCCCCEEEEESC-CTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCC-CccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            34566799999999 8899999999999999999999996      4899999999999999999999999999999999


Q ss_pred             EeeeCCC
Q 014384          219 YAVRDDD  225 (425)
Q Consensus       219 ~a~~~~~  225 (425)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2cqi_A           89 WATTPSS   95 (103)
T ss_dssp             ECCCTTC
T ss_pred             ECCCCcc
Confidence            9988543

>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=99.60  E-value=1.9e-15  Score=123.16  Aligned_cols=79  Identities=15%  Similarity=0.281  Sum_probs=69.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecC------C
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGR------K  116 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~------~  116 (425)
                      .....++|||+|||+.+|+++|.++|..||.|..|.|.       +|||||+|.+.++|.+|+..|||..|..      .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            34567899999999999999999999999999999983       6899999999999999999999998821      3


Q ss_pred             CcEEEEEEeccc
Q 014384          117 GRRLRVEWTKHE  128 (425)
Q Consensus       117 gr~l~V~~a~~~  128 (425)
                      +++|.|.|+.+.
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            778999998753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.60  E-value=1.8e-15  Score=133.23  Aligned_cols=78  Identities=15%  Similarity=0.348  Sum_probs=72.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+.+|+++|+++|++||+|+.|.|.       +|||||+|.+.++|++|+..|||..|  +|+.|.|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l--~Gr~l~V  161 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL--DGRPMDI  161 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBC--SSSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            34567899999999999999999999999999999993       69999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      +|+....
T Consensus       162 ~~a~~~~  168 (177)
T 2f3j_A          162 QLVASQI  168 (177)
T ss_dssp             EEESSGG
T ss_pred             EEecCCC
Confidence            9998654

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.60  E-value=2e-15  Score=116.61  Aligned_cols=70  Identities=21%  Similarity=0.478  Sum_probs=65.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRY----G-------KVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~----G-------~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      ...++|||+|||+.+|+++|.++|.+|    |       .|..|.+.  +|||||+|.+.++|.+|+ .|||..|  +|+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~--~g~   80 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQ   80 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEE--TTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEE--CCe
Confidence            356899999999999999999999999    8       99999985  899999999999999999 9999999  899


Q ss_pred             EEEEEE
Q 014384          119 RLRVEW  124 (425)
Q Consensus       119 ~l~V~~  124 (425)
                      .|.|+.
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999974

>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=99.60  E-value=1.1e-15  Score=140.37  Aligned_cols=74  Identities=18%  Similarity=0.336  Sum_probs=67.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYG--KVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G--~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ..++|||+||++.+|+++|+++|.+||  +|+.|.|        ++|||||+|.+.++|++||..|||+.|  +|+.|.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~--~Gr~l~V  144 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL--HGQNPVV  144 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCB--TTBCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeE--CCEEeEE
Confidence            567999999999999999999999999  9999998        378999999999999999999999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      .|+...
T Consensus       145 ~~a~~~  150 (229)
T 3q2s_C          145 TPVNKQ  150 (229)
T ss_dssp             EECCHH
T ss_pred             EECCCC
Confidence            998753

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.5e-15  Score=121.05  Aligned_cols=77  Identities=17%  Similarity=0.352  Sum_probs=70.5

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCC--CccCCeEEEEEEeee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNM--SKLTDRVISVEYAVR  222 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~i~v~~a~~  222 (425)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.|+  +|||||+|.+.++|..|++.|++  ..|.|+.|.|.|+..
T Consensus        13 ~~~~~~LfV~nL-p~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~   91 (105)
T 1sjq_A           13 GVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH   91 (105)
T ss_dssp             CCCCCEEEECSC-CTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSS
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCC
Confidence            456789999999 8899999999999999999999997  68999999999999999998864  789999999999987


Q ss_pred             CC
Q 014384          223 DD  224 (425)
Q Consensus       223 ~~  224 (425)
                      +.
T Consensus        92 ~~   93 (105)
T 1sjq_A           92 KE   93 (105)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.60  E-value=2.8e-15  Score=133.74  Aligned_cols=118  Identities=16%  Similarity=0.255  Sum_probs=82.7

Q ss_pred             eeeEEEEeCCCCcccccccCCccee-----ecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEE
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLY-----VLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV   84 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v   84 (425)
                      ..||||.|.+...+..+........     ...+................++|||+|||+.+|+++|.++|+.||.|..|
T Consensus        55 ~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v  134 (196)
T 1l3k_A           55 RGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI  134 (196)
T ss_dssp             EEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEE
T ss_pred             cceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEE
Confidence            3499999998776555554322111     11111111111111233456899999999999999999999999999999


Q ss_pred             EEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccC
Q 014384           85 DMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERG  130 (425)
Q Consensus        85 ~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~  130 (425)
                      .|.        +|||||+|.+.++|.+|+.. +|..|  +|+.|.|.|+.....
T Consensus       135 ~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~--~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTV--NGHNCEVRKALSKQE  185 (196)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEE--TTEECEEEECC----
T ss_pred             EEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEE--CCEEEEEEecCChhH
Confidence            883        68999999999999999965 89999  899999999987653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.60  E-value=5e-15  Score=134.17  Aligned_cols=117  Identities=16%  Similarity=0.282  Sum_probs=88.9

Q ss_pred             eeeEEEEeCCCCccccccc-CCc------ceeecccccccch-----hhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhh
Q 014384           10 CHYLLIVYSHSVWPVQKKY-LPR------RLYVLGFRRSHSQ-----LSIAAFEAMMRPIFCGNFEYDARQSDLERLFRR   77 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~-~~~------~~~~~~~~~~~~~-----~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~   77 (425)
                      ..||||.|.+...+..+.. ++.      .+.+. .......     ..........++|||+|||..+|+++|.++|++
T Consensus        70 ~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~-~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~  148 (216)
T 2qfj_A           70 KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVG-RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA  148 (216)
T ss_dssp             CSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEE-CCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTT
T ss_pred             CceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEe-cCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhc
Confidence            3599999988766544442 111      11111 1111110     112234567799999999999999999999999


Q ss_pred             cCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           78 YGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        78 ~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+....
T Consensus       149 ~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~--~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDL--GGQYLRVGKAVTPP  206 (216)
T ss_dssp             SSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBC--SSSBCEEEECSSCS
T ss_pred             cCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEe--CCcEEEEEEecCCC
Confidence            9999999983        68999999999999999999999999  89999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.60  E-value=2e-15  Score=134.94  Aligned_cols=76  Identities=18%  Similarity=0.365  Sum_probs=70.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||..+|+++|.++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|.|.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~--~g~~l~v~  189 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQ  189 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            566999999999999999999999999999999883        68999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus       190 ~a~~~~  195 (198)
T 2yh0_A          190 RASVGA  195 (198)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            997643

>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=99.60  E-value=7.6e-16  Score=133.80  Aligned_cols=113  Identities=14%  Similarity=0.238  Sum_probs=85.1

Q ss_pred             eeEEEEeCCCCcccccccCCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---
Q 014384           11 HYLLIVYSHSVWPVQKKYLPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---   87 (425)
                      .||||.|.+...+..+......+....+....  ...........+|||+|||+.+|+++|.++|++||.|..|.|.   
T Consensus        46 g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~--~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~  123 (167)
T 2cjk_A           46 GFGFLSFEKPSSVDEVVKTQHILDGKVIDPKR--AIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK  123 (167)
T ss_dssp             SCEEEEESSTHHHHHHHHSCCEETTEECCCEE--CCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS
T ss_pred             ceEEEEEccHHHHHHHHhcccccCCeEccccc--ccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC
Confidence            59999999887665555422111111111111  1111223456799999999999999999999999999999983   


Q ss_pred             -----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           88 -----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        88 -----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                           +|||||+|.+.++|.+|++ |||..|  .|+.|.|.|+.+.
T Consensus       124 ~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~--~g~~i~V~~a~pk  166 (167)
T 2cjk_A          124 DTGQSRGFGFVTYDSADAVDRVCQ-NKFIDF--KDRKIEIKRAEPR  166 (167)
T ss_dssp             SSSTTSEEEEEEESSHHHHHHHHH-CSEECS--SSSCEEEEECCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHHh-CCCEEe--CCeEEEEeecCCC
Confidence                 5899999999999999996 899999  8999999998753

>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=99.60  E-value=1.2e-15  Score=121.97  Aligned_cols=76  Identities=17%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .+...++|||+|||+++|+++|+++|..||.| .|.|       ++|||||+|.+.++|++|| .+|+..|  .|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~--~gr~i~V   86 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANM--QHRYVEL   86 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCS--SSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeE--CCcEEEE
Confidence            34567899999999999999999999999955 7877       3789999999999999999 6899999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        87 ~~~~~~~   93 (102)
T 1wez_A           87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            9887544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=6.1e-15  Score=117.58  Aligned_cols=80  Identities=33%  Similarity=0.482  Sum_probs=73.3

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+..+|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.||+..|+|+.|.
T Consensus         7 ~~~~~~~~l~v~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 1x5s_A            7 GMASDEGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   85 (102)
T ss_dssp             CCCCCCSEEEEESC-CTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            34567799999999 8899999999999999999999995        46999999999999999999999999999999


Q ss_pred             EEEeeeCCC
Q 014384          217 VEYAVRDDD  225 (425)
Q Consensus       217 v~~a~~~~~  225 (425)
                      |.++.....
T Consensus        86 v~~a~~~~~   94 (102)
T 1x5s_A           86 VDQAGKSSD   94 (102)
T ss_dssp             EEEEECCCC
T ss_pred             EEECCCCCC
Confidence            999988643

>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=99.59  E-value=6.2e-16  Score=128.15  Aligned_cols=75  Identities=13%  Similarity=0.262  Sum_probs=67.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+++|+++|.++|..||.|.. +.|       ++|||||+|.+.++|++||. |||..|  +|+.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~--~gr~i~V   98 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYM--GNRFIQV   98 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS--TTSCBEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeE--CCcEEEE
Confidence            456689999999999999999999999999876 333       37999999999999999997 999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      .++...
T Consensus        99 ~~a~~~  104 (124)
T 1wel_A           99 HPITKK  104 (124)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998654

>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=99.59  E-value=8.5e-15  Score=116.08  Aligned_cols=78  Identities=27%  Similarity=0.469  Sum_probs=72.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            5 SSGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCSCEEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            456789999999 8899999999999999999999995        4799999999999999999999999999999999


Q ss_pred             EeeeCCC
Q 014384          219 YAVRDDD  225 (425)
Q Consensus       219 ~a~~~~~  225 (425)
                      ++..+..
T Consensus        84 ~a~~~~~   90 (99)
T 1whw_A           84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             EcCCCcc
Confidence            9988644

>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=99.59  E-value=7.9e-15  Score=117.58  Aligned_cols=81  Identities=21%  Similarity=0.311  Sum_probs=73.6

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.||+..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A            9 ISERNQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCCTTTEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             cccCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            345567899999999 8899999999999999999999995        4699999999999999999999999999999


Q ss_pred             EEEEeeeCCC
Q 014384          216 SVEYAVRDDD  225 (425)
Q Consensus       216 ~v~~a~~~~~  225 (425)
                      .|.++..+..
T Consensus        88 ~v~~a~~~~~   97 (105)
T 1x5u_A           88 RVNKASAHNK   97 (105)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEECCCCCc
Confidence            9999987643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.59  E-value=1.8e-14  Score=117.55  Aligned_cols=82  Identities=24%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+..+|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.||+..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDL-SPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   87 (115)
T ss_dssp             CCCSTTCEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            344567899999999 8899999999999999999999995        4699999999999999999999999999999


Q ss_pred             EEEEeeeCCCC
Q 014384          216 SVEYAVRDDDD  226 (425)
Q Consensus       216 ~v~~a~~~~~~  226 (425)
                      .|.|+..+...
T Consensus        88 ~V~~a~~~~~~   98 (115)
T 2dgo_A           88 RTNWATRKPPA   98 (115)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999876433

>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=99.59  E-value=3.6e-15  Score=121.81  Aligned_cols=73  Identities=29%  Similarity=0.481  Sum_probs=68.7

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..+|||+|| |..+++++|+++|.+||.|..|.|+      +|||||+|.+.++|.+|++.|||..|+|+.|.|.++...
T Consensus         5 ~~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCC-CCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            568999999 8899999999999999999999986      679999999999999999999999999999999998764

>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=99.59  E-value=8.9e-16  Score=115.21  Aligned_cols=67  Identities=18%  Similarity=0.445  Sum_probs=62.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.+.++|++|+. +++..|  .|+.|.|.+|
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-KKYHNV--GLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCB--TTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeE--CCEEEEEEEC
Confidence            69999999999999999999999999999883        7899999999999999995 588888  8999999875

>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=99.59  E-value=1.3e-14  Score=116.41  Aligned_cols=79  Identities=24%  Similarity=0.389  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCC---eEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTD---RVI  215 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g---~~i  215 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|.+|++.||+..|.|   +.|
T Consensus        11 ~~~~~~~l~v~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGML-NKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            3456899999999 8899999999999999999999996       5799999999999999999999999998   999


Q ss_pred             EEEEeeeCCC
Q 014384          216 SVEYAVRDDD  225 (425)
Q Consensus       216 ~v~~a~~~~~  225 (425)
                      .|.++..+..
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999988643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=1.2e-14  Score=115.21  Aligned_cols=78  Identities=21%  Similarity=0.432  Sum_probs=71.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++ ||+..|+|+.|.|
T Consensus         6 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            6 SGSKSNKIFVGGI-PHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCSSCCEEEEESC-CSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            4566789999999 8899999999999999999999995        5799999999999999998 9999999999999


Q ss_pred             EEeeeCCC
Q 014384          218 EYAVRDDD  225 (425)
Q Consensus       218 ~~a~~~~~  225 (425)
                      .++..+..
T Consensus        84 ~~a~~~~~   91 (99)
T 2dgs_A           84 KRAEPRDS   91 (99)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCcc
Confidence            99987543

>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=99.59  E-value=2.3e-15  Score=131.55  Aligned_cols=116  Identities=13%  Similarity=0.226  Sum_probs=83.2

Q ss_pred             eeeEEEEeCCCCccccccc-CCc-ceeecccccc--cchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEE
Q 014384           10 CHYLLIVYSHSVWPVQKKY-LPR-RLYVLGFRRS--HSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVD   85 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~-~~~-~~~~~~~~~~--~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~   85 (425)
                      ..||||.|.+...+..+.. +.. .+........  .............++|||+|||+.+|+++|.++|++||.|..|.
T Consensus        47 ~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~  126 (175)
T 3nmr_A           47 KGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECR  126 (175)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             ceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEE
Confidence            4599999988766444431 111 1110000000  00011112233568999999999999999999999999999999


Q ss_pred             Ee-------CCEEEEEEcCHHHHHHHHHhcCCCeecCC--CcEEEEEEec
Q 014384           86 MK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRK--GRRLRVEWTK  126 (425)
Q Consensus        86 i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~--gr~l~V~~a~  126 (425)
                      |.       +|||||+|.+.++|.+|+..|||..+. .  +++|.|.||.
T Consensus       127 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~-~g~~~~l~V~~ad  175 (175)
T 3nmr_A          127 ILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTM-EGCSSPMVVKFAD  175 (175)
T ss_dssp             EEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCC-TTCSSCCEEEECC
T ss_pred             EEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCccc-CCCCCCeEEEecC
Confidence            83       789999999999999999999998773 3  4999999974

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=9.7e-15  Score=116.01  Aligned_cols=79  Identities=19%  Similarity=0.413  Sum_probs=72.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.+.       +|||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus        12 ~~~~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   90 (100)
T 2do4_A           12 STSLEKHKLFISGL-PFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34566789999999 8899999999999999999999996       389999999999999999999999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++..+.
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9998753

>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=99.59  E-value=5.1e-15  Score=116.79  Aligned_cols=76  Identities=26%  Similarity=0.320  Sum_probs=71.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHH----hhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLE----RHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~----~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....++|||+|| |..+++++|+    ++|.+||.|..|.|+     ++||||+|.+.++|.+|++.|||..|+|+.|.|
T Consensus         6 ~~~~~~l~V~nL-~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            6 SGNGADVQVSNI-DYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             CSSCEEEEEESC-CTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            445689999999 8999999999    999999999999998     889999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      .++...
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            999764

>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=99.59  E-value=1e-14  Score=119.33  Aligned_cols=77  Identities=27%  Similarity=0.363  Sum_probs=71.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec-------cEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR-------NFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~-------g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..+..+|||+|| |..+++++|+++|++||.|..|.|..       |||||+|.+.++|.+|++.|||..|+|+.|.|++
T Consensus         4 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGL-NRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECC-TTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999 88999999999999999999999963       8999999999999999999999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98753

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=6.1e-15  Score=117.87  Aligned_cols=79  Identities=34%  Similarity=0.449  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.||+..|+|+.|.
T Consensus         8 ~~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            8 PDVDGMITLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SCCSCCCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCeEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34566799999999 8899999999999999999999985        57999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++....
T Consensus        87 V~~a~~~~   94 (103)
T 2dnm_A           87 VQVARYGR   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEECCcCC
Confidence            99998753

>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=99.59  E-value=2e-15  Score=130.87  Aligned_cols=112  Identities=21%  Similarity=0.283  Sum_probs=82.3

Q ss_pred             eeEEEEeCCCCccccccc-CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--
Q 014384           11 HYLLIVYSHSVWPVQKKY-LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--   87 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--   87 (425)
                      .||||.|.+...+..+.. ++..... ...................+|||+|||..+|+++|.++|++||.|..|.+.  
T Consensus        45 g~afV~f~~~~~A~~a~~~l~~~~~~-g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~  123 (167)
T 1fxl_A           45 GYGFVNYIDPKDAEKAINTLNGLRLQ-TKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD  123 (167)
T ss_dssp             EEEEEEESSHHHHHHHHHHHTTCEET-TEECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCccC-CceEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEec
Confidence            699999988776555442 1221111 110000000111233456899999999999999999999999999999883  


Q ss_pred             ------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc--EEEEEEe
Q 014384           88 ------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR--RLRVEWT  125 (425)
Q Consensus        88 ------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr--~l~V~~a  125 (425)
                            +|||||+|.+.++|.+|+..|||..|  .|+  .|.|.||
T Consensus       124 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~~~i~v~~A  167 (167)
T 1fxl_A          124 QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP--SGATEPITVKFA  167 (167)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC--TTCSSCCEEEEC
T ss_pred             CCCCCccceEEEEeCCHHHHHHHHHHhcCCcc--CCCccceEEEeC
Confidence                  68999999999999999999999999  675  5888876

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=8.3e-15  Score=114.94  Aligned_cols=78  Identities=29%  Similarity=0.488  Sum_probs=71.3

Q ss_pred             CCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       143 ~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      ......+.++|||+|| |..+++++|+++|++||.|..|.++        ++||||+|.+.++|.+|++.||+..|.|+.
T Consensus         9 ~~~~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   87 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRV   87 (94)
T ss_dssp             CCSCCCCTTSEEEESC-CTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            3445667889999999 8899999999999999999999995        479999999999999999999999999999


Q ss_pred             EEEEEee
Q 014384          215 ISVEYAV  221 (425)
Q Consensus       215 i~v~~a~  221 (425)
                      |.|.||+
T Consensus        88 l~v~~ak   94 (94)
T 2e5h_A           88 IKASIAI   94 (94)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999974

>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=1.5e-15  Score=128.96  Aligned_cols=77  Identities=22%  Similarity=0.402  Sum_probs=69.1

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEE-----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCC
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--------VDM-----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKG  117 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--------v~i-----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~g  117 (425)
                      ..+.++|||+|||+.+|+++|.++|..||.|..        |.+     .+|||||+|.+.++|.+|+..|||..|  .|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~--~g  119 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL--FG  119 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEE--TT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEe--CC
Confidence            456789999999999999999999999998865        333     379999999999999999999999999  89


Q ss_pred             cEEEEEEecccc
Q 014384          118 RRLRVEWTKHER  129 (425)
Q Consensus       118 r~l~V~~a~~~~  129 (425)
                      +.|.|.|+....
T Consensus       120 ~~l~V~~a~~~~  131 (143)
T 3egn_A          120 KPMVVQFARSAR  131 (143)
T ss_dssp             EECEEEECCCSC
T ss_pred             cEEEEEECCCCC
Confidence            999999997654

>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=99.59  E-value=6.1e-15  Score=113.40  Aligned_cols=74  Identities=35%  Similarity=0.573  Sum_probs=69.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|..|++.|||..|+|+.|.|.
T Consensus         4 ~~~~~~l~V~nl-~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            4 ATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCSSEEEEECC-CTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            456799999999 7889999999999999999999983        6799999999999999999999999999999999


Q ss_pred             Eee
Q 014384          219 YAV  221 (425)
Q Consensus       219 ~a~  221 (425)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            974

>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=99.58  E-value=1.1e-14  Score=116.57  Aligned_cols=79  Identities=25%  Similarity=0.450  Sum_probs=71.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      .....+..+|||+|| |..+++++|+++|.+|| |..|.|+         +|||||+|.+.++|.+|+ .||+..|+|+.
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~   85 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR   85 (104)
T ss_dssp             CCCSSSCEEEEEESC-CSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE
T ss_pred             CCCCCCCCEEEEeCC-CCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcE
Confidence            344567799999999 88999999999999999 9999985         569999999999999999 99999999999


Q ss_pred             EEEEEeeeCCC
Q 014384          215 ISVEYAVRDDD  225 (425)
Q Consensus       215 i~v~~a~~~~~  225 (425)
                      |.|.++..+..
T Consensus        86 l~V~~a~~~~~   96 (104)
T 1wi8_A           86 IRVDVADQAQD   96 (104)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEccCCCC
Confidence            99999988643

>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=99.58  E-value=5.6e-15  Score=114.12  Aligned_cols=76  Identities=24%  Similarity=0.387  Sum_probs=67.7

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+..+|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.|||..|+|+.|.|.
T Consensus         3 ~~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (87)
T 3bs9_A            3 LGSHFHVFVGDL-SPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   81 (87)
T ss_dssp             ---CEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCceEEEEeCC-CCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            346789999999 7889999999999999999999995        4699999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ++..+
T Consensus        82 ~a~~k   86 (87)
T 3bs9_A           82 WATRK   86 (87)
T ss_dssp             EEC--
T ss_pred             ecCCC
Confidence            99764

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.58  E-value=2.8e-15  Score=121.01  Aligned_cols=79  Identities=27%  Similarity=0.520  Sum_probs=72.8

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.+.+|||||+|.+.++|.+|++.|||..|+|+.|.|.++....
T Consensus        26 ~~~~~~~~l~V~nL-p~~~t~~~L~~~F~~~G~i~~v~i~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           26 EGELSNTRLFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             --CCSCSEEEECSS-CTTCCHHHHHHHHTTTSCCCEEEEETTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            34566789999999 88999999999999999999999999999999999999999999999999999999999998753

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.36  E-value=1.3e-16  Score=130.71  Aligned_cols=80  Identities=20%  Similarity=0.358  Sum_probs=71.9

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEE--------eCCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR--------VDM--------KSGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~--------v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      ...+.++|||+|||..+|+++|.++|++||.|..        |.|        .+|||||+|.+.++|.+|+..|||..|
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            3456789999999999999999999999999988        666        268999999999999999999999999


Q ss_pred             cCCCcEEEEEEeccccCC
Q 014384          114 GRKGRRLRVEWTKHERGI  131 (425)
Q Consensus       114 g~~gr~l~V~~a~~~~~~  131 (425)
                        .|+.|.|.++......
T Consensus        83 --~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           83 --SGNPIKVSFATRRADF   98 (116)
Confidence              8999999999876543

>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=99.58  E-value=3.7e-15  Score=121.70  Aligned_cols=78  Identities=17%  Similarity=0.349  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcC--CCccCCeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATN--MSKLTDRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~i~v~~a~  221 (425)
                      ...+.++|||+|| |..+++++|+++|++||.|+.|.|+  +|||||+|.+.++|.+|++.|+  +..|.|+.|.|.|+.
T Consensus        27 ~~~ps~~LfVgNL-p~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  105 (119)
T 2ad9_A           27 AGVPSRVIHIRKL-PIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN  105 (119)
T ss_dssp             CSSCCSEEEEESC-CTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEcc
Confidence            4567889999999 8889999999999999999999997  6899999999999999999887  468999999999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      .+.
T Consensus       106 ~k~  108 (119)
T 2ad9_A          106 HKE  108 (119)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            754

>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=99.58  E-value=1.1e-14  Score=115.44  Aligned_cols=80  Identities=25%  Similarity=0.372  Sum_probs=73.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.+.  ++||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A            9 EKTFTQRSRLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             SCCCCCTTEEEEESC-CTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCcCCCCCEEEEeCC-CCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            344567789999999 8889999999999999999999997  5899999999999999999999999999999999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      .+.
T Consensus        88 ~~~   90 (99)
T 2cpj_A           88 HSA   90 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.58  E-value=7.9e-15  Score=118.43  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=70.9

Q ss_pred             CCCCCCcEEEEEcCCCCC-CCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcC--CCccCCeEEEEEE
Q 014384          145 TNTRPSKTLFVINFDPYH-TRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATN--MSKLTDRVISVEY  219 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~-~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~i~v~~  219 (425)
                      ....+.++|||+|| |.. +++++|+++|++||.|..|.|.  +|||||+|.+.++|..|++.|+  +..|.|+.|.|.|
T Consensus        20 ~~~~p~~~l~V~NL-p~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           20 QKQELGRVIHLSNL-PHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             CSSCCCCEEEEESC-CCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             ccCCCCCEEEEeCC-CCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            34667899999999 786 9999999999999999999997  6899999999999999999886  4669999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        99 a~~~~  103 (112)
T 1x4f_A           99 SEKYK  103 (112)
T ss_dssp             ECSCS
T ss_pred             Ccccc
Confidence            98754

>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=99.58  E-value=1.3e-15  Score=133.63  Aligned_cols=116  Identities=15%  Similarity=0.196  Sum_probs=85.4

Q ss_pred             eeEEEEeCCCCcccccccCCcceeeccccc-ccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---
Q 014384           11 HYLLIVYSHSVWPVQKKYLPRRLYVLGFRR-SHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---   86 (425)
Q Consensus        11 ~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---   86 (425)
                      .||||.|.+...+..+..++........+. ..............++|||+|||..+|+++|.++|+.||.|..+..   
T Consensus        55 g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~  134 (175)
T 1fje_B           55 KFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGK  134 (175)
T ss_dssp             TEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSS
T ss_pred             cEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCC
Confidence            599999998776555443222211110000 0000001123345689999999999999999999999999988822   


Q ss_pred             eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           87 KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        87 ~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ++|||||+|.+.++|.+|+..|||..|  .|+.|.|.|+...
T Consensus       135 ~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~i~v~~a~~k  174 (175)
T 1fje_B          135 SKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTGEK  174 (175)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHTEEEE--TTEEEEEEECSSC
T ss_pred             CceEEEEEECCHHHHHHHHHHhCCCEE--CCeEEEEEecCCC
Confidence            379999999999999999999999999  8999999999753

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=5.7e-15  Score=117.77  Aligned_cols=79  Identities=33%  Similarity=0.505  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.||+..|+|+.|.
T Consensus         7 ~~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A            7 GMATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             CSCCCCSCEEEESC-CSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CcCCCCCEEEEeCC-CCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34567899999999 8889999999999999999999984        67999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++....
T Consensus        86 V~~a~~~~   93 (102)
T 2cqb_A           86 VNLAKPMR   93 (102)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99998764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.2e-15  Score=119.99  Aligned_cols=71  Identities=17%  Similarity=0.242  Sum_probs=65.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ..+|||+|||+++|+++|+++|+.| .|..|.|.       +|||||+|.+.++|++|| .||+..|  .|+.|.|..+.
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-KRNRMLM--IQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEE--TTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeE--CCeEEEEEECC
Confidence            4799999999999999999999999 89999883       899999999999999999 7999999  79999998876


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=2e-15  Score=122.12  Aligned_cols=75  Identities=16%  Similarity=0.140  Sum_probs=69.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ....+|||+|| |..+++++|+++|.+|| .|..+.+.    +|||||+|.+.++|.+|++.|||..|+|+.|.|+++..
T Consensus        26 ~~~~~l~VgnL-p~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           26 AKRYRITMKNL-PEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCEEEEEECS-SCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            34689999999 89999999999999999 89999985    79999999999999999999999999999999999875


Q ss_pred             C
Q 014384          223 D  223 (425)
Q Consensus       223 ~  223 (425)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.58  E-value=9.5e-15  Score=113.01  Aligned_cols=74  Identities=16%  Similarity=0.369  Sum_probs=69.3

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE---------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~---------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..++|||+|| |..+++++|+++|.+||.|..|.+         .+|||||+|.+.++|.+|++.|||..|+|+.|.|.+
T Consensus         3 ~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            3 KPTKVHIGRL-TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            4579999999 889999999999999999999988         478999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      +...
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            9764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=8.9e-15  Score=115.75  Aligned_cols=76  Identities=28%  Similarity=0.411  Sum_probs=70.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .+.++|||+|| |..+++++|+++|++||.|..|.|.           +|||||+|.+.++|.+|++.||+..|+|+.|.
T Consensus         3 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            3 SGSSGLFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            45789999999 8899999999999999999999885           36999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++....
T Consensus        82 V~~a~~~~   89 (98)
T 2cpf_A           82 VRISERAT   89 (98)
T ss_dssp             EECSSCSS
T ss_pred             EEEccCCC
Confidence            99998754

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.58  E-value=7.1e-16  Score=129.95  Aligned_cols=76  Identities=17%  Similarity=0.240  Sum_probs=67.0

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....++|||+|||+++|+++|+++|++|| |..|.|.       +|||||+|.+.++|++|| .||+..|  .|+.|.|
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l--~gR~i~V  117 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANM--QHRYIEL  117 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSS--SSCCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEE--CCEEEEE
Confidence            445678999999999999999999999999 6688883       799999999999999999 8999999  7999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus       118 ~~a~~~~  124 (139)
T 2hgn_A          118 FLNSTTG  124 (139)
T ss_dssp             EECCCSC
T ss_pred             EECCCCC
Confidence            9887654

>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=99.57  E-value=1.8e-14  Score=116.70  Aligned_cols=80  Identities=29%  Similarity=0.495  Sum_probs=73.2

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcC------CCc
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATN------MSK  209 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~------g~~  209 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++.||      +..
T Consensus         9 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCcCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            345567889999999 8899999999999999999999995        6799999999999999999999      999


Q ss_pred             cCCeEEEEEEeeeCC
Q 014384          210 LTDRVISVEYAVRDD  224 (425)
Q Consensus       210 ~~g~~i~v~~a~~~~  224 (425)
                      |+|+.|.|.++..+.
T Consensus        88 ~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRD  102 (111)
T ss_dssp             SSSCEEEEECCCCCC
T ss_pred             EcCEEEEEEECCCCc
Confidence            999999999998754

>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=99.57  E-value=1.1e-14  Score=125.65  Aligned_cols=79  Identities=27%  Similarity=0.410  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|+        ++||||+|.+.++|.+||+.||+..|+|+.|.|
T Consensus        35 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           35 LLKKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTCCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3456789999999 8899999999999999999999994        579999999999999999999999999999999


Q ss_pred             EEeeeCCC
Q 014384          218 EYAVRDDD  225 (425)
Q Consensus       218 ~~a~~~~~  225 (425)
                      +|+.....
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99987543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=5.9e-15  Score=116.28  Aligned_cols=76  Identities=26%  Similarity=0.474  Sum_probs=70.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEE-EEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV-RIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v-~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..| .|+        +|||||+|.+.++|.+|++.||+..|+|+.|.|.
T Consensus         3 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            3 SGSSGIFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             SCCCEEEEECC-CTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45789999999 8889999999999999999988 875        5799999999999999999999999999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      ++..+.
T Consensus        82 ~a~~~~   87 (96)
T 1x5t_A           82 YAFKKD   87 (96)
T ss_dssp             ESCCCC
T ss_pred             EecccC
Confidence            998754

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=9.7e-15  Score=114.74  Aligned_cols=79  Identities=35%  Similarity=0.451  Sum_probs=71.9

Q ss_pred             CCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       143 ~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      ......+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|++.||+..|+|+.
T Consensus         8 ~~~~~~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR   86 (95)
T ss_dssp             CCCSCCGGGCEEEESC-CSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            3445677899999999 8889999999999999999999985        469999999999999999999999999999


Q ss_pred             EEEEEeee
Q 014384          215 ISVEYAVR  222 (425)
Q Consensus       215 i~v~~a~~  222 (425)
                      |.|.+++.
T Consensus        87 l~v~~a~~   94 (95)
T 2cqc_A           87 IRVSGPSS   94 (95)
T ss_dssp             EEEECCSC
T ss_pred             EEEEecCC
Confidence            99999864

>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=99.57  E-value=1.1e-14  Score=111.30  Aligned_cols=72  Identities=24%  Similarity=0.438  Sum_probs=68.1

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .+|||+|| |..+++++|+++|.+||.|..+.++        +|||||+|.+.++|.+|+..|||..|+|+.|.|.++..
T Consensus         2 ~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            2 FNLFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECC-CTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            58999999 8899999999999999999999986        67999999999999999999999999999999999987


Q ss_pred             C
Q 014384          223 D  223 (425)
Q Consensus       223 ~  223 (425)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.4e-14  Score=116.42  Aligned_cols=78  Identities=23%  Similarity=0.448  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|+..|||..|+|+.|.|
T Consensus        19 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           19 RSVEGWILFVTGV-HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CBTTBEEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            3456789999999 8899999999999999999999996        579999999999999999999999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++..+.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
Confidence            9998753

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.56  E-value=1e-14  Score=113.94  Aligned_cols=78  Identities=26%  Similarity=0.388  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.+.      +|||||+|.+.++|.+|++.||+..|+|+.|.|.+
T Consensus         4 ~~~~~~~l~V~nl-p~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            4 GSSGACQIFVRNL-PFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSSCCEEEECSC-CTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3456789999999 8899999999999999999999986      58999999999999999999999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98754

>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=99.56  E-value=1e-14  Score=119.07  Aligned_cols=80  Identities=21%  Similarity=0.431  Sum_probs=72.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.||+..|+|+.|
T Consensus        19 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           19 QKEGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CCCCSTTCCEEEESC-CSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CcCCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            344556789999999 8899999999999999999999885        4699999999999999999999999999999


Q ss_pred             EEEEeeeCC
Q 014384          216 SVEYAVRDD  224 (425)
Q Consensus       216 ~v~~a~~~~  224 (425)
                      .|.|+..+.
T Consensus        98 ~V~~a~~~~  106 (115)
T 2cpz_A           98 KVQLKRSKN  106 (115)
T ss_dssp             EEECCCCSC
T ss_pred             EEEEcCCCC
Confidence            999998764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=2.6e-14  Score=114.90  Aligned_cols=81  Identities=25%  Similarity=0.554  Sum_probs=73.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHc-CCCccCCe
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDAT-NMSKLTDR  213 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l-~g~~~~g~  213 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|+         +|||||+|.+.++|.+|++.| |+..|.|+
T Consensus         9 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A            9 VPKKQTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SCCSSCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             cccCCCCCEEEEeCC-CCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            344567799999999 8899999999999999999999984         469999999999999999999 99999999


Q ss_pred             EEEEEEeeeCCC
Q 014384          214 VISVEYAVRDDD  225 (425)
Q Consensus       214 ~i~v~~a~~~~~  225 (425)
                      .|.|.++..+..
T Consensus        88 ~l~v~~a~~~~~   99 (107)
T 2cph_A           88 RLVLEWADSEVT   99 (107)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEeCCCCCC
Confidence            999999988643

>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=1.2e-15  Score=123.04  Aligned_cols=76  Identities=18%  Similarity=0.191  Sum_probs=68.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGK---VDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~---V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ......+|||+|||+++|+++|.++|..||.   |..|.|.       +|||||+|.+.++|++||. ||+..|  .|+.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~--~gr~   83 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYM--GQRY   83 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCS--SSSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCccee--CCeE
Confidence            4466789999999999999999999999998   8888883       7899999999999999997 999999  7999


Q ss_pred             EEEEEeccc
Q 014384          120 LRVEWTKHE  128 (425)
Q Consensus       120 l~V~~a~~~  128 (425)
                      |.|.++...
T Consensus        84 i~V~~a~~~   92 (107)
T 2lmi_A           84 VEVYEINNE   92 (107)
T ss_dssp             CCCEECCHH
T ss_pred             EEEEECCHH
Confidence            999988653

>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=99.56  E-value=9.8e-15  Score=115.10  Aligned_cols=75  Identities=20%  Similarity=0.467  Sum_probs=70.1

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      |.++|||+|| |..+++++|+++|.+||.|..|.+.        +|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus         1 P~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   79 (96)
T 2x1f_A            1 PSRVVYLGSI-PYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS   79 (96)
T ss_dssp             CCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEc
Confidence            4689999999 8899999999999999999999995        579999999999999999999999999999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        80 ~~~~   83 (96)
T 2x1f_A           80 SNSD   83 (96)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8753

>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=99.56  E-value=1.4e-14  Score=111.43  Aligned_cols=75  Identities=23%  Similarity=0.413  Sum_probs=69.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc-CCCccCCeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT-NMSKLTDRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~i~v~~a~  221 (425)
                      ...+..+|||+|| |..+++++|+++|.+||.|..|.+.  +|||||+|.+.++|.+|+..| ++..++|+.|.|+|++
T Consensus         8 ~~~~~~~l~V~~l-~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGL-GDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECC-TTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCC-CCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            3466789999999 7889999999999999999999997  589999999999999999999 9999999999999974

>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=99.56  E-value=1.4e-14  Score=116.51  Aligned_cols=76  Identities=20%  Similarity=0.349  Sum_probs=70.9

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+..+|||+|| |..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|.+|++.||+..|.|+.|.|
T Consensus        24 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            44567899999999 8899999999999999999999986       679999999999999999999999999999999


Q ss_pred             EEee
Q 014384          218 EYAV  221 (425)
Q Consensus       218 ~~a~  221 (425)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.56  E-value=3.6e-14  Score=119.76  Aligned_cols=79  Identities=25%  Similarity=0.410  Sum_probs=72.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| +..+++++|+++|+.||.|..|.|.        +|||||+|.+.++|.+|++.||+..|.|+.|.
T Consensus        37 ~~~~~~~~l~V~nL-p~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           37 PEPDVLRNLMVNYI-PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             CCTTTTSEEEEESC-STTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            44566789999999 8899999999999999999999985        67999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++....
T Consensus       116 v~~a~~~~  123 (139)
T 1u6f_A          116 VALAASGH  123 (139)
T ss_dssp             EEESSCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=99.56  E-value=1.4e-14  Score=117.11  Aligned_cols=79  Identities=22%  Similarity=0.437  Sum_probs=72.8

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|+..|||..|+|+.|.
T Consensus        21 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           21 QRSVEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             CCBTTBEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34566789999999 8899999999999999999999995        58999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++..+.
T Consensus       100 V~~a~~~~  107 (110)
T 1oo0_B          100 VDWCFVKG  107 (110)
T ss_dssp             EEESEESS
T ss_pred             EEEcccCC
Confidence            99998864

>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=99.56  E-value=7e-15  Score=115.19  Aligned_cols=77  Identities=22%  Similarity=0.380  Sum_probs=69.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCc-EEEEEE-eccEEEEEEcCHHHHHHHHHHcCC-CccCCeEEEEEEeeeC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGK-IISVRI-RRNFAFVQYEVQEDATRALDATNM-SKLTDRVISVEYAVRD  223 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~-v~~v~~-~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~i~v~~a~~~  223 (425)
                      ..+.++|||+|| |..+++++|+++|.+||. |..+.+ .+|||||+|.+.++|.+|++.||| ..|+|+.|.|.++..+
T Consensus         5 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~vv~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~   83 (93)
T 2cqh_A            5 SSGMNKLYIGNL-SPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   83 (93)
T ss_dssp             CCCCCCEEEECC-CTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHHcCCceEEEEEcCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCc
Confidence            456789999999 889999999999999999 665555 489999999999999999999999 9999999999999875


Q ss_pred             C
Q 014384          224 D  224 (425)
Q Consensus       224 ~  224 (425)
                      .
T Consensus        84 ~   84 (93)
T 2cqh_A           84 K   84 (93)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.56  E-value=1.4e-14  Score=117.01  Aligned_cols=77  Identities=17%  Similarity=0.414  Sum_probs=72.0

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.|.  +|||||+|.+.++|.+|+..|||..|+|+.|.|.|+....
T Consensus        22 ~~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           22 SPKNCTVYCGGI-ASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             CSSCCEEEEECC-SSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            456789999999 7899999999999999999999997  6899999999999999999999999999999999998864

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=3.6e-14  Score=113.38  Aligned_cols=78  Identities=28%  Similarity=0.466  Sum_probs=70.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+.++|||+|| |..+++++|+++|.+|| |..|.|+        +|||||+|.+.++|.+|+ .||+..|+|+.|
T Consensus         9 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A            9 ELPTEPPYTAYVGNL-PFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             CCCSSSCEEEEEESC-CTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCCCCeEEEEeCC-CCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            344566799999999 89999999999999997 9999985        569999999999999999 899999999999


Q ss_pred             EEEEeeeCC
Q 014384          216 SVEYAVRDD  224 (425)
Q Consensus       216 ~v~~a~~~~  224 (425)
                      .|.++....
T Consensus        86 ~V~~a~~~~   94 (103)
T 2dng_A           86 RVDIAEGRK   94 (103)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEecCCC
Confidence            999998754

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=7.5e-14  Score=113.58  Aligned_cols=78  Identities=27%  Similarity=0.364  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|.       ++||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANL-DYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            34566789999999 8899999999999999999999986       479999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      .++...
T Consensus        89 ~~a~~~   94 (114)
T 2do0_A           89 KMDERA   94 (114)
T ss_dssp             EECSCC
T ss_pred             EEcccC
Confidence            998764

>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=99.55  E-value=1.2e-14  Score=137.58  Aligned_cols=72  Identities=19%  Similarity=0.325  Sum_probs=68.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCC-CcEEEEEEec
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRK-GRRLRVEWTK  126 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~-gr~l~V~~a~  126 (425)
                      ..++|||+||+..+|+++|.++|++||.|..|.|.   +|||||+|.+.++|.+|+..|||..|  . |+.|.|.|++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~~g~~l~v~~ak  281 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKI--TQNNAMKISFAK  281 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEe--CCCCEEEEEEec
Confidence            46889999999999999999999999999999994   59999999999999999999999999  6 9999999986

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.55  E-value=3.2e-15  Score=119.30  Aligned_cols=74  Identities=20%  Similarity=0.556  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ...++|||+|||+.+|+++|.++|++||.|..|.|.       +|||||+|.+.++|++|+.  ++..|  +|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~--~g~~l~v~~   82 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINF--HGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEE--TTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeE--CCEEEEEEE
Confidence            456899999999999999999999999999999983       6999999999999999996  99999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus        83 a~~~~   87 (102)
T 2xs2_A           83 AIRKQ   87 (102)
T ss_dssp             EEECC
T ss_pred             CCcCc
Confidence            97654

>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=99.55  E-value=2.4e-14  Score=116.06  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=72.6

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHH---hhhccCCcEEEEEEec-----------cEEEEEEcCHHHHHHHHHHcCCCc
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLE---RHFEPYGKIISVRIRR-----------NFAFVQYEVQEDATRALDATNMSK  209 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~---~~f~~~G~v~~v~~~~-----------g~afV~f~~~~~A~~A~~~l~g~~  209 (425)
                      .......++|||+|| |..+++++|.   ++|.+||.|..|.|+.           |||||+|.+.++|.+|++.|||..
T Consensus         9 ~~r~~~~~~l~V~nL-p~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   87 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGL-SQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV   87 (111)
T ss_dssp             CCCCCCSSCEEEEEE-CTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             cccccCCCEEEEECC-CCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE
Confidence            344566789999999 8899999999   9999999999999962           699999999999999999999999


Q ss_pred             cCCeEEEEEEeeeCC
Q 014384          210 LTDRVISVEYAVRDD  224 (425)
Q Consensus       210 ~~g~~i~v~~a~~~~  224 (425)
                      |+|+.|.|.+|..+.
T Consensus        88 ~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           88 VDGRTLKASLGTTKY  102 (111)
T ss_dssp             ETTEEEEEESCCCCS
T ss_pred             ECCEEEEEEeccccc
Confidence            999999999998864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.55  E-value=2.1e-14  Score=113.85  Aligned_cols=78  Identities=18%  Similarity=0.270  Sum_probs=70.8

Q ss_pred             CCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE--------EEEe--------ccEEEEEEcCHHHHHHHHHHcC
Q 014384          143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS--------VRIR--------RNFAFVQYEVQEDATRALDATN  206 (425)
Q Consensus       143 ~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~--------v~~~--------~g~afV~f~~~~~A~~A~~~l~  206 (425)
                      ......+.++|||+|| |..+++++|+++|.+||.|..        |.+.        +|||||+|.+.++|.+|++.||
T Consensus         6 ~~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            6 HHHSHSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             SCCSCCCCSEEEEECC-CSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC
Confidence            3445677899999999 889999999999999999998        8774        5799999999999999999999


Q ss_pred             CCccCCeEEEEEEee
Q 014384          207 MSKLTDRVISVEYAV  221 (425)
Q Consensus       207 g~~~~g~~i~v~~a~  221 (425)
                      |..|+|+.|.|++|+
T Consensus        85 g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           85 GKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TCBSSSSBCEEEECC
T ss_pred             CCEeCCcEEEEEecC
Confidence            999999999999874

>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=99.55  E-value=5.6e-15  Score=114.56  Aligned_cols=74  Identities=22%  Similarity=0.358  Sum_probs=63.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ...++|||+|||+++|+++|.++|++||+|..|.|.   +|||||+|.+.++|++|    ++..+.+.|+.|.|.++...
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCC
Confidence            457899999999999999999999999999999994   89999999999999754    44444338999999998765


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        79 ~   79 (88)
T 1wf0_A           79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=2.1e-14  Score=116.76  Aligned_cols=80  Identities=18%  Similarity=0.232  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEE--------EEEEe--------ccEEEEEEcCHHHHHHHHHHcCCC
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII--------SVRIR--------RNFAFVQYEVQEDATRALDATNMS  208 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~--------~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~  208 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|.        .|.|.        +|||||+|.+.++|.+|++.||+.
T Consensus        10 ~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A           10 DEDSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCEEEEECC-CTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             ccCCCCCEEEEcCC-CCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            44567899999999 89999999999999999998        57774        579999999999999999999999


Q ss_pred             ccCCeEEEEEEeeeCCC
Q 014384          209 KLTDRVISVEYAVRDDD  225 (425)
Q Consensus       209 ~~~g~~i~v~~a~~~~~  225 (425)
                      .|.|+.|.|.++.....
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999988643

>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=99.55  E-value=2.2e-14  Score=115.22  Aligned_cols=80  Identities=28%  Similarity=0.412  Sum_probs=72.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCcc---CCe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKL---TDR  213 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~---~g~  213 (425)
                      ....+..+|||+|| |..+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.||+..+   .|+
T Consensus         8 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            8 MKDHDAIKLFIGQI-PRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             CCCTTCEEEEEESC-CTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            34566789999999 8899999999999999999999985        47999999999999999999999988   899


Q ss_pred             EEEEEEeeeCCC
Q 014384          214 VISVEYAVRDDD  225 (425)
Q Consensus       214 ~i~v~~a~~~~~  225 (425)
                      .|.|.++..+..
T Consensus        87 ~l~v~~a~~~~~   98 (106)
T 2dgp_A           87 PIQVKPADSESR   98 (106)
T ss_dssp             CCEEEECCCCSC
T ss_pred             eEEEEECCcccc
Confidence            999999987643

>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=99.54  E-value=1.4e-14  Score=117.54  Aligned_cols=74  Identities=19%  Similarity=0.279  Sum_probs=69.6

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..++|||+|| |..+++++|+++|.+||.|..|.|+  ++||||+|.+.++|..|++.|||..|+|+.|.|+|+...
T Consensus         9 ~~~~l~V~nL-p~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            9 SKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            3579999999 8899999999999999999999995  789999999999999999999999999999999999874

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.1e-14  Score=117.65  Aligned_cols=79  Identities=34%  Similarity=0.541  Sum_probs=72.7

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      .....+.++|||+|| +..+++++|+++|++||.|..|.+.      +|||||+|.+.++|.+|++.|||..|+|+.|.|
T Consensus        23 ~~~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           23 TENKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             CSCTTCCCEEEEESC-CTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCCEEEEECC-CCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344567789999999 8899999999999999999999996      789999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      .++..+
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=7.2e-14  Score=110.31  Aligned_cols=77  Identities=30%  Similarity=0.456  Sum_probs=70.2

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ....+.++|||+||   .+++++|+++|.+||.|..|.|.  +|||||+|.+.++|.+|+..||+..|+|+.|.|.++..
T Consensus        10 ~~~~~~~~l~V~n~---~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE---DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             CCCCCCSEEEEECS---SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             CCCCCCCEEEEcCC---CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            34556789999997   57899999999999999999996  78999999999999999999999999999999999977


Q ss_pred             CC
Q 014384          223 DD  224 (425)
Q Consensus       223 ~~  224 (425)
                      +.
T Consensus        87 ~~   88 (97)
T 1x5p_A           87 QP   88 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2e-14  Score=113.51  Aligned_cols=77  Identities=23%  Similarity=0.386  Sum_probs=69.5

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ......++|||+|| |..+++++|+++|.+||.|. +.+.    +|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus        14 ~~~~~~~~l~V~nL-~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           14 EGAPLAADVYVGNL-PRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SSSCCCCEEEEECC-CTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCCCEEEEeCC-CCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34556789999999 88999999999999999986 5554    789999999999999999999999999999999999


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      ..+
T Consensus        92 ~~~   94 (97)
T 2e5j_A           92 RQQ   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=3.1e-14  Score=113.28  Aligned_cols=78  Identities=27%  Similarity=0.377  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE----eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI----RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..+..    .+|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           11 WSGESKTLVLSNL-SYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CSCCCSEEEEESC-CTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            4567899999999 888999999999999999844333    36899999999999999999999999999999999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      .+.
T Consensus        90 ~~~   92 (101)
T 2fc9_A           90 PRG   92 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            753

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=6.9e-14  Score=114.22  Aligned_cols=79  Identities=28%  Similarity=0.406  Sum_probs=71.6

Q ss_pred             CCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       143 ~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      ......+.++|||+|| |..+++++|+++|.+||.|..|.|+        ++||||+|.+.++|.+|++.|++ .|.|+.
T Consensus        10 ~~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CCCCSCSSSEEEEECC-CSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCcCCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            3445667899999999 8899999999999999999999995        46999999999999999999998 899999


Q ss_pred             EEEEEeeeC
Q 014384          215 ISVEYAVRD  223 (425)
Q Consensus       215 i~v~~a~~~  223 (425)
                      |.|.++...
T Consensus        88 l~V~~a~~~   96 (116)
T 2cqd_A           88 ANVNLAYLG   96 (116)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcccC
Confidence            999999764

>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=99.54  E-value=3e-14  Score=114.98  Aligned_cols=78  Identities=23%  Similarity=0.418  Sum_probs=71.5

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|..|++.|||..|+|+.|.
T Consensus        21 ~~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           21 KGSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CSCSSCEEEEEECC-CSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34556789999999 7889999999999999999999985        57999999999999999999999999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.++..+
T Consensus       100 V~~a~~k  106 (108)
T 2jrs_A          100 VGHVTER  106 (108)
T ss_dssp             EECSCSS
T ss_pred             EEEcccC
Confidence            9998765

>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=99.54  E-value=1.5e-14  Score=113.64  Aligned_cols=77  Identities=26%  Similarity=0.324  Sum_probs=70.3

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+..+|||+|| |..+++++|+++|.+||.|..|.|+       +|||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus        11 ~~~~~~~~l~v~nl-p~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           11 AQEEADRTVFVGNL-EARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             -CTTGGGEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            34566789999999 7889999999999999999999996       579999999999999999999999999999999


Q ss_pred             EEeee
Q 014384          218 EYAVR  222 (425)
Q Consensus       218 ~~a~~  222 (425)
                      .++..
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99864

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.54  E-value=9.6e-15  Score=116.27  Aligned_cols=73  Identities=27%  Similarity=0.383  Sum_probs=68.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ++|||+|| |..+++++|+++|++||.|..|.+.   +|||||+|.+.++|.+|++.||+..|+|+.|.|.++....
T Consensus         1 ~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNL-GTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECC-CSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            48999999 8899999999999999999999995   6899999999999999999999999999999999998864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2.2e-14  Score=114.73  Aligned_cols=79  Identities=18%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhcc-CCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCc-cCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEP-YGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSK-LTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~-~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~i~  216 (425)
                      ...+..+|||+|| |..+++++|+++|.+ ||.|..|.|+       +|||||+|.+.++|.+|++.||+.. |+|+.|.
T Consensus         5 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDL-TPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECC-CTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCC-CCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456789999999 889999999999999 9999999995       6799999999999999999999999 9999999


Q ss_pred             EEEeeeCCC
Q 014384          217 VEYAVRDDD  225 (425)
Q Consensus       217 v~~a~~~~~  225 (425)
                      |.++.....
T Consensus        84 v~~a~~~~~   92 (104)
T 2dhg_A           84 LSVAIPKAS   92 (104)
T ss_dssp             CCBCCCCCS
T ss_pred             EEEccCCCc
Confidence            999977543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=2.2e-14  Score=118.96  Aligned_cols=77  Identities=16%  Similarity=0.290  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHH----hhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLE----RHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~----~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ...+.++|||+|| +..+++++|+    ++|++||.|..|.+.     +|||||+|.+.++|..|+..|||..|.|+.|.
T Consensus        25 ~~~p~~~LfV~nL-~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           25 HTEPSQVVLITNI-NPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CCSCCSEEEEESC-CTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            3566889999999 7888898876    699999999999885     68999999999999999999999999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.|+..+
T Consensus       104 V~~a~~~  110 (127)
T 2a3j_A          104 ITFSETP  110 (127)
T ss_dssp             EEECCCC
T ss_pred             EEEccCc
Confidence            9999875

>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=99.53  E-value=2.2e-14  Score=113.13  Aligned_cols=78  Identities=27%  Similarity=0.502  Sum_probs=71.3

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHH----hhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLE----RHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~----~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ...+.++|||+|| |..+++++|+    ++|.+||.|..|.+.     +|||||+|.+.++|..|++.|||..|+|+.|.
T Consensus         4 ~~~~~~~l~V~nL-p~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            4 ETRPNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             --CCCSEEEEESC-CTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            3467799999999 8899999999    999999999999986     68999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++..+.
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99998753

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.53  E-value=9.6e-15  Score=114.83  Aligned_cols=75  Identities=25%  Similarity=0.427  Sum_probs=66.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCc--EEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCc----cCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGK--IISVRIR--------RNFAFVQYEVQEDATRALDATNMSK----LTD  212 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~--v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~----~~g  212 (425)
                      ...-.+|||+|| |..+|+++|+++|++||.  |..|.++        +|||||+|.+.++|.+|++.|||..    |+|
T Consensus         6 ~~~m~tlfV~nL-~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            6 HHHMDTIILRNI-APHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SCCCCEEEEESC-CTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             CCccCEEEEeCC-CCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            345579999999 789999999999999995  5677764        6799999999999999999999974    899


Q ss_pred             eEEEEEEeee
Q 014384          213 RVISVEYAVR  222 (425)
Q Consensus       213 ~~i~v~~a~~  222 (425)
                      +.|.|+||+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999874

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=8.1e-15  Score=120.84  Aligned_cols=74  Identities=14%  Similarity=0.209  Sum_probs=65.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCe----eEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKV----DRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V----~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      .....+|||+|||+++|+++|+++|++||.|    ..|.|       ++|||||+|.+.++|++||.. |+..|  .|+.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l--~gR~   96 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLL--GKRY   96 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEES--SSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCee--CCeE
Confidence            4667899999999999999999999999975    57777       379999999999999999964 99988  7999


Q ss_pred             EEEEEecc
Q 014384          120 LRVEWTKH  127 (425)
Q Consensus       120 l~V~~a~~  127 (425)
                      |.|..+..
T Consensus        97 i~V~~a~~  104 (123)
T 2dha_A           97 IELFRSTA  104 (123)
T ss_dssp             ECCEEECH
T ss_pred             EEEEECCH
Confidence            99988754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=4.3e-14  Score=112.64  Aligned_cols=81  Identities=26%  Similarity=0.440  Sum_probs=70.5

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+.++|||+|| |..+++++|+++|.+|+.|..+...     +|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus         9 ~~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A            9 NARSQPSKTLFVKGL-SEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSSSCCCSSEEEECC-CTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCCEEEEeCC-CCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345567899999999 8899999999999999766555442     5899999999999999999999999999999999


Q ss_pred             EeeeCCC
Q 014384          219 YAVRDDD  225 (425)
Q Consensus       219 ~a~~~~~  225 (425)
                      ++..+..
T Consensus        88 ~a~~~~~   94 (102)
T 2fc8_A           88 WAKPKGE   94 (102)
T ss_dssp             ECCCCCS
T ss_pred             EecCCCC
Confidence            9988643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.53  E-value=3.5e-15  Score=116.58  Aligned_cols=74  Identities=24%  Similarity=0.429  Sum_probs=66.6

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcC-CCccCCeEEEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIR--------RNFAFVQYEVQEDATRALDATN-MSKLTDRVISVEY  219 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~i~v~~  219 (425)
                      +++|||+|| |..+++++|+++|++|| .|..|.|+        +|||||+|.+.++|.+|++.|+ +..|+|+.|.|+|
T Consensus         1 S~~i~v~nL-p~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~   79 (91)
T 2lxi_A            1 SNIVMLRML-PQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY   79 (91)
T ss_dssp             CCEEEEETC-CSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEEC
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEE
Confidence            368999999 89999999999999999 79998884        6899999999999999999874 5679999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      |.++.
T Consensus        80 a~~~~   84 (91)
T 2lxi_A           80 SDPKP   84 (91)
T ss_dssp             CCSCC
T ss_pred             cCCCC
Confidence            98753

>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=99.53  E-value=2.1e-14  Score=119.71  Aligned_cols=80  Identities=35%  Similarity=0.519  Sum_probs=73.0

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.|||..|+|+.|
T Consensus        40 ~~~~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           40 RANPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             SSCCCCSSCBCEETC-TTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            345567899999999 8899999999999999999999995        5799999999999999999999999999999


Q ss_pred             EEEEeeeCC
Q 014384          216 SVEYAVRDD  224 (425)
Q Consensus       216 ~v~~a~~~~  224 (425)
                      .|.|+..+.
T Consensus       119 ~V~~a~~~~  127 (129)
T 2kxn_B          119 RVDFSITKR  127 (129)
T ss_dssp             EESCCSSSS
T ss_pred             EEEEecCCC
Confidence            999997753

>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=99.53  E-value=1.4e-14  Score=132.95  Aligned_cols=75  Identities=23%  Similarity=0.339  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCC-CcEEEEEEec
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRK-GRRLRVEWTK  126 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~-gr~l~V~~a~  126 (425)
                      .+.++|||+|||..+|+++|.++|.+|| +|..|.|   .+|||||+|.+.++|.+|+..|||..|  . |+.|.|.|++
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~~g~~l~v~~a~  226 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL--GENHHLRVSFSK  226 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBS--SSSCBCEEEECS
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCcc--CCCCeEEEEEec
Confidence            3468999999999999999999999999 9999999   589999999999999999999999999  6 9999999987


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus       227 ~~  228 (229)
T 2adc_A          227 ST  228 (229)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.52  E-value=1.1e-14  Score=115.81  Aligned_cols=75  Identities=16%  Similarity=0.235  Sum_probs=69.2

Q ss_pred             CCCcEEEEEcCCCC------CCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCC-
Q 014384          148 RPSKTLFVINFDPY------HTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTD-  212 (425)
Q Consensus       148 ~~~~~l~V~nl~p~------~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g-  212 (425)
                      ...++|||+|| |.      .+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.|||..|.| 
T Consensus         4 ~~~~~vfV~nL-p~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            4 GSDQYIVVNGA-PVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             CGGGEEEEESC-CCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CcCcEEEEeCC-CcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34689999999 88      88899999999999999999985        6899999999999999999999999999 


Q ss_pred             eEEEEEEeeeC
Q 014384          213 RVISVEYAVRD  223 (425)
Q Consensus       213 ~~i~v~~a~~~  223 (425)
                      +.|.|.++.+.
T Consensus        83 r~l~V~~a~~~   93 (100)
T 3ns6_A           83 HRLFLYTMKDV   93 (100)
T ss_dssp             CBCEEEESHHH
T ss_pred             eEEEEEECchh
Confidence            99999998653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.52  E-value=3.9e-14  Score=116.06  Aligned_cols=76  Identities=24%  Similarity=0.450  Sum_probs=69.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|++.|||..|+|+.|.
T Consensus        35 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           35 IEGPEGCNLFIYHL-PQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             CCCCCSEEEEEECS-CTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34566789999999 8899999999999999999999995        57999999999999999999999999999999


Q ss_pred             EEEee
Q 014384          217 VEYAV  221 (425)
Q Consensus       217 v~~a~  221 (425)
                      |+|++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99874

>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=99.52  E-value=1.4e-14  Score=119.76  Aligned_cols=75  Identities=15%  Similarity=0.211  Sum_probs=65.5

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCee--EEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVD--RVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~--~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      ......+|||+|||+++|+++|+++|+.| .|.  .|.|.       +|||||+|.+.++|++||. +++..|  .|+.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l--~gR~I  113 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERI--GHRYI  113 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCB--TTBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEE--CCEEE
Confidence            34567899999999999999999999999 566  78873       7999999999999999995 578888  79999


Q ss_pred             EEEEeccc
Q 014384          121 RVEWTKHE  128 (425)
Q Consensus       121 ~V~~a~~~  128 (425)
                      .|.++...
T Consensus       114 ~V~~a~~~  121 (126)
T 2hgm_A          114 EVFKSSQE  121 (126)
T ss_dssp             CCEEECHH
T ss_pred             EEEECCHH
Confidence            99988643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.52  E-value=1.4e-14  Score=132.60  Aligned_cols=80  Identities=20%  Similarity=0.415  Sum_probs=70.0

Q ss_pred             hcCCCceEEEcCCCCCC---------CHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecC---
Q 014384           50 FEAMMRPIFCGNFEYDA---------RQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGR---  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~---------t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~---  115 (425)
                      .....++|||+||+..+         |+++|.++|++||+|+.|.|  .+|||||+|.+.++|+.|+++|||..|.+   
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         79999999999999999998  48999999999999999999999998822   


Q ss_pred             -------CCcEEEEEEecccc
Q 014384          116 -------KGRRLRVEWTKHER  129 (425)
Q Consensus       116 -------~gr~l~V~~a~~~~  129 (425)
                             .|+.|.|.||....
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC---
T ss_pred             ccccccCCCCEEEEEEccCCC
Confidence                   58999999998654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3.3e-14  Score=109.36  Aligned_cols=76  Identities=22%  Similarity=0.371  Sum_probs=67.7

Q ss_pred             CCCCcE-EEEEcCCCCCCCHHH----HHhhhccCC-cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          147 TRPSKT-LFVINFDPYHTRTRD----LERHFEPYG-KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       147 ~~~~~~-l~V~nl~p~~~~~~~----L~~~f~~~G-~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .+|..+ |||.|| |+.+++++    |.++|.+|| +|..|.  .|+|||+|.+.++|..|++.|||..|.|+.|.|.||
T Consensus         5 ~~p~~T~lYV~NL-~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt--gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A   81 (96)
T 2diu_A            5 SSGCHTLLYVYNL-PANKDGKSVSNRLRRLSDNCGGKVLSIT--GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFT   81 (96)
T ss_dssp             CCCSSEEEEEESC-CTTSCHHHHHHHHHHHHHTTTCCEEECC--TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESS
T ss_pred             CCCcceEEEEeCC-CCcCCHHHHHHHHHHHHHHcCCeeEEEe--cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEec
Confidence            455666 899999 89999887    558999994 999994  499999999999999999999999999999999999


Q ss_pred             eeCCC
Q 014384          221 VRDDD  225 (425)
Q Consensus       221 ~~~~~  225 (425)
                      +...+
T Consensus        82 ~~~sd   86 (96)
T 2diu_A           82 PKNRE   86 (96)
T ss_dssp             CCSCC
T ss_pred             CCCcc
Confidence            98654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=1.5e-14  Score=115.09  Aligned_cols=75  Identities=19%  Similarity=0.333  Sum_probs=69.7

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ....++|||+|| +..+++++|+++|.+||.|..|.+.  +|||||+|.+.++|..|+..|||..|+|+.|.|.|++.
T Consensus        24 ~~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           24 PPRVTTAYIGNI-PHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             CSSCCEEEEESC-CTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCCEEEEcCC-CcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            345689999999 7899999999999999999999996  78999999999999999999999999999999999865

>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=99.52  E-value=2.7e-14  Score=115.43  Aligned_cols=79  Identities=14%  Similarity=0.224  Sum_probs=70.7

Q ss_pred             CCCCCcEEEE--EcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCcc-----CCeEEE
Q 014384          146 NTRPSKTLFV--INFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKL-----TDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V--~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~-----~g~~i~  216 (425)
                      ...+..+|||  +|| +..+++++|+++|++||.|..|.|+  +|||||+|.+.++|.+|++.|||..|     .|.+|.
T Consensus        21 ~~~pt~~L~V~Ng~L-~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGL-GNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTG-GGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCC-CCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            3456789999  669 7899999999999999999999987  67999999999999999999999988     689999


Q ss_pred             EEEeeeCCC
Q 014384          217 VEYAVRDDD  225 (425)
Q Consensus       217 v~~a~~~~~  225 (425)
                      |.|+..-..
T Consensus       100 v~~a~~~p~  108 (114)
T 2cq2_A          100 LNFVEKVQW  108 (114)
T ss_dssp             EEEESCCCC
T ss_pred             EEecccCcc
Confidence            999987543

>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=99.51  E-value=4.8e-14  Score=114.95  Aligned_cols=79  Identities=27%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcE----EEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI----ISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v----~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|    ..+.+.    +|||||+|.+.++|..|++.||+..|+|+.|.
T Consensus        20 ~~~~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           20 NPGEPNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CCCSCCSEEEEECC-CTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34457799999999 8899999999999999998    566654    68999999999999999999999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.++....
T Consensus        99 v~~a~~~~  106 (115)
T 2cpx_A           99 IEFGKNKK  106 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEccCCC
Confidence            99998864

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=3.2e-14  Score=114.04  Aligned_cols=80  Identities=21%  Similarity=0.336  Sum_probs=72.2

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|++. ++..|+|+.|
T Consensus        10 ~~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   87 (105)
T 2dh8_A           10 NSGADEIGKLFVGGL-DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI   87 (105)
T ss_dssp             CCCSSSSSEECCBSC-CTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEE
T ss_pred             cCCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEE
Confidence            345667899999999 8899999999999999999999985        36999999999999999998 9999999999


Q ss_pred             EEEEeeeCCC
Q 014384          216 SVEYAVRDDD  225 (425)
Q Consensus       216 ~v~~a~~~~~  225 (425)
                      .|.++..+..
T Consensus        88 ~V~~a~~~~~   97 (105)
T 2dh8_A           88 DPKPCTPRGM   97 (105)
T ss_dssp             BCCCSCCSSC
T ss_pred             EEEEccCCCC
Confidence            9999987643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.51  E-value=1.5e-14  Score=129.51  Aligned_cols=75  Identities=23%  Similarity=0.339  Sum_probs=70.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCC-CcEEEEEEec
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRK-GRRLRVEWTK  126 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~-gr~l~V~~a~  126 (425)
                      .+.++|||+|||..+|+++|.++|..|| .|..|.|   .+|+|||+|.+.++|.+|+..|||..|  . |+.|.|.|++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~~g~~l~v~~a~  195 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL--GENHHLRVSFSK  195 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCC--SSCCSCCEEEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCcc--CCCCeEEEEeec
Confidence            3478999999999999999999999999 9999999   479999999999999999999999999  6 9999999987


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus       196 ~~  197 (198)
T 1qm9_A          196 ST  197 (198)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=99.51  E-value=6.2e-14  Score=114.31  Aligned_cols=76  Identities=28%  Similarity=0.466  Sum_probs=71.0

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..|.++     +|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus         5 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            5 PEVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TTCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            456789999999 8899999999999999999999995     5799999999999999999999999999999999998


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        84 ~~   85 (115)
T 3lqv_A           84 AN   85 (115)
T ss_dssp             HH
T ss_pred             CC
Confidence            64

>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=99.51  E-value=3.6e-14  Score=112.22  Aligned_cols=77  Identities=18%  Similarity=0.212  Sum_probs=68.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      .....++|||+|| |..+++++|+++|.+||.|..+.++        +|||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus        11 ~~~~~~~l~v~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   89 (98)
T 2cqp_A           11 GKPGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (98)
T ss_dssp             CCCSSEEEEEESC-CTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3456689999999 8999999999999999998755442        689999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      +++...
T Consensus        90 ~~a~~~   95 (98)
T 2cqp_A           90 VLGSGP   95 (98)
T ss_dssp             EESSCS
T ss_pred             EEcCCC
Confidence            998764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.50  E-value=3.7e-14  Score=113.75  Aligned_cols=77  Identities=18%  Similarity=0.257  Sum_probs=69.8

Q ss_pred             CCCCCcEEEEEcCCCCCC------CHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCe
Q 014384          146 NTRPSKTLFVINFDPYHT------RTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDR  213 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~------~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~  213 (425)
                      .....++|||+|| |..+      ++++|+++|.+||.|..|.|+      +|||||+|.+.++|.+|+..|||..|+|+
T Consensus        11 ~~~~~~~l~V~nL-p~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           11 ADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CCSCCSEEEEESC-CCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCCEEEEeCC-CcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3445689999999 7777      689999999999999999986      68999999999999999999999999998


Q ss_pred             -EEEEEEeeeC
Q 014384          214 -VISVEYAVRD  223 (425)
Q Consensus       214 -~i~v~~a~~~  223 (425)
                       .|.|.++...
T Consensus        90 ~~l~V~~a~~~  100 (105)
T 2nlw_A           90 HTFRVNLFTDF  100 (105)
T ss_dssp             CEEEEECSCCC
T ss_pred             ceEEEEEcchH
Confidence             9999998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=3.2e-14  Score=112.73  Aligned_cols=77  Identities=19%  Similarity=0.331  Sum_probs=70.4

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEE-EEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE--
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII-SVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRV--  214 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~-~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~--  214 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|. .|.++        +|||||+|.+.++|.+|++.|||..|.|+.  
T Consensus         5 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            5 SSGMAASLWMGDL-EPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCSSSSEEEECSC-CTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCccEEEEeCC-CCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            3456799999999 78899999999999999999 99885        479999999999999999999999999999  


Q ss_pred             --EEEEEeeeC
Q 014384          215 --ISVEYAVRD  223 (425)
Q Consensus       215 --i~v~~a~~~  223 (425)
                        |.|.|+...
T Consensus        84 ~~l~v~~a~~~   94 (99)
T 2div_A           84 KRFKLNYATYS   94 (99)
T ss_dssp             EECCEEETTCC
T ss_pred             eeEEEeecCCC
Confidence              999998764

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.7e-14  Score=112.72  Aligned_cols=73  Identities=16%  Similarity=0.408  Sum_probs=67.8

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ....+|||+|| |..+++++|+++|++||.|..|.|+       +|||||+|.+.++|.+|+. +++..|+|+.|.|.++
T Consensus         9 ~~~~~lfV~~L-p~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECC-CTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            45689999999 8899999999999999999999996       5899999999999999999 9999999999999987


Q ss_pred             ee
Q 014384          221 VR  222 (425)
Q Consensus       221 ~~  222 (425)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>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=99.49  E-value=1.1e-14  Score=113.38  Aligned_cols=73  Identities=18%  Similarity=0.310  Sum_probs=62.9

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCC--cEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYG--KIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G--~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .+|||+|| +..+++++|+++|++||  .|..|.++        +|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus         2 ~~l~V~nL-~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~   80 (90)
T 3p5t_L            2 IALYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS   80 (90)
T ss_dssp             --CEEESC-CTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC
T ss_pred             eEEEEeCC-CCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEEC
Confidence            47999999 88999999999999999  99999885        579999999999999999999999999999999998


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ....
T Consensus        81 ~~~~   84 (90)
T 3p5t_L           81 NKLE   84 (90)
T ss_dssp             ----
T ss_pred             CCCc
Confidence            8753

>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=99.49  E-value=2.2e-13  Score=108.70  Aligned_cols=78  Identities=18%  Similarity=0.477  Sum_probs=69.3

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+|+.  ++..|+|+.|.
T Consensus        10 ~~~~~~~~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~   86 (103)
T 2cqg_A           10 RAVQKTSDLIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCD   86 (103)
T ss_dssp             CCCCCCCCEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEE
T ss_pred             CccCCCCEEEEEcC-CCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEE
Confidence            34566789999999 8999999999999999999999985        4699999999999999998  46789999999


Q ss_pred             EEEeeeCCC
Q 014384          217 VEYAVRDDD  225 (425)
Q Consensus       217 v~~a~~~~~  225 (425)
                      |.++..+..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cqg_A           87 CKLPNSKQS   95 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EEecCCCCc
Confidence            999987643

>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=1.4e-13  Score=111.66  Aligned_cols=78  Identities=19%  Similarity=0.253  Sum_probs=68.9

Q ss_pred             hcCCCceEEEcCCCCCCC-----------HHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeec
Q 014384           50 FEAMMRPIFCGNFEYDAR-----------QSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFG  114 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t-----------~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig  114 (425)
                      .+.+.++|+|.||....+           +++|.++|++||+|..|.|.    +|||||+|.+.++|.+|+..|||..| 
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~-   89 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF-   89 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE-
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEE-
Confidence            456789999999954432           68999999999999999884    89999999999999999999999999 


Q ss_pred             CCCcEEEEEEecccc
Q 014384          115 RKGRRLRVEWTKHER  129 (425)
Q Consensus       115 ~~gr~l~V~~a~~~~  129 (425)
                       +|+.|.|.|+....
T Consensus        90 -~gr~l~v~~a~~~~  103 (112)
T 2dit_A           90 -GGRQITAQAWDGTT  103 (112)
T ss_dssp             -TTEECEEEECCSCC
T ss_pred             -CCcEEEEEEeCCCC
Confidence             89999999997654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.48  E-value=1.3e-13  Score=110.36  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=67.9

Q ss_pred             hcCCCceEEEcCCCC-----CCCHHHHHHHHhhcCCeeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecC
Q 014384           50 FEAMMRPIFCGNFEY-----DARQSDLERLFRRYGKVDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGR  115 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~-----~~t~~~L~~lF~~~G~V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~  115 (425)
                      ...++++|+|.||..     +.++++|+++|++||+|..|.|.         +|||||+|.+.++|.+|+..|||..|  
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~--   81 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYF--   81 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEE--
T ss_pred             CCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEE--
Confidence            346788999999963     23789999999999999999883         68999999999999999999999999  


Q ss_pred             CCcEEEEEEeccc
Q 014384          116 KGRRLRVEWTKHE  128 (425)
Q Consensus       116 ~gr~l~V~~a~~~  128 (425)
                      +|+.|.|.++...
T Consensus        82 ~Gr~i~v~~a~~~   94 (105)
T 2pe8_A           82 GGRVVKACFYNLD   94 (105)
T ss_dssp             TTEECEEEECCHH
T ss_pred             CCcEEEEEEcCHH
Confidence            8999999998754

>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=99.48  E-value=1.4e-13  Score=106.29  Aligned_cols=73  Identities=26%  Similarity=0.541  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|++ +++..|+|+.|.|
T Consensus         7 ~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v   84 (87)
T 3s7r_A            7 NEEDAGKMFVGGL-SWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDP   84 (87)
T ss_dssp             CCSCTTEEEEECC-CTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEE
Confidence            3456789999999 8899999999999999999999985        5799999999999999996 5888899999999


Q ss_pred             EEe
Q 014384          218 EYA  220 (425)
Q Consensus       218 ~~a  220 (425)
                      .+|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.48  E-value=1.2e-13  Score=114.15  Aligned_cols=78  Identities=18%  Similarity=0.325  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+.++|||+|| +..+++++|+++|.+||.|..|.|.       +|||||+|.+.++|.+|++.|||..|+|+.|.|
T Consensus        30 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           30 EGVETGAKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCCSSCEEEEEESC-CSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34567789999999 8899999999999999999999995       589999999999999999999999999999999


Q ss_pred             EEeeeC
Q 014384          218 EYAVRD  223 (425)
Q Consensus       218 ~~a~~~  223 (425)
                      .+|...
T Consensus       109 ~~a~~~  114 (124)
T 2kt5_A          109 QLVASQ  114 (124)
T ss_dssp             EEECCT
T ss_pred             EEeCCC
Confidence            999875

>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=99.48  E-value=8.4e-14  Score=107.90  Aligned_cols=72  Identities=26%  Similarity=0.459  Sum_probs=67.1

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|+ .||+..|.|+.|.|.++.
T Consensus         6 ~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            6 ARSIYVGNV-DYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HTEEEEESC-CTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            479999999 8899999999999999999999985        569999999999999999 999999999999999987


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=99.48  E-value=4.5e-14  Score=112.89  Aligned_cols=76  Identities=28%  Similarity=0.538  Sum_probs=70.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.+.        +|||||+|.+.++|.+|++.|||..|+|+.|.|.+
T Consensus         6 ~~~~~l~V~nl-p~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            6 RSLRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHSCEEEESC-CTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCccEEEEeCC-CCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            34579999999 8899999999999999999999885        67999999999999999999999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        85 a~~~~   89 (104)
T 1p1t_A           85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCcc
Confidence            87753

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.7e-13  Score=106.80  Aligned_cols=75  Identities=20%  Similarity=0.360  Sum_probs=68.9

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .....+|||+|| |..+++++|+++|.+| .|..|.|+       +|||||+|.+.++|.+|+. ||+..|+|+.|.|.+
T Consensus         7 ~~~~~~l~v~nL-p~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGA-PFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECC-CSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECC-CCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            456789999999 8999999999999999 99999885       5699999999999999999 999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98753

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.48  E-value=5.6e-14  Score=114.28  Aligned_cols=71  Identities=17%  Similarity=0.214  Sum_probs=62.7

Q ss_pred             CceEEEcCC----CCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcC----HHH----HHHHHH--hcCCC
Q 014384           54 MRPIFCGNF----EYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDD----ERD----AEDAIR--GLDRT  111 (425)
Q Consensus        54 ~~~l~V~nL----~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~----~~~----A~~A~~--~lng~  111 (425)
                      .++|||+||    ++.+|+++|.++|+.||+|.+|.+        ++|||||+|.+    +++    |.+|+.  .|||.
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            368999999    999999999999999999999998        48999999996    433    788988  78999


Q ss_pred             eecCCCcEEEEEEec
Q 014384          112 EFGRKGRRLRVEWTK  126 (425)
Q Consensus       112 ~ig~~gr~l~V~~a~  126 (425)
                      .|  +|+.|.|.+-.
T Consensus        82 ~I--~Gr~irV~ln~   94 (136)
T 2j8a_A           82 FI--MGFKFEVILNK   94 (136)
T ss_dssp             EE--TTEEEEEEECC
T ss_pred             ee--cCcEEEEEECc
Confidence            99  89999999754

>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=99.47  E-value=3e-14  Score=111.98  Aligned_cols=75  Identities=19%  Similarity=0.216  Sum_probs=65.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .++..+|||+|| |..+++++|+++|.+||.|..+.++        +|||||+|.+.++|.+|++.||+..|+|+.|.|+
T Consensus        12 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~   90 (95)
T 2ek1_A           12 KPGPTVIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLS   90 (95)
T ss_dssp             ---CEEEEEECC-CTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEE
Confidence            345689999999 8999999999999999998766553        5899999999999999999999999999999999


Q ss_pred             Eeee
Q 014384          219 YAVR  222 (425)
Q Consensus       219 ~a~~  222 (425)
                      ++..
T Consensus        91 ~a~s   94 (95)
T 2ek1_A           91 GPSS   94 (95)
T ss_dssp             CCC-
T ss_pred             eccC
Confidence            8753

>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=99.47  E-value=3e-13  Score=108.20  Aligned_cols=77  Identities=19%  Similarity=0.309  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE-EEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS-VRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~-v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ......+|||+|| |..+++++|+++|.+||.|.. |.|+       +|||||+|.+.++|.+||.. ++..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESC-CTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999 899999999999999999987 7774       68999999999999999997 999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++....
T Consensus        89 ~~~~~~~   95 (104)
T 1wg5_A           89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9987643

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.47  E-value=1.5e-13  Score=113.63  Aligned_cols=72  Identities=17%  Similarity=0.288  Sum_probs=66.5

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccE-EEEEEcCHHHHHHHHHHcCCCccCC--eEEEEEEeeeC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNF-AFVQYEVQEDATRALDATNMSKLTD--RVISVEYAVRD  223 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~-afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a~~~  223 (425)
                      ..|||+|| ++.+++++|.++|++||.|..|.+.   +|| |||+|.+.++|..|++.|||..|.|  +.|+|+|++..
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 LRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             EEEEEESC-CSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             EEEEECCC-CCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            46679999 8999999999999999999999886   467 9999999999999999999999998  89999999875

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.47  E-value=7.1e-14  Score=110.03  Aligned_cols=78  Identities=21%  Similarity=0.407  Sum_probs=69.8

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE---eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ...+..+|||+|| |..+++++|+++|.+||.|..+..   .+|||||+|.+.++|.+|++.|||..|+|+.|.|.++..
T Consensus        12 ~~~~~~~l~V~nL-~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           12 KVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESC-CSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            3456789999999 889999999999999999887722   378999999999999999999999999999999999977


Q ss_pred             CC
Q 014384          223 DD  224 (425)
Q Consensus       223 ~~  224 (425)
                      ..
T Consensus        91 ~~   92 (96)
T 1fjc_A           91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.47  E-value=3.2e-13  Score=109.83  Aligned_cols=78  Identities=21%  Similarity=0.425  Sum_probs=70.2

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCcc-------
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKL-------  210 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~-------  210 (425)
                      ....+.++|||+|| |..+++++|+++|.+||.|..|.|+       +|||||+|.+.++|.+|++.|||..|       
T Consensus        20 ~~~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            34456789999999 8889999999999999999999995       47999999999999999999999999       


Q ss_pred             -CCeEEEEEEeeeC
Q 014384          211 -TDRVISVEYAVRD  223 (425)
Q Consensus       211 -~g~~i~v~~a~~~  223 (425)
                       .+++|.|.|+.+.
T Consensus        99 ~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           99 APTEPLLCKFSGPS  112 (114)
T ss_dssp             CCSSCBEEEECCCS
T ss_pred             CCCCceeEEccCCC
Confidence             5788999999853

>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=99.47  E-value=8e-14  Score=112.44  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=70.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCc-EEEEEEe---------ccEEEEEEcCHHHHHHHHHHcC--CCccCCeE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGK-IISVRIR---------RNFAFVQYEVQEDATRALDATN--MSKLTDRV  214 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~-v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~  214 (425)
                      ..+.++|||+|| |..+++++|+++|.+||. |..|.++         +|||||+|.+.++|..|++.|+  +..|+|+.
T Consensus         5 s~~~~~l~V~nL-p~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            5 SSGNCRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCCSEEEEEECC-CTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             ccCCCEEEEeCC-CCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            346789999999 889999999999999998 9999986         5799999999999999999996  58999999


Q ss_pred             EEEEEeeeCC
Q 014384          215 ISVEYAVRDD  224 (425)
Q Consensus       215 i~v~~a~~~~  224 (425)
                      |.|.|+....
T Consensus        84 l~V~~a~~~~   93 (109)
T 2dis_A           84 IAVDWAEPEI   93 (109)
T ss_dssp             CEEEESCSSC
T ss_pred             EEEEEcCCCC
Confidence            9999998754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.47  E-value=2.9e-13  Score=111.35  Aligned_cols=75  Identities=25%  Similarity=0.255  Sum_probs=67.0

Q ss_pred             CCCcE--EEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccE-EEEEEcCHHHHHHHHHHcCCCccCC--eEEEEEEe
Q 014384          148 RPSKT--LFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNF-AFVQYEVQEDATRALDATNMSKLTD--RVISVEYA  220 (425)
Q Consensus       148 ~~~~~--l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~-afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a  220 (425)
                      +++++  |||+|| ++.+++++|.++|++||.|..|.|.  .|| |||+|.+.++|..|++.|||..|.|  +.|.|+||
T Consensus        21 ~ps~vl~l~V~NL-~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           21 GGNKVLLLSIQNP-LYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             CCCSEEEEEEESC-CSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             CCCcEEEEEEcCc-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            44554  578999 8999999999999999999999886  476 9999999999999999999999987  68999999


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      +..
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=2.1e-13  Score=107.28  Aligned_cols=76  Identities=24%  Similarity=0.342  Sum_probs=69.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEE-Ee----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVR-IR----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~-~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ....++|||+|| |..+++++|+++|.+||.|..|. ++    .+.|||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nl-p~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           12 RQRIRKLQIRNI-PPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             CCSCCCEEEEEE-CSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCCEEEEEcC-CCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            345689999999 88999999999999999999994 65    3459999999999999999999999999999999998


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      .+
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.47  E-value=4.8e-14  Score=107.46  Aligned_cols=66  Identities=21%  Similarity=0.348  Sum_probs=61.4

Q ss_pred             cEEEEEcCCCCCC------CHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCe-EEEE
Q 014384          151 KTLFVINFDPYHT------RTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDR-VISV  217 (425)
Q Consensus       151 ~~l~V~nl~p~~~------~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~-~i~v  217 (425)
                      ++|||+|| |..+      ++++|+++|++||.|..|.++      +|||||+|.+.++|.+|++.|||..|+|+ .|.|
T Consensus         2 ~~l~V~nL-p~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESC-CCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCC-CCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            68999999 7787      679999999999999999986      68999999999999999999999999999 8865

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.47  E-value=2e-13  Score=115.11  Aligned_cols=76  Identities=34%  Similarity=0.566  Sum_probs=69.4

Q ss_pred             CCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      .....+..+|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|++.|||..|+|+.|
T Consensus        57 ~~~~~~~~~l~v~nl-p~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           57 GGSATTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             CSSCSSCCEEEEECC-CTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCCcEEEEEeC-CCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            345567899999999 8899999999999999999999984        6799999999999999999999999999999


Q ss_pred             EEEEe
Q 014384          216 SVEYA  220 (425)
Q Consensus       216 ~v~~a  220 (425)
                      .|.+|
T Consensus       136 ~v~~A  140 (140)
T 2ku7_A          136 RVNLA  140 (140)
T ss_dssp             EEEC-
T ss_pred             EEEeC
Confidence            99875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=2.9e-14  Score=109.63  Aligned_cols=72  Identities=24%  Similarity=0.419  Sum_probs=66.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|..|++.|||..|.|+.|++.+
T Consensus         3 ~~~~~l~v~nl-p~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            3 SGSSGLYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCEEEEESC-CTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            56789999999 8899999999999999999999985        57999999999999999999999999999887755


Q ss_pred             e
Q 014384          220 A  220 (425)
Q Consensus       220 a  220 (425)
                      +
T Consensus        82 ~   82 (85)
T 1x4e_A           82 P   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.47  E-value=1.8e-13  Score=109.13  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=68.0

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ....+..+|||+|| |+.+++++|+++|.+||.| .|.|+       +|||||+|.+.++|.+||+ +|+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (102)
T 1wez_A           10 FQSTTGHCVHMRGL-PYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESC-CTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            34566789999999 8999999999999999955 88875       6799999999999999995 7999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++....
T Consensus        87 ~~~~~~~   93 (102)
T 1wez_A           87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            9987754

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.47  E-value=9.8e-14  Score=119.47  Aligned_cols=74  Identities=16%  Similarity=0.300  Sum_probs=67.9

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCC--cEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYG--KIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G--~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...+|||+|| +..+++++|+++|.+||  .|..|.|+        +|||||+|.+.++|.+||+.|||..|+|+.|.|.
T Consensus        54 ~~~~lfVgnL-p~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           54 RRAAVYVGSF-SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             --CEEEEECC-CTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            4579999999 89999999999999999  99999985        5799999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ++...
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            98653

>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=99.47  E-value=5.9e-14  Score=117.78  Aligned_cols=77  Identities=17%  Similarity=0.219  Sum_probs=69.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc---EEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK---IISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~---v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      .......+|||+|| |+.+++++|+++|++||.   |..|.|+       +|||||+|.+.++|.+||+ ||+..|+|+.
T Consensus        39 ~~~~~~~~lfVgnL-p~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGL-PWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESC-CTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34456789999999 899999999999999999   7788875       6799999999999999999 9999999999


Q ss_pred             EEEEEeeeC
Q 014384          215 ISVEYAVRD  223 (425)
Q Consensus       215 i~v~~a~~~  223 (425)
                      |.|.++...
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999998653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=1.1e-13  Score=113.10  Aligned_cols=76  Identities=22%  Similarity=0.457  Sum_probs=69.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|.+||+. ++..|+|+.|.|.+
T Consensus        25 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           25 EQFRKLFIGGL-SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHTEEEEECC-TTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEEC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEE
Confidence            34589999999 8899999999999999999999985        46999999999999999997 99999999999999


Q ss_pred             eeeCCC
Q 014384          220 AVRDDD  225 (425)
Q Consensus       220 a~~~~~  225 (425)
                      +..+..
T Consensus       103 a~~~~~  108 (116)
T 1x4b_A          103 AVAREE  108 (116)
T ss_dssp             CSSCCC
T ss_pred             CCCCcc
Confidence            987643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.46  E-value=1.7e-13  Score=113.21  Aligned_cols=72  Identities=24%  Similarity=0.465  Sum_probs=67.5

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| |..+++++|+++|.+||.|..|.+.        +|||||+|.+.++|.+|+ .|||..|+|+.|.|.++.
T Consensus        36 ~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           36 KRSVYVGNV-DYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HTEEEEEEE-CTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            579999999 8899999999999999999999985        579999999999999999 899999999999999987


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus       114 ~~  115 (124)
T 2jwn_A          114 TN  115 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=2.2e-13  Score=106.83  Aligned_cols=75  Identities=20%  Similarity=0.323  Sum_probs=66.5

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec--c-EEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--N-FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~--g-~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ....+|||+|| |..+++++|+++|.+||.|..|.+.+  + ||||+|.+.++|.+|+. ||+..|+|+.|.|.++....
T Consensus         6 ~~~~~l~V~nl-~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A            6 SGLRSVFVSGF-PRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             TTCCEEEEECC-CTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            44579999999 89999999999999999999984432  2 99999999999999999 99999999999999886643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=9.6e-14  Score=113.08  Aligned_cols=70  Identities=23%  Similarity=0.419  Sum_probs=59.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      ....++|||+|||+++|+++|+++|++||+|. +.+.           +|||||+|.+.++|++||..|++  +  +|+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~--~G~~   79 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--E--DGKL   79 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--E--TTEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--c--CCcE
Confidence            35678999999999999999999999999999 6551           68999999999999999998843  4  6676


Q ss_pred             EEEEEe
Q 014384          120 LRVEWT  125 (425)
Q Consensus       120 l~V~~a  125 (425)
                      |.|..+
T Consensus        80 ~~~~~~   85 (114)
T 2dnl_A           80 YLCVSS   85 (114)
T ss_dssp             EEEECC
T ss_pred             EEeccC
Confidence            666644

>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=99.46  E-value=5.6e-14  Score=111.66  Aligned_cols=76  Identities=26%  Similarity=0.453  Sum_probs=66.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      ......++|||+|| +..+++++|+++|.+|| |..|.|.         +|||||+|.+.++|.+|+ .|||..|+|+.|
T Consensus        14 ~~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l   90 (100)
T 2j76_E           14 LPKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             ------CEEEESCC-SSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCC
T ss_pred             CCCCCCcEEEEeCC-CCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEE
Confidence            44566799999999 88999999999999999 9999984         579999999999999999 899999999999


Q ss_pred             EEEEeeeC
Q 014384          216 SVEYAVRD  223 (425)
Q Consensus       216 ~v~~a~~~  223 (425)
                      .|.++...
T Consensus        91 ~V~~a~~~   98 (100)
T 2j76_E           91 RVDVADQA   98 (100)
T ss_dssp             CCEECCCS
T ss_pred             EEEeccCC
Confidence            99998764

>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=99.46  E-value=1.3e-13  Score=123.09  Aligned_cols=74  Identities=19%  Similarity=0.333  Sum_probs=66.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ..++|||+|||+.+|+++|.++|++||+|..|.|.       +|||||+|.+.++|.+|+..++ ..|  +|+.|.|.|+
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~--~Gr~l~V~~~  184 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKY--KETDLLILFK  184 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEE--TTEECEEEET
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeE--CCEEEEEEEh
Confidence            45899999999999999999999999999999884       7999999999999999996655 578  8999999998


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus       185 ~~y~  188 (193)
T 2voo_A          185 DDYF  188 (193)
T ss_dssp             TTC-
T ss_pred             HHHH
Confidence            7643

>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=99.46  E-value=1e-13  Score=107.34  Aligned_cols=73  Identities=18%  Similarity=0.278  Sum_probs=68.1

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ...+|||+|| |..+++++|+++|.+| .|..+.+.  +|||||+|.+.++|.+|++.|||..++|+.|.|+++..+
T Consensus         4 ~~~~l~V~nL-p~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            4 GSSGILVKNL-PQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESC-CSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            4678999999 8999999999999999 99998885  789999999999999999999999999999999998764

>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=99.46  E-value=7.8e-14  Score=113.54  Aligned_cols=73  Identities=26%  Similarity=0.419  Sum_probs=68.2

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ..++|||+|| |..+++++|+++|.+||.|..|.|.        +|||||+|.+.++|.+|+ .||+..|+|+.|.|.++
T Consensus        24 ~~~~l~V~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           24 DARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHTEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            3479999999 8899999999999999999999995        579999999999999999 99999999999999998


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      ...
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.45  E-value=2.5e-13  Score=109.65  Aligned_cols=77  Identities=18%  Similarity=0.348  Sum_probs=66.7

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..|.+.        +|||||+|.+.++|.+|++.+ +..|+|+.|.|
T Consensus        21 ~~~~~~~lfV~nL-p~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           21 MGSSGCKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             -----CCEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            3456789999999 8899999999999999999999995        579999999999999999986 49999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++....
T Consensus        99 ~~a~~~~  105 (109)
T 2rs2_A           99 KVAFPRR  105 (109)
T ss_dssp             EECCCCC
T ss_pred             EEccCCC
Confidence            9998753

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.44  E-value=1.6e-13  Score=112.44  Aligned_cols=77  Identities=18%  Similarity=0.255  Sum_probs=69.6

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc---EEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGK---IISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~---v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      .......+|||+|| |..+++++|+++|..||.   |..|.|+       +|||||+|.+.++|.+||+ ||+..|+|+.
T Consensus        12 ~~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~   89 (118)
T 2db1_A           12 PEGGEGYVVKLRGL-PWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRY   89 (118)
T ss_dssp             SCBCCCCEEEEESC-CTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEE
T ss_pred             CCCCCCcEEEEeCC-CCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeE
Confidence            34456789999999 899999999999999998   8888875       6799999999999999999 9999999999


Q ss_pred             EEEEEeeeC
Q 014384          215 ISVEYAVRD  223 (425)
Q Consensus       215 i~v~~a~~~  223 (425)
                      |.|.++..+
T Consensus        90 i~V~~a~~~   98 (118)
T 2db1_A           90 IEVFKSHRT   98 (118)
T ss_dssp             EEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999998664

>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=99.44  E-value=2.2e-13  Score=116.93  Aligned_cols=73  Identities=15%  Similarity=0.224  Sum_probs=67.2

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCC--eEEEEEEeeeC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTD--RVISVEYAVRD  223 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a~~~  223 (425)
                      ..+|||+|| ++.+++++|+++|++||.|..|.|.    ++||||+|.+.++|.+|++.|||..|.|  +.|.|+|++..
T Consensus        46 vl~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           46 VLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             EEEEEECSC-CSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             eEEEEEeCc-CCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            456889999 8999999999999999999999985    4699999999999999999999999965  99999999875

>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=99.43  E-value=1.5e-13  Score=128.57  Aligned_cols=113  Identities=15%  Similarity=0.119  Sum_probs=84.7

Q ss_pred             eeeEEEEeCCCCccccccc-CCcceeecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--
Q 014384           10 CHYLLIVYSHSVWPVQKKY-LPRRLYVLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--   86 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--   86 (425)
                      ..||||.|.+...+..+.. ++...... ...      .........+|||+|||+.+|+++|.++|..||.|..|.|  
T Consensus        58 kg~afV~f~~~~~A~~A~~~l~g~~i~g-~~l------~v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~  130 (261)
T 3sde_A           58 RGFGFIRLESRTLAEIAKAELDGTILKS-RPL------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV  130 (261)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETT-EEC------EEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEE
T ss_pred             CcEEEEEECCHHHHHHHHHHcCCcEECC-cee------EeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeee
Confidence            3599999988776555542 22222211 110      1122345789999999999999999999999999999998  


Q ss_pred             -----eCCEEEEEEcCHHHHHHHHHhcCC-Cee-cCCCcEEEEEEecccc
Q 014384           87 -----KSGFAFIYMDDERDAEDAIRGLDR-TEF-GRKGRRLRVEWTKHER  129 (425)
Q Consensus        87 -----~kg~aFV~F~~~~~A~~A~~~lng-~~i-g~~gr~l~V~~a~~~~  129 (425)
                           ++|||||+|.+.++|.+|+..||+ ..+ +..+++|.|.++....
T Consensus       131 ~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          131 DDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             ETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             CCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence                 379999999999999999999954 444 1249999999998654

>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=99.43  E-value=3.4e-14  Score=119.66  Aligned_cols=117  Identities=14%  Similarity=0.199  Sum_probs=66.8

Q ss_pred             CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHH
Q 014384           88 SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRD  167 (425)
Q Consensus        88 kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~  167 (425)
                      +++||.+|..++.+..|+..+..+.=   |...--..              .............+|||+|| |+.+++++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~g---g~~~g~~~--------------g~~~~~~~~~~~~~lfV~nL-p~~~te~d   62 (139)
T 2hgn_A            1 MGSSHHHHHHSSGLVPRGSHMASMTG---GQQMGRGS--------------GDSEFTVQSTTGHCVHMRGL-PYKATEND   62 (139)
T ss_dssp             -------------------------------------------------------------CCCCEECCSC-CTTCCHHH
T ss_pred             CCcccccccCccccchhcccchhccC---CCCCCCCC--------------CCcccCCCCCCCCEEEEeCC-CCCCCHHH
Confidence            47889999988888877765544321   11110000              00111223455689999999 89999999


Q ss_pred             HHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          168 LERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       168 L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      |+++|++|| |+.|.|+       +|||||+|.+.++|.+|| .+|+..|+|+.|.|.++....
T Consensus        63 L~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           63 IYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             HHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             HHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            999999999 6688885       689999999999999999 799999999999999987754

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.43  E-value=8.2e-14  Score=104.37  Aligned_cols=67  Identities=21%  Similarity=0.489  Sum_probs=62.4

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      +|||+|| |..+++++|+++|.+||.|..|.++        +|||||+|.+.++|.+|++ ||+..|+|+.|.|.+|
T Consensus         1 ~l~v~nl-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGL-SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECC-CSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecC-CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            4899999 8899999999999999999999885        4799999999999999998 9999999999999875

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=1.9e-13  Score=111.26  Aligned_cols=77  Identities=19%  Similarity=0.229  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcE-EEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI-ISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v-~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ...+..+|||+|| |..+++++|+++|..||.| ..|.|+       +|||||+|.+.++|.+||+. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESC-CTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCc-CCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            3456789999999 8999999999999999999 778774       78999999999999999987 999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .++..+.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998753

>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=99.43  E-value=8.7e-14  Score=115.11  Aligned_cols=77  Identities=14%  Similarity=0.274  Sum_probs=67.8

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEE-EE-------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV-RI-------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v-~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .......+|||+|| |..+++++|+++|..||.|..+ .+       .+|||||+|.+.++|.+||+ ||+..|+|+.|.
T Consensus        20 ~~~~~~~~l~V~nL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   97 (124)
T 1wel_A           20 SPHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   97 (124)
T ss_dssp             SCCCCCCEEEEECC-CTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            34556789999999 8999999999999999998653 33       26899999999999999999 999999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |.++..+
T Consensus        98 V~~a~~~  104 (124)
T 1wel_A           98 VHPITKK  104 (124)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.43  E-value=1.6e-13  Score=114.65  Aligned_cols=77  Identities=25%  Similarity=0.435  Sum_probs=69.5

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE--EEEe--------ccEEEEEEcCHHHHHHHHHHcCCC----cc
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS--VRIR--------RNFAFVQYEVQEDATRALDATNMS----KL  210 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~--v~~~--------~g~afV~f~~~~~A~~A~~~l~g~----~~  210 (425)
                      ....+..+|||+|| |..+++++|+++|.+||.|..  |.|+        +|||||+|.+. +|.+|+..|||.    .|
T Consensus        18 ~~~~~~~~lfV~nL-~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           18 SSENANDTIILRNL-NPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCSCCCCEEEECSC-CTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            34466789999999 889999999999999999966  7774        68999999999 999999999999    99


Q ss_pred             CCeEEEEEEeeeC
Q 014384          211 TDRVISVEYAVRD  223 (425)
Q Consensus       211 ~g~~i~v~~a~~~  223 (425)
                      +|+.|.|.++...
T Consensus        96 ~gr~l~V~~a~~~  108 (131)
T 2m2b_A           96 DGKTINVEFAKGS  108 (131)
T ss_dssp             GGCCCCCEECCCS
T ss_pred             CCEEEEEEECCCC
Confidence            9999999999775

>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=99.43  E-value=6.5e-14  Score=108.88  Aligned_cols=72  Identities=21%  Similarity=0.473  Sum_probs=64.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ++|||+|| |..+++++|+++|.+||.|..|.+.        +|||||+|.+.+ |.+|+..|||..|+|+.|.|.+|..
T Consensus         2 ~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            2 RNIYVGNL-VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             EEEEEEEE-CTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             cEEEECCC-CCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            58999999 8899999999999999999999995        579999999999 9999999999999999999999987


Q ss_pred             CC
Q 014384          223 DD  224 (425)
Q Consensus       223 ~~  224 (425)
                      ..
T Consensus        80 ~~   81 (90)
T 2ki2_A           80 KK   81 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>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=99.42  E-value=4.2e-13  Score=120.96  Aligned_cols=76  Identities=18%  Similarity=0.184  Sum_probs=70.2

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      .++++|||+||++..+++++|+++|.+||.|..|.++   +|||||+|.+.++|..|++.|||..|.|+.|.|.+++.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            4578999999943889999999999999999999996   589999999999999999999999999999999998764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.42  E-value=1.3e-13  Score=103.82  Aligned_cols=68  Identities=21%  Similarity=0.423  Sum_probs=63.7

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ++|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.++ ..++|+.|.|.+|
T Consensus         1 ~~l~v~nl-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESC-CSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCC-CCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            47999999 8899999999999999999999885        4799999999999999999999 9999999999986

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.13  E-value=1.6e-14  Score=118.02  Aligned_cols=78  Identities=21%  Similarity=0.314  Sum_probs=70.6

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE--------EEEe--------ccEEEEEEcCHHHHHHHHHHcCCCcc
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS--------VRIR--------RNFAFVQYEVQEDATRALDATNMSKL  210 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~--------v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~  210 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..        |.|+        +|||||+|.+.++|.+|+..||+..|
T Consensus         4 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            4 NSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            456789999999 889999999999999999988        6664        57999999999999999999999999


Q ss_pred             CCeEEEEEEeeeCCC
Q 014384          211 TDRVISVEYAVRDDD  225 (425)
Q Consensus       211 ~g~~i~v~~a~~~~~  225 (425)
                      .|+.|.|.++..+..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999988643

>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=99.41  E-value=4.5e-13  Score=103.25  Aligned_cols=69  Identities=22%  Similarity=0.503  Sum_probs=64.9

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccC----C-------cEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPY----G-------KIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~----G-------~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      .+..+|||+|| |..+++++|+++|.+|    |       .|..+.+.  +|||||+|.+.++|.+|+ .|||..|+|+.
T Consensus         4 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~   81 (87)
T 2hzc_A            4 GSARRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQS   81 (87)
T ss_dssp             GGGGEEEEESC-CTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeE
Confidence            45789999999 8899999999999999    8       99999997  799999999999999999 99999999999


Q ss_pred             EEEE
Q 014384          215 ISVE  218 (425)
Q Consensus       215 i~v~  218 (425)
                      |.|+
T Consensus        82 l~V~   85 (87)
T 2hzc_A           82 LKIR   85 (87)
T ss_dssp             CEEE
T ss_pred             EEEe
Confidence            9986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.41  E-value=4.4e-13  Score=117.88  Aligned_cols=77  Identities=18%  Similarity=0.330  Sum_probs=71.2

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...+.++|||+|| +..+++++|+++|.+||.|+.|.|.       +|||||+|.+.++|.+|++.||+..|+|+.|.|+
T Consensus        84 ~~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNL-DFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECC-CSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4456789999999 8899999999999999999999995       5899999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      |+...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            99764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.40  E-value=1.2e-13  Score=109.87  Aligned_cols=76  Identities=21%  Similarity=0.284  Sum_probs=66.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE-------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..+..+|||+|| |..+++++|+++|.+||.|..+.+       .+|||||+|.+.++|.+|++ ||+..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECC-CTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            446789999999 899999999999999997655111       27899999999999999998 999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      +....
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            97753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=3.8e-13  Score=108.41  Aligned_cols=72  Identities=18%  Similarity=0.272  Sum_probs=66.1

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ...+|||+|| |+.+++++|+++|+.| .|..|.|+       +|||||+|.+.++|.+|| .||+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nL-p~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGM-PFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECC-CSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3579999999 8999999999999999 89999985       689999999999999999 699999999999998886


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            54

>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=99.40  E-value=3.2e-13  Score=114.54  Aligned_cols=76  Identities=25%  Similarity=0.399  Sum_probs=68.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE--------EEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCe
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS--------VRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDR  213 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~--------v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~  213 (425)
                      ..+.++|||+|| |..+++++|+++|.+||.|..        +.+.     +|||||+|.+.++|.+|+..|||..|.|+
T Consensus        42 ~~~~~~l~V~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNL-AKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEE-CTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            567789999999 889999999999999998765        3332     68999999999999999999999999999


Q ss_pred             EEEEEEeeeC
Q 014384          214 VISVEYAVRD  223 (425)
Q Consensus       214 ~i~v~~a~~~  223 (425)
                      .|.|.++...
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999999764

>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=99.40  E-value=7.7e-13  Score=102.66  Aligned_cols=74  Identities=20%  Similarity=0.327  Sum_probs=60.3

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCc--cCCeEEEEEEe
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSK--LTDRVISVEYA  220 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~--~~g~~i~v~~a  220 (425)
                      ...+.++|||+|| |..+++++|+++|++||.|..|.|+   +|||||+|.+.++|.+    |++..  +.|+.|.|.++
T Consensus         7 ~~~~~~~l~V~~L-p~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            7 HHHHGSKVFVGRC-TEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             ----CCEEEEESC-CTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            4566789999999 8999999999999999999999997   7999999999999983    45554  45999999998


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7643

>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=99.40  E-value=3.2e-13  Score=123.75  Aligned_cols=74  Identities=18%  Similarity=0.307  Sum_probs=67.8

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCC--cEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYG--KIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G--~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..++|||+|| +..+++++|+++|.+||  .|+.|.|+        +|||||+|.+.++|.+||+.||+..|.|+.|.|.
T Consensus        67 ~~~~lfVgnL-~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNL-TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESC-CTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CccEEEEeCC-CCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            4678999999 89999999999999999  99999985        5799999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ++...
T Consensus       146 ~a~~~  150 (229)
T 3q2s_C          146 PVNKQ  150 (229)
T ss_dssp             ECCHH
T ss_pred             ECCCC
Confidence            98753

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.39  E-value=5.6e-13  Score=128.41  Aligned_cols=79  Identities=15%  Similarity=0.290  Sum_probs=68.3

Q ss_pred             hhcCCCceEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCee-cCCCc--EEE
Q 014384           49 AFEAMMRPIFCGN--FEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEF-GRKGR--RLR  121 (425)
Q Consensus        49 ~~~~~~~~l~V~n--L~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~i-g~~gr--~l~  121 (425)
                      ....++.+|||+|  |+..+|+++|+++|++||+|..|.|  .+|||||+|.+.++|++|++.|||+.+ +..|+  .|.
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            3467789999999  5789999999999999999999998  589999999999999999999999987 22345  677


Q ss_pred             EEEecc
Q 014384          122 VEWTKH  127 (425)
Q Consensus       122 V~~a~~  127 (425)
                      |.|+..
T Consensus        93 ~~~~~~   98 (345)
T 3tht_A           93 LNFVEK   98 (345)
T ss_dssp             EEECSS
T ss_pred             EEEeec
Confidence            788753

>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=99.38  E-value=2.6e-13  Score=109.14  Aligned_cols=76  Identities=14%  Similarity=0.200  Sum_probs=69.0

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCc---EEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGK---IISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~---v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      ......+|||+|| |..+++++|+++|..||.   |..|.|.       +|||||+|.+.++|.+||. ||+..|+|+.|
T Consensus         7 ~~~~~~~l~V~nL-p~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGL-PWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECC-CSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCC-CCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999 899999999999999998   8888885       6799999999999999999 99999999999


Q ss_pred             EEEEeeeC
Q 014384          216 SVEYAVRD  223 (425)
Q Consensus       216 ~v~~a~~~  223 (425)
                      .|.++...
T Consensus        85 ~V~~a~~~   92 (107)
T 2lmi_A           85 EVYEINNE   92 (107)
T ss_dssp             CCEECCHH
T ss_pred             EEEECCHH
Confidence            99998764

>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=99.38  E-value=3.2e-12  Score=103.60  Aligned_cols=80  Identities=16%  Similarity=0.199  Sum_probs=69.2

Q ss_pred             CCCCCCcEEEEEcCCCCCCC-----------HHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCc
Q 014384          145 TNTRPSKTLFVINFDPYHTR-----------TRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSK  209 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~-----------~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~  209 (425)
                      ....+..+|+|.|| .....           +++|+++|.+||.|..|.|.    +|||||+|.+.++|.+|+..|||..
T Consensus        10 ~~~~~s~~l~l~Nl-~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           10 SRMRHERVVIIKNM-FHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCCCSCCEEEEESS-CCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCCCceEEEEEcC-CCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            34567899999999 33322           57999999999999999875    7999999999999999999999999


Q ss_pred             cCCeEEEEEEeeeCCC
Q 014384          210 LTDRVISVEYAVRDDD  225 (425)
Q Consensus       210 ~~g~~i~v~~a~~~~~  225 (425)
                      |+|+.|.|.++.....
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999977543

>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=99.37  E-value=1.2e-12  Score=104.86  Aligned_cols=75  Identities=17%  Similarity=0.308  Sum_probs=65.2

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCC
Q 014384           52 AMMRPIFCGNF--EYDAR--------QSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRT  111 (425)
Q Consensus        52 ~~~~~l~V~nL--~~~~t--------~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~  111 (425)
                      .++++|.|.|+  +..+.        +++|+++|++||+|..|.|.          +|+|||+|.++++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46788999998  33333        47899999999999999983          599999999999999999999999


Q ss_pred             eecCCCcEEEEEEeccc
Q 014384          112 EFGRKGRRLRVEWTKHE  128 (425)
Q Consensus       112 ~ig~~gr~l~V~~a~~~  128 (425)
                      .|  .|+.|.|.|+...
T Consensus        83 ~f--~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KF--ANRVVVTKYCDPD   97 (105)
T ss_dssp             EE--TTEECEEEEECHH
T ss_pred             Ee--CCCEEEEEEeCHH
Confidence            99  8999999998654

>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=99.37  E-value=4.6e-13  Score=103.59  Aligned_cols=74  Identities=22%  Similarity=0.286  Sum_probs=63.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.|+   +|||||+|.+.++|++|+..  ...+.|..|.|.++..+.
T Consensus         3 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            3 SGSSGVFVGRC-TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCCEEEEESC-CSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CCCcEEEEeCC-CCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            45689999999 8999999999999999999999996   78999999999999754321  344589999999987754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.35  E-value=1.4e-12  Score=119.22  Aligned_cols=77  Identities=25%  Similarity=0.305  Sum_probs=68.9

Q ss_pred             CCCCcEEEEEcCCCCCC---------CHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCcc-----
Q 014384          147 TRPSKTLFVINFDPYHT---------RTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKL-----  210 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~---------~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~-----  210 (425)
                      .....+|||+|| +..+         ++++|+++|++||.|..|.|.  +|||||+|.+.++|+.|++.|+|..|     
T Consensus       131 ~~~~rtLfVgnL-~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGI-DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECT-TGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCC-ChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            456789999999 6666         699999999999999999996  89999999999999999999999999     


Q ss_pred             -------CCeEEEEEEeeeCC
Q 014384          211 -------TDRVISVEYAVRDD  224 (425)
Q Consensus       211 -------~g~~i~v~~a~~~~  224 (425)
                             .|+.|.|.||....
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC---
T ss_pred             ccccccCCCCEEEEEEccCCC
Confidence                   89999999998754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=4.7e-12  Score=100.15  Aligned_cols=62  Identities=23%  Similarity=0.349  Sum_probs=55.5

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           64 YDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        64 ~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..+|+++|+++|++||+|..|.|   ++|||||+|.+.++|+.||..+++  +  .|+.|.|.|+....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~--~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--L--VDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--C--SSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--C--CCCeEEEEEccCCC
Confidence            56899999999999999999999   489999999999999999988655  4  68999999987654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.34  E-value=1e-12  Score=104.56  Aligned_cols=74  Identities=18%  Similarity=0.382  Sum_probs=68.1

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .+.++|||+|| |..+++++|+++|.+||.|..|.++       +|||||+|.+.++|.+|+.  ++..|+|+.|.|.++
T Consensus         7 ~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGI-DVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            34689999999 8899999999999999999999995       4899999999999999998  999999999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ....
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            8754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.34  E-value=3.8e-12  Score=101.82  Aligned_cols=76  Identities=21%  Similarity=0.230  Sum_probs=66.3

Q ss_pred             CCCCcEEEEEcCC-CC---CCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCe
Q 014384          147 TRPSKTLFVINFD-PY---HTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDR  213 (425)
Q Consensus       147 ~~~~~~l~V~nl~-p~---~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~  213 (425)
                      ..++.+|+|.||- +.   ..++++|+++|++||.|..|.|+         +|||||+|.+.++|.+|++.|||..|+|+
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            4567899999992 11   23589999999999999999985         47999999999999999999999999999


Q ss_pred             EEEEEEeee
Q 014384          214 VISVEYAVR  222 (425)
Q Consensus       214 ~i~v~~a~~  222 (425)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999875

>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=99.32  E-value=3.6e-13  Score=100.81  Aligned_cols=67  Identities=16%  Similarity=0.388  Sum_probs=62.0

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      +|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++. ++..++|+.|.|.+|
T Consensus         1 ~l~v~nL-p~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGL-SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCC-CSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCC-CCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            5899999 8899999999999999999999885        57999999999999999984 899999999999875

>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=99.31  E-value=2.4e-12  Score=106.27  Aligned_cols=75  Identities=20%  Similarity=0.351  Sum_probs=65.9

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEE--EEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKII--SVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~--~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ......+|||+|| |+.+++++|+++|++| .|+  .|.|+       +|||||+|.+.++|.+||+. ++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnL-p~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGL-PFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECC-CTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            4456789999999 8999999999999999 666  78875       68999999999999999984 77999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |..+..+
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9888653

>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=99.31  E-value=6.1e-13  Score=106.34  Aligned_cols=65  Identities=20%  Similarity=0.476  Sum_probs=57.6

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE
Q 014384           59 CGNFEYDARQSDLERLF------------RRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR  119 (425)
Q Consensus        59 V~nL~~~~t~~~L~~lF------------~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~  119 (425)
                      +.||+..+|+++|.++|            ++||+|..|.|.       +|||||+|.++++|.+|+..|||..|  +|+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~--~Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF--NGQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEE--TTEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEE--CCEE
Confidence            56777777877777666            999999999994       79999999999999999999999999  8999


Q ss_pred             EEEEEe
Q 014384          120 LRVEWT  125 (425)
Q Consensus       120 l~V~~a  125 (425)
                      |.|+|+
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999986

>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=99.30  E-value=6.7e-12  Score=102.45  Aligned_cols=77  Identities=19%  Similarity=0.244  Sum_probs=66.4

Q ss_pred             hcCCCceEEEcCCCC--CC---CHHHHHHHHhhcCCeeEEEEe------------CCEEEEEEcCHHHHHHHHHhcCCCe
Q 014384           50 FEAMMRPIFCGNFEY--DA---RQSDLERLFRRYGKVDRVDMK------------SGFAFIYMDDERDAEDAIRGLDRTE  112 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~--~~---t~~~L~~lF~~~G~V~~v~i~------------kg~aFV~F~~~~~A~~A~~~lng~~  112 (425)
                      ...++++|+|.|+-.  .+   .+++|+++|++||+|..|.|.            +|+|||+|.++++|.+|+..|||..
T Consensus        16 ~~~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~   95 (118)
T 3ue2_A           16 RKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW   95 (118)
T ss_dssp             HHHSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCE
Confidence            334789999999942  22   378999999999999999883            2899999999999999999999999


Q ss_pred             ecCCCcEEEEEEeccc
Q 014384          113 FGRKGRRLRVEWTKHE  128 (425)
Q Consensus       113 ig~~gr~l~V~~a~~~  128 (425)
                      |  +|+.|.|.|+...
T Consensus        96 f--~GR~i~v~~~~~~  109 (118)
T 3ue2_A           96 F--AGRKVVAEVYDQE  109 (118)
T ss_dssp             E--TTEECEEEEECHH
T ss_pred             E--CCcEEEEEEcChH
Confidence            9  8999999998653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=1.2e-12  Score=107.81  Aligned_cols=74  Identities=18%  Similarity=0.203  Sum_probs=65.5

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcE----EEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKI----ISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v----~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ....+|||+|| |+.+++++|+++|++||.|    ..|.|+       +|||||+|.+.++|.+||+. |+..|+|+.|.
T Consensus        21 ~~~~~v~V~nL-p~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGL-PFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSC-CTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            45689999999 8999999999999999975    466664       68999999999999999986 99999999999


Q ss_pred             EEEeeeC
Q 014384          217 VEYAVRD  223 (425)
Q Consensus       217 v~~a~~~  223 (425)
                      |..+...
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988653

>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=99.29  E-value=7.9e-12  Score=101.33  Aligned_cols=76  Identities=13%  Similarity=0.128  Sum_probs=64.8

Q ss_pred             cCCCceEEEcCCCCCC----------CHHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeecCC
Q 014384           51 EAMMRPIFCGNFEYDA----------RQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFGRK  116 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~----------t~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~~  116 (425)
                      +.++++|.|.|+=...          .+++|.++|++||+|..|.|.    +|||||+|.+.++|.+|+..|||..|  +
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f--~   81 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWF--A   81 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEE--T
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEE--C
Confidence            4567788888883321          246889999999999999994    79999999999999999999999999  8


Q ss_pred             CcEEEEEEeccc
Q 014384          117 GRRLRVEWTKHE  128 (425)
Q Consensus       117 gr~l~V~~a~~~  128 (425)
                      |+.|.|.|+...
T Consensus        82 GR~i~v~~~~~~   93 (114)
T 3s6e_A           82 GKMITAAYVPLP   93 (114)
T ss_dssp             TEECEEEEECHH
T ss_pred             CEEEEEEEEcHH
Confidence            999999998643

>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=99.29  E-value=1.9e-11  Score=108.99  Aligned_cols=71  Identities=15%  Similarity=0.445  Sum_probs=64.6

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .++|||+|| |..+++++|+++|.+||.|..|.|+       +|||||+|.+.++|.+|+..++ ..|+|+.|.|.++..
T Consensus       109 ~~~l~V~nL-p~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECC-CTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             cCEEEecCC-CCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            579999999 8889999999999999999999986       6899999999999999998654 589999999998654

>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=99.26  E-value=1.3e-11  Score=98.75  Aligned_cols=77  Identities=23%  Similarity=0.400  Sum_probs=66.0

Q ss_pred             CCCCcEEEEEcC-CCCCCC--------HHHHHhhhccCCcEEEEEEe----------ccEEEEEEcCHHHHHHHHHHcCC
Q 014384          147 TRPSKTLFVINF-DPYHTR--------TRDLERHFEPYGKIISVRIR----------RNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       147 ~~~~~~l~V~nl-~p~~~~--------~~~L~~~f~~~G~v~~v~~~----------~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                      ..|+.+|+|.|+ ++....        .++|+++|++||.|..|.|+          +|+|||+|.+.++|.+|++.|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            357889999997 222222        36899999999999999995          48999999999999999999999


Q ss_pred             CccCCeEEEEEEeeeC
Q 014384          208 SKLTDRVISVEYAVRD  223 (425)
Q Consensus       208 ~~~~g~~i~v~~a~~~  223 (425)
                      ..|+|+.|.|.++...
T Consensus        82 ~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPD   97 (105)
T ss_dssp             CEETTEECEEEEECHH
T ss_pred             CEeCCCEEEEEEeCHH
Confidence            9999999999998653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=2.2e-11  Score=98.91  Aligned_cols=70  Identities=16%  Similarity=0.339  Sum_probs=58.6

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVI  215 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  215 (425)
                      ....++|||+|| |..+++++|+++|.+||.|. +.++           +|||||+|.+.++|.+|++.|++  ++|..|
T Consensus         5 ~~~~~~lfVgnL-p~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~   80 (114)
T 2dnl_A            5 SSGSRKVFVGGL-PPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLY   80 (114)
T ss_dssp             SSCCCCEEEECC-CTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEE
T ss_pred             CCCCCEEEEcCC-CCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEE
Confidence            345689999999 89999999999999999998 6653           57999999999999999999843  666666


Q ss_pred             EEEEe
Q 014384          216 SVEYA  220 (425)
Q Consensus       216 ~v~~a  220 (425)
                      .+..+
T Consensus        81 ~~~~~   85 (114)
T 2dnl_A           81 LCVSS   85 (114)
T ss_dssp             EEECC
T ss_pred             EeccC
Confidence            66543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=1e-10  Score=92.39  Aligned_cols=62  Identities=16%  Similarity=0.235  Sum_probs=55.6

Q ss_pred             CCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          161 YHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ..+++++|+++|.+||.|..|.|+   +|||||+|.+.++|..|++.+++  +.|+.|.|.|+....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            567899999999999999999995   78999999999999999998655  679999999988754

>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=99.16  E-value=1e-10  Score=95.39  Aligned_cols=74  Identities=19%  Similarity=0.283  Sum_probs=64.2

Q ss_pred             CCcEEEEEcC-CCC---CCCHHHHHhhhccCCcEEEEEEe------------ccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 014384          149 PSKTLFVINF-DPY---HTRTRDLERHFEPYGKIISVRIR------------RNFAFVQYEVQEDATRALDATNMSKLTD  212 (425)
Q Consensus       149 ~~~~l~V~nl-~p~---~~~~~~L~~~f~~~G~v~~v~~~------------~g~afV~f~~~~~A~~A~~~l~g~~~~g  212 (425)
                      ++.+|+|.|+ ++.   ..-+++|++.|++||.|..|.|+            +|++||+|.+.++|.+|++.|||..|+|
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            6789999998 221   12368999999999999999885            2799999999999999999999999999


Q ss_pred             eEEEEEEeee
Q 014384          213 RVISVEYAVR  222 (425)
Q Consensus       213 ~~i~v~~a~~  222 (425)
                      +.|.|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999865

>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=99.15  E-value=1.2e-10  Score=94.43  Aligned_cols=77  Identities=14%  Similarity=0.228  Sum_probs=65.1

Q ss_pred             CCCCcEEEEEcC-CCCCC--------CHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCCe
Q 014384          147 TRPSKTLFVINF-DPYHT--------RTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTDR  213 (425)
Q Consensus       147 ~~~~~~l~V~nl-~p~~~--------~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~  213 (425)
                      ..++.+|.|.|+ ++...        -+++|+++|++||.|..|.|.    +|++||+|.+.++|.+|++.|||..|+|+
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            456788999998 22211        135789999999999999995    68999999999999999999999999999


Q ss_pred             EEEEEEeeeC
Q 014384          214 VISVEYAVRD  223 (425)
Q Consensus       214 ~i~v~~a~~~  223 (425)
                      .|.|.|+...
T Consensus        84 ~i~v~~~~~~   93 (114)
T 3s6e_A           84 MITAAYVPLP   93 (114)
T ss_dssp             ECEEEEECHH
T ss_pred             EEEEEEEcHH
Confidence            9999998653

>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=99.13  E-value=7.6e-11  Score=113.53  Aligned_cols=76  Identities=16%  Similarity=0.268  Sum_probs=65.6

Q ss_pred             CCCCCcEEEEEcCC-CCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccC---Ce--EEEE
Q 014384          146 NTRPSKTLFVINFD-PYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLT---DR--VISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~-p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~---g~--~i~v  217 (425)
                      ...|+.+|||+|+. +..+++++|+++|++||.|..|.++  +|||||+|.+.++|++|++.|||..+.   |.  .|.|
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~   93 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL   93 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEE
Confidence            46778999999941 6789999999999999999999884  889999999999999999999999873   44  5777


Q ss_pred             EEee
Q 014384          218 EYAV  221 (425)
Q Consensus       218 ~~a~  221 (425)
                      .|+.
T Consensus        94 ~~~~   97 (345)
T 3tht_A           94 NFVE   97 (345)
T ss_dssp             EECS
T ss_pred             EEee
Confidence            7763

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.12  E-value=5.9e-11  Score=96.55  Aligned_cols=71  Identities=14%  Similarity=0.157  Sum_probs=61.0

Q ss_pred             cEEEEEcC----CCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcC----HHH----HHHHHH--HcCCC
Q 014384          151 KTLFVINF----DPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEV----QED----ATRALD--ATNMS  208 (425)
Q Consensus       151 ~~l~V~nl----~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~----~~~----A~~A~~--~l~g~  208 (425)
                      ..|||+||    + ..+++++|+++|..||+|..|.+.        +|||||+|.+    +++    |.+|+.  .|+|.
T Consensus         3 ~kI~VgnL~~~~~-~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            3 CEIVVYPAQDSTT-TNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CEEEEEESSSSCC-CCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             cEEEEeCCCCCCC-CCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            68999999    6 677799999999999999999984        7899999996    323    788888  78999


Q ss_pred             ccCCeEEEEEEeee
Q 014384          209 KLTDRVISVEYAVR  222 (425)
Q Consensus       209 ~~~g~~i~v~~a~~  222 (425)
                      .|+|+.|.|.+...
T Consensus        82 ~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           82 FIMGFKFEVILNKH   95 (136)
T ss_dssp             EETTEEEEEEECCT
T ss_pred             eecCcEEEEEECcc
Confidence            99999999998543

>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=99.12  E-value=1.2e-10  Score=92.90  Aligned_cols=64  Identities=19%  Similarity=0.340  Sum_probs=54.3

Q ss_pred             EcCCCCCCCHHHHHhhh------------ccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          156 INFDPYHTRTRDLERHF------------EPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       156 ~nl~p~~~~~~~L~~~f------------~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .|| +..+++++|+++|            ++||.|..|.|+       +|||||+|.+.++|.+|+..|||..|+|+.|.
T Consensus        21 ~~l-~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           21 DGL-RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             CHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             CCc-ccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            344 3445566565555            999999999996       68999999999999999999999999999999


Q ss_pred             EEEe
Q 014384          217 VEYA  220 (425)
Q Consensus       217 v~~a  220 (425)
                      |.|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=2.7e-10  Score=92.54  Aligned_cols=75  Identities=15%  Similarity=0.197  Sum_probs=65.6

Q ss_pred             hcCCCceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcC-HHHHHHHHHhcC--CCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDD-ERDAEDAIRGLD--RTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~-~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~-~~~A~~A~~~ln--g~~ig~~gr~l~V~  123 (425)
                      .-.....|||+||+.. ++.++|+++|++||+|..|.+.  ...|||.|.+ ..+|.+|+..||  +..|  +|..+.++
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i--~g~~~~~e   91 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQL--RNKEVTWE   91 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCT--TSSSEEEE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEE--eCcEEEEE
Confidence            3456789999999999 9999999999999999999996  4489999999 899999999996  5666  78888888


Q ss_pred             Eec
Q 014384          124 WTK  126 (425)
Q Consensus       124 ~a~  126 (425)
                      +..
T Consensus        92 vL~   94 (121)
T 1owx_A           92 VLE   94 (121)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.08  E-value=2.9e-10  Score=86.66  Aligned_cols=73  Identities=11%  Similarity=0.171  Sum_probs=61.9

Q ss_pred             CCceEEEcCCC----CCCCH----HHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFE----YDARQ----SDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~----~~~t~----~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      +..||+|.-++    .++-.    .+|.+.|.+||+|..|++..+.+||+|.+.++|.+|+. |||..|  .|+.|+|.+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~~fVtF~d~~sAlaAi~-mnG~~v--~Gr~LkV~l   82 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLS-LNGKEL--LNRTITIAL   82 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSSEEEEESSHHHHHHGGG-GTTCEE--TTEEEEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCCEEEEECChHHHHHHHh-cCCeEe--CCeEEEEEe
Confidence            44577776655    23333    67999999999999999998999999999999999996 999999  899999999


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      +.+.
T Consensus        83 kt~d   86 (91)
T 2dnr_A           83 KSPS   86 (91)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=9.4e-10  Score=89.33  Aligned_cols=78  Identities=17%  Similarity=0.112  Sum_probs=69.0

Q ss_pred             CCCCCCCcEEEEEcCCCCC-CCHHHHHhhhccCCcEEEEEEecc--EEEEEEcC-HHHHHHHHHHcC--CCccCCeEEEE
Q 014384          144 STNTRPSKTLFVINFDPYH-TRTRDLERHFEPYGKIISVRIRRN--FAFVQYEV-QEDATRALDATN--MSKLTDRVISV  217 (425)
Q Consensus       144 ~~~~~~~~~l~V~nl~p~~-~~~~~L~~~f~~~G~v~~v~~~~g--~afV~f~~-~~~A~~A~~~l~--g~~~~g~~i~v  217 (425)
                      ....+++..|+|+|| +.. ++.++|+++|.+||.|.+|.+..+  .|||+|.+ ..+|..|+..||  +..|+|..+.+
T Consensus        12 ~~~~~~G~il~v~~l-~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~   90 (121)
T 1owx_A           12 SLEEKIGCLLKFSGD-LDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   90 (121)
T ss_dssp             CCSCCCCCEEEEEES-CCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             cccccCCeEEEEecC-CCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEE
Confidence            455778899999999 566 999999999999999999999865  99999999 899999999995  78899999999


Q ss_pred             EEeee
Q 014384          218 EYAVR  222 (425)
Q Consensus       218 ~~a~~  222 (425)
                      +....
T Consensus        91 evL~G   95 (121)
T 1owx_A           91 EVLEG   95 (121)
T ss_dssp             EECCH
T ss_pred             EECCC
Confidence            87544

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=5.9e-10  Score=84.91  Aligned_cols=77  Identities=18%  Similarity=0.275  Sum_probs=64.6

Q ss_pred             CCCCCcEEEEEcCCC---CCCCH----HHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          146 NTRPSKTLFVINFDP---YHTRT----RDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p---~~~~~----~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+|..||+|.-++.   ...-+    .+|.+.|.+||.|..+++..+.+||+|.+.++|.+|+. |||.+++|+.|+|.
T Consensus         3 ~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            3 SGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSSEEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCCEEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            356677888877621   11223    57899999999999999999999999999999999998 99999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ++.++
T Consensus        82 lkt~d   86 (91)
T 2dnr_A           82 LKSPS   86 (91)
T ss_dssp             ECCCS
T ss_pred             eCCCC
Confidence            98763

>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=98.86  E-value=5.6e-09  Score=79.90  Aligned_cols=73  Identities=15%  Similarity=0.264  Sum_probs=61.9

Q ss_pred             cCCCceEEEcCCCCC-----CCH----HHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           51 EAMMRPIFCGNFEYD-----ARQ----SDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~-----~t~----~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      -.+..||+|..++..     +-.    .+|.+.|.+||+|..|++...-+||+|.+.++|.+||. |||..|  .|+.|+
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 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKV--KGRAVK   88 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHHH-GGGSEE--TTEEEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCcEEEEEcChHHHHHHHh-cCCeee--CCeEEE
Confidence            345678888877643     322    56899999999999999988889999999999999997 999999  899999


Q ss_pred             EEEec
Q 014384          122 VEWTK  126 (425)
Q Consensus       122 V~~a~  126 (425)
                      |.+..
T Consensus        89 V~~k~   93 (95)
T 1ufw_A           89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EeccC
Confidence            98753

>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=98.76  E-value=9.2e-09  Score=78.70  Aligned_cols=75  Identities=21%  Similarity=0.283  Sum_probs=63.6

Q ss_pred             CCCCCCcEEEEEcCCCC-----CCC---HHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPY-----HTR---TRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~-----~~~---~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ...+|..||+|.-+++.     +..   -.+|.+.|.+||.|..+++..+-+||+|.+.++|.+|+. |||.+++|+.|+
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~   88 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCcEEEEEcChHHHHHHHh-cCCeeeCCeEEE
Confidence            45678889999887321     121   156899999999999999999999999999999999998 999999999999


Q ss_pred             EEEe
Q 014384          217 VEYA  220 (425)
Q Consensus       217 v~~a  220 (425)
                      |.+.
T Consensus        89 V~~k   92 (95)
T 1ufw_A           89 ISGP   92 (95)
T ss_dssp             EECC
T ss_pred             Eecc
Confidence            9864

>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=98.57  E-value=8.2e-08  Score=87.13  Aligned_cols=73  Identities=21%  Similarity=0.279  Sum_probs=60.9

Q ss_pred             CceEEEcCCCC-----CCCHHHHHHHHhhcCCeeEEEEe------------CCEEEEEEcCHHHHHHHHHhcCCCeecCC
Q 014384           54 MRPIFCGNFEY-----DARQSDLERLFRRYGKVDRVDMK------------SGFAFIYMDDERDAEDAIRGLDRTEFGRK  116 (425)
Q Consensus        54 ~~~l~V~nL~~-----~~t~~~L~~lF~~~G~V~~v~i~------------kg~aFV~F~~~~~A~~A~~~lng~~ig~~  116 (425)
                      ...|.+.|+-.     .-.+++|.+.|++||+|..|.|.            +|++||+|.+.++|.+|+..|||..|  .
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~--~  201 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF--A  201 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBS--S
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceE--C
Confidence            34555555532     33568999999999999999983            58999999999999999999999999  8


Q ss_pred             CcEEEEEEeccc
Q 014384          117 GRRLRVEWTKHE  128 (425)
Q Consensus       117 gr~l~V~~a~~~  128 (425)
                      |+.|.|.++...
T Consensus       202 gr~i~~~~~~~~  213 (222)
T 3dxb_A          202 GRKVVAEVYDQE  213 (222)
T ss_dssp             SSBCEEEECCHH
T ss_pred             CeEEEEEEcCHH
Confidence            999999998643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.52  E-value=4.7e-07  Score=70.57  Aligned_cols=71  Identities=14%  Similarity=0.165  Sum_probs=65.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRY-----GKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~-----G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ++..++|-+-|||..+++..|..|++.+     |.|..|.|-  -+-|+|+|.|...|.+|.-+|||.+|  .|++|+|.
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef--~gr~Lr~g   95 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQF--QGKVIRSG   95 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEE--TTEEEEEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeee--cCeEEEec
Confidence            4457899999999999999999999999     999999884  68899999999999999999999999  89999986

>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=98.42  E-value=2.4e-06  Score=77.34  Aligned_cols=59  Identities=17%  Similarity=0.241  Sum_probs=54.8

Q ss_pred             CHHHHHhhhccCCcEEEEEEe------------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          164 RTRDLERHFEPYGKIISVRIR------------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       164 ~~~~L~~~f~~~G~v~~v~~~------------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .+++|.+.|.+||.|..+.++            +|++||+|.+.++|.+|++.|||..|+|+.|.+.+...
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            478999999999999999985            47999999999999999999999999999999999865

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.18  E-value=3.8e-06  Score=65.51  Aligned_cols=69  Identities=13%  Similarity=0.094  Sum_probs=63.7

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccC-----CcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPY-----GKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~-----G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ..+|-+-|| |..++...|+.+++.+     |.|+.|.+.  -+-|+|+|.+...|.+|.-.|+|.+|+|+.|.+.-
T Consensus        21 ~rtiaL~~i-pDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           21 ETLICLFPL-SDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TSCEEEECC-CTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CcEEEEecC-CCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            578899999 8999999999999999     999999886  56899999999999999999999999999999863

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.07  E-value=8e-06  Score=63.50  Aligned_cols=74  Identities=22%  Similarity=0.257  Sum_probs=62.7

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           53 MMRPIFCGNFEYDA-R----QSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        53 ~~~~l~V~nL~~~~-t----~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ..++|+|+||+..| +    .+.|++||..|+++....+-  =.=..|.|.++++|.+|...|++..|  +|+.|+|.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f--~g~~~r~YFg   81 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF--LGKEMKLYFA   81 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEE--TTEECEEECC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhcccee--cCceeEEEec
Confidence            35789999998865 2    26789999999998877763  34568999999999999999999999  8999999999


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        82 q~~   84 (104)
T 1wey_A           82 QTL   84 (104)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            844

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.06  E-value=2.5e-05  Score=60.40  Aligned_cols=71  Identities=14%  Similarity=0.076  Sum_probs=58.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRY-----GKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~-----G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ....+|.|.|||+.+.++.|+-+|+.-     |+|..|....+-|+|+|.+.+.|+..|. -....|  ++..|.|...
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 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLA-QADHEL--HGAQLSLRPA   81 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEETTEEEEEESSHHHHHHHHT-CSCCBS--SSSBCEEEEC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcCCcEEEEEcChHHHHHHhc-CCccee--cCeEEEEEcC
Confidence            345799999999999999999999982     6899999877999999999999999983 334455  6778888654

>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=97.87  E-value=3.8e-05  Score=58.67  Aligned_cols=58  Identities=17%  Similarity=0.270  Sum_probs=50.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcC
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD  109 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~ln  109 (425)
                      +.-.+.++| ++|+.+...||.++|..||.|.--+|.-..|||.|.+++.|..|+..++
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            334456666 9999999999999999999877677789999999999999999998774

>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=97.74  E-value=3.5e-05  Score=59.07  Aligned_cols=54  Identities=19%  Similarity=0.321  Sum_probs=47.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcC
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD  109 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~ln  109 (425)
                      +.++| ++|+.+...||.++|+.||.|.--+|.-..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            35666 9999999999999999999766666679999999999999999998775

>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=97.49  E-value=0.00028  Score=53.89  Aligned_cols=59  Identities=12%  Similarity=0.117  Sum_probs=52.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      ++|.|.+||+.+|++++.+.++.+.++......          -.-|||.|.+.+++....+.++|..|
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            689999999999999999999999877655542          35799999999999999999999988

>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=97.47  E-value=0.00045  Score=55.20  Aligned_cols=73  Identities=18%  Similarity=0.157  Sum_probs=59.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ....+-|.|-++|+.. ...|...|++||+|.+....  .....|.|.+..+|++|| ..||+.|+ .+-.|-|.+..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL-~kNG~ii~-g~~mIGV~p~~   95 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIFG-ESIMIGVKPCI   95 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHH-TTTTCEET-TTEECEEEECC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHH-HhCCeEec-CCEEEEEEECC
Confidence            3456789999999885 67888999999999998883  679999999999999999 88999993 24556666643

>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=97.46  E-value=9.8e-05  Score=57.38  Aligned_cols=73  Identities=12%  Similarity=0.103  Sum_probs=61.4

Q ss_pred             CcEEEEEcCCCCCCCH----HHHHhhhccCCcEEEEEEecc--EEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          150 SKTLFVINFDPYHTRT----RDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~----~~L~~~f~~~G~v~~v~~~~g--~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .++|+|.||++..-..    +.++++|..|+++....+.+.  -..|.|.++++|.+|-..||+..|.|..|+|-|+..
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            4789999995433232    567899999999888877654  578999999999999999999999999999999874

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.09  E-value=0.0047  Score=47.70  Aligned_cols=72  Identities=19%  Similarity=0.132  Sum_probs=60.4

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhcc-----CCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEP-----YGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~-----~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ...+|.|.|| |..+.++.|.-+|+.     -|+|..+....+-|+|+|.+.+.|+..++. ....|.|..|.|.-...
T Consensus         7 ~~~~I~V~~l-Pp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            7 GGVAVEVRGL-PPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCCEEEEESC-CTTSCHHHHHHHHHCTTTTCCCCEEEEEEETTEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             CccEEEEECC-CCCCChhHheEEEeCCCcCCCceeeEEEEcCCcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            4579999999 778889999999986     258999998889999999999999999873 36778889998866444

>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=97.01  E-value=0.0039  Score=47.56  Aligned_cols=55  Identities=29%  Similarity=0.430  Sum_probs=47.8

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN  206 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~  206 (425)
                      .+.++| ++ |......||.++|+.||.|.--.|.-..|||.|.+.+.|..|+..+.
T Consensus        16 ~HVf~l-~F-P~ewKt~DI~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-EC-CTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eC-ChhhhhHHHHHHhhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            456666 99 77788999999999999887778888999999999999999998763

>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=96.89  E-value=0.0024  Score=50.92  Aligned_cols=71  Identities=20%  Similarity=0.337  Sum_probs=58.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCC-eEEEEEEe
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTD-RVISVEYA  220 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g-~~i~v~~a  220 (425)
                      ......|.|.++ |... ...|..+|++||.|.....+  .+...|.|.+..+|++||. .||..|+| ..|-|...
T Consensus        21 ~~~~~wVtVFGF-p~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           21 HLDDTWVTVFGF-PQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             CGGGGEEEEECC-CGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCCCEEEEECC-CHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            344678999999 5554 77899999999999999985  4699999999999999997 59999985 55666653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.75  E-value=0.0022  Score=49.17  Aligned_cols=60  Identities=15%  Similarity=0.099  Sum_probs=48.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCCee
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRTEF  113 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~~i  113 (425)
                      .-+|.|..||+.+|++++.+.++.+-++......          -.-|||.|.+.+++....+.++|..|
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            4689999999999999988887765443222211          35789999999999999999999887

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.67  E-value=0.0026  Score=48.74  Aligned_cols=54  Identities=30%  Similarity=0.435  Sum_probs=46.5

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN  206 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~  206 (425)
                      +.++| ++ |......||.++|..||.|.--.|--..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~F-P~ewKt~Di~~lFs~fggv~I~WidDTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-EC-CTTCCHHHHHHHTTTSEEEEEEEEETTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eC-ChhhhhHHHHHHHhccCCEEEEEEcCCeEEEEecCHHHHHHHHHhcc
Confidence            44555 99 77777999999999999777777778899999999999999999774

>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=96.21  E-value=0.024  Score=43.09  Aligned_cols=70  Identities=19%  Similarity=0.230  Sum_probs=56.2

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec----------cEEEEEEcCHHHHHHHHHHcCCCccCCe-----EE
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR----------NFAFVQYEVQEDATRALDATNMSKLTDR-----VI  215 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~----------g~afV~f~~~~~A~~A~~~l~g~~~~g~-----~i  215 (425)
                      ++|.|.+| |-.+|++++.+.+..+..+.......          .-|||.|.+.+++..-.+.++|..|-+.     ..
T Consensus         2 ~KvVIRrL-PP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a   80 (91)
T 1uw4_A            2 SKVVIRRL-PPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             cEEEEeCC-CCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeee
Confidence            47899999 77788999999999998877776643          3799999999999999999999877532     33


Q ss_pred             EEEEee
Q 014384          216 SVEYAV  221 (425)
Q Consensus       216 ~v~~a~  221 (425)
                      .|++|.
T Consensus        81 ~VE~AP   86 (91)
T 1uw4_A           81 IVEFAP   86 (91)
T ss_dssp             EEEECS
T ss_pred             EEEEcC
Confidence            456553

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.13  E-value=0.011  Score=47.71  Aligned_cols=72  Identities=17%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE---------------------eCCEEEEEEcCHHHHHHHHHhcC
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM---------------------KSGFAFIYMDDERDAEDAIRGLD  109 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i---------------------~kg~aFV~F~~~~~A~~A~~~ln  109 (425)
                      ....-|.|-+.|+.. ...+.+.|++||.|.+ +.+                     -.+...|.|.+..+|.+|| ..|
T Consensus         5 ~~e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LEN   82 (132)
T ss_dssp             ---CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTT
T ss_pred             cCceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhC
Confidence            344677888886554 5677889999999876 211                     1457799999999999999 899


Q ss_pred             CCeecCCCcEEEEEEecc
Q 014384          110 RTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus       110 g~~ig~~gr~l~V~~a~~  127 (425)
                      |..|  .|..|-|.+...
T Consensus        83 G~ii--~G~mIGV~Py~~   98 (132)
T 3p3d_A           83 GAVF--NGVLLGVIPYTK   98 (132)
T ss_dssp             TCEE--TTEECEEEECCH
T ss_pred             CeEe--CcEEEEEEECCH
Confidence            9999  788888876643

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.44  E-value=0.016  Score=46.78  Aligned_cols=69  Identities=16%  Similarity=0.311  Sum_probs=54.8

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEE-EEE---------------------eccEEEEEEcCHHHHHHHHHHcCC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIIS-VRI---------------------RRNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~-v~~---------------------~~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                      ...|.|.++ |... ...+.+.|++||.|.+ +.+                     -.+...|+|.+..+|.+||. .||
T Consensus         7 e~~VtVFGF-p~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            7 ELAILVFGY-PETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             -CEEEEECC-CGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             ceEEEEEec-CHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            457888899 6666 6788899999999876 211                     13577899999999999997 699


Q ss_pred             CccCCeEEEEEEee
Q 014384          208 SKLTDRVISVEYAV  221 (425)
Q Consensus       208 ~~~~g~~i~v~~a~  221 (425)
                      ..|+|..|-|....
T Consensus        84 ~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           84 AVFNGVLLGVIPYT   97 (132)
T ss_dssp             CEETTEECEEEECC
T ss_pred             eEeCcEEEEEEECC
Confidence            99999888887753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.35  E-value=0.0072  Score=60.02  Aligned_cols=55  Identities=7%  Similarity=0.148  Sum_probs=42.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHH
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIR  106 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~  106 (425)
                      ....++|+|. .+..+++.+|.++|.+||+|..+.+-   ..||.|||.+.++|..++.
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            4456899997 79999999999999999999999983   4599999999999998773

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.22  E-value=0.089  Score=40.25  Aligned_cols=71  Identities=17%  Similarity=0.176  Sum_probs=53.7

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEec----------cEEEEEEcCHHHHHHHHHHcCCCccCC-----eE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR----------NFAFVQYEVQEDATRALDATNMSKLTD-----RV  214 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~----------g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~  214 (425)
                      .-+|.|..| |-.+|++++.+.+..+-.+.......          .-|||.|.+.+++..-.+.++|..|-+     -.
T Consensus         9 ~~KvVIRrL-PP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            9 SHMVVIRRL-PPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCEEEECC-CSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             ceeEEEeCC-CCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            457999999 67777999998888766654443322          378999999999999999999977653     24


Q ss_pred             EEEEEee
Q 014384          215 ISVEYAV  221 (425)
Q Consensus       215 i~v~~a~  221 (425)
                      ..|++|.
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            5566654

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.75  E-value=0.12  Score=52.31  Aligned_cols=56  Identities=18%  Similarity=0.275  Sum_probs=49.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCC
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDR  110 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng  110 (425)
                      ...++|+ ++..+...+|.++|+.||.|.-.+|....|||.|.+.+.|..|+..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~widdt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEECSSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEEcCCeEEEEECCHHHHHHHHHHHHh
Confidence            3567776 9999999999999999998777777889999999999999999998863

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.22  E-value=0.1  Score=51.81  Aligned_cols=51  Identities=14%  Similarity=0.220  Sum_probs=38.6

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--c-cEEEEEEcCHHHHHHHHH
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--R-NFAFVQYEVQEDATRALD  203 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~-g~afV~f~~~~~A~~A~~  203 (425)
                      ..|+|. + +..+++.+|.+.|++||.|..+.+-  + .||.|||.+.+++..++.
T Consensus        54 rsv~v~-~-~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-C-PEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-E-CCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-c-CCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            689997 6 6778899999999999999999885  3 399999999999887765

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=87.78  E-value=5.7  Score=29.39  Aligned_cols=69  Identities=19%  Similarity=0.145  Sum_probs=54.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++-|.|-|||..+-..++.-.....|---.|....|.|.|.|.+.++...|+..|-+.    +...|.++.
T Consensus        10 kqnclikiinipqgtlkaevvlavrhlgyefycdyidgqamirfqnsdeqrlaiqkllnh----nnnklqiei   78 (129)
T 4eyt_A           10 KQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYIDGQAMIRFQNSDEQRLAIQKLLNH----NNNKLQIEI   78 (129)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEECSSCEEEEESSHHHHHHHHHHHEET----TTTEEEEEE
T ss_pred             hhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeeecCeeEEEecCChHHHHHHHHHHhc----CCCEEEEEE
Confidence            456788899999999999888888888877778888999999999999999998765322    344555554

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=84.16  E-value=1.8  Score=31.05  Aligned_cols=60  Identities=15%  Similarity=0.159  Sum_probs=40.8

Q ss_pred             CCCCHHHHHhhhccCC-----cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          161 YHTRTRDLERHFEPYG-----KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       161 ~~~~~~~L~~~f~~~G-----~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+...+|..++..-+     .|-.|.+...|.||+-... .|..++..|++..+.|+.+.|+.+.
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~s~v~v~~~-~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNG-KGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECSSCEEEEECTT-CHHHHHHHHTTCCC---CCCEEECC
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeCCcEEEEECHH-HHHHHHHHhccccCcCceEEEEECC
Confidence            4455666666665433     5788999999999998764 4677888899999999999887654

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=83.55  E-value=2.6  Score=30.17  Aligned_cols=68  Identities=10%  Similarity=0.267  Sum_probs=45.2

Q ss_pred             eEEEcC-CCCCCCHHHHHHHHhhcC-----CeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           56 PIFCGN-FEYDARQSDLERLFRRYG-----KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        56 ~l~V~n-L~~~~t~~~L~~lF~~~G-----~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      +|||.. -...++..+|..++..-+     .|-.|.|...|.||+-... .|..++..|++..+  .|+.+.|+.+.
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~s~v~v~~~-~~~~~~~~l~~~~i--~g~~~~v~~~~   75 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNG-KGPHVLKVMKNTTV--KGKQLKVNKAN   75 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECSSCEEEEECTT-CHHHHHHHHTTCCC-----CCCEEECC
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeCCcEEEEECHH-HHHHHHHHhccccC--cCceEEEEECC
Confidence            455531 234677778888777654     3667888899999998765 46778889999988  89999988764

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=82.47  E-value=9.7  Score=28.15  Aligned_cols=56  Identities=13%  Similarity=0.162  Sum_probs=48.3

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHc
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDAT  205 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l  205 (425)
                      .++.|.|-|+ |..+-..++.-...-.|---.|....|.|+|.|.+.++..-|+..|
T Consensus        11 qnclikiini-pqgtlkaevvlavrhlgyefycdyidgqamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A           11 QNCLIKIINI-PQGTLKAEVVLAVRHLGYEFYCDYIDGQAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             CSCEEEEECC-CTTCCHHHHHHHHHTTCCCEEEEECSSCEEEEESSHHHHHHHHHHH
T ss_pred             hCcEEEEEec-CCCceeeeeEEeehhcCeeEeeeeecCeeEEEecCChHHHHHHHHH
Confidence            4567889999 7888788887777888888899999999999999999999898876

>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=81.90  E-value=3.2  Score=41.73  Aligned_cols=56  Identities=29%  Similarity=0.414  Sum_probs=46.6

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNM  207 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g  207 (425)
                      ...++|+ + +..+...+|.++|+.||.|.-.++....|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f-~~~~~~~~i~~~fs~fg~v~V~widdt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-F-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-C-CTTCCHHHHHHHGGGGCCCEEEECSSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-C-CCCCCHHHHHHHHHhcCCEEEEEEcCCeEEEEECCHHHHHHHHHHHHh
Confidence            3566665 7 566678999999999998777777788999999999999999998853

---

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	425
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-18
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-13
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-09
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	8e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	9e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 9e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	0.001
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	7e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	4e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.004
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.002
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	7e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.002

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.1 bits (187), Expect = 9e-18
 Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 2/97 (2%)

Query: 137 GSSARRPSTNTR-PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQ 195
           GSS     T+ R  +  +F+ N +    +  D+E  F  YGKI+   + + FAFVQY  +
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNE 60

Query: 196 EDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            +A  A+   +   +  +V+ +  A  +    R+G S
Sbjct: 61  RNARAAVAGEDGRMIAGQVLDINLA-AEPKVNRSGPS 96

>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 = 67.2 bits (164), Expect = 1e-14
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 57  IFCGNF-EYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +F GN      ++SD+E +F +YGK+    +  GFAF+   +ER+A  A+ G D      
Sbjct: 18  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIA- 76

Query: 116 KGRRLRVEWTKHERGIRRPGGGS 138
            G+ L +      +   R G  S
Sbjct: 77  -GQVLDINLAAEPKV-NRSGPSS 97

>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 = 63.8 bits (155), Expect = 1e-13
 Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++  N         L+ +F +YG + + ++          G AF+  +   +A++AI  L
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 109 DRTEFGRKGRRLRVEW 124
           +        + L V  
Sbjct: 69  NNVIPEGGSQPLSVRL 84

>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 = 56.1 bits (135), Expect = 6e-11
 Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 11/79 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------NFAFVQYEVQEDATRALD 203
            L+V N  P       L+  F  YG I+   I R          AFV+Y  +E+A  A+ 
Sbjct: 8   NLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 204 ATNMSKL--TDRVISVEYA 220
           A N        + +SV  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>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 = 61.9 bits (150), Expect = 6e-13
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++ G+   D  ++ L   F   G +  + +          G+A++      DAE A+  +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +       G+ +R+ W++
Sbjct: 63  NFDVIK--GKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------NFAFVQYEVQEDATRALD 203
           +L+V +          L   F P G I+S+R+ R         +A+V ++   DA RALD
Sbjct: 2   SLYVGDL-HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 204 ATNMSKLTDRVISVEYAVRD 223
             N   +  + + + ++ RD
Sbjct: 61  TMNFDVIKGKPVRIMWSQRD 80

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (141), Expect = 1e-11
 Identities = 14/84 (16%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--FAFVQYEVQEDATRA 201
           + ++  + T++           + + + F P+G+I+ +R+     ++FV++   E A  A
Sbjct: 12  NQSSPKNCTVYCGGI-ASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHA 70

Query: 202 LDATNMSKLTDRVISVEYAVRDDD 225
           + + N + +   V+   +     D
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKESPD 94

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.7 bits (134), Expect = 1e-10
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 4/72 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++CG          + + F  +G++  + +    G++F+       A  AI  ++ T   
Sbjct: 21  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE 80

Query: 115 RKGRRLRVEWTK 126
             G  ++  W K
Sbjct: 81  --GHVVKCYWGK 90

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV--DMKSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           +F GN   D  + ++ +LF +YGK   V      GF FI ++    AE A   LD     
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 70

Query: 115 RKGRRLRVEWTKH 127
             G++LRV +  H
Sbjct: 71  --GKQLRVRFACH 81

>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 = 51.5 bits (123), Expect = 3e-09
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 3/71 (4%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSK 209
            LFV N  P      ++ + FE YGK   V I   + F F++ E +  A  A    +   
Sbjct: 10  RLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 68

Query: 210 LTDRVISVEYA 220
           L  + + V +A
Sbjct: 69  LRGKQLRVRFA 79

>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 = 56.9 bits (137), Expect = 3e-11
 Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 9/75 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLD 109
           +   N ++    +D++ LF  +G + +  +         G A ++ + + DA  A++  +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 110 RTEFGRKGRRLRVEW 124
                  GR + ++ 
Sbjct: 63  GVPLD--GRPMNIQL 75

>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 = 55.3 bits (133), Expect = 9e-11
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN-------FAFVQYEVQEDATRALDAT 205
           L V N   +     D++  F  +G +    +  +        A V +E + DA +A+   
Sbjct: 3   LLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 206 NMSKLTDRVISVEYA 220
           N   L  R ++++  
Sbjct: 62  NGVPLDGRPMNIQLV 76

>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 = 57.3 bits (138), Expect = 3e-11
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 12/86 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRG 107
           I   N  + A Q ++  LF  +G++  V +           GF F+    ++DA+ A   
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 70

Query: 108 L-DRTEFGRKGRRLRVEWTKHERGIR 132
           L   T     GRRL +EW   E  ++
Sbjct: 71  LCHSTHLY--GRRLVLEWADSEVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.5 bits (136), Expect = 6e-11
 Identities = 19/87 (21%), Positives = 42/87 (48%), Gaps = 11/87 (12%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN---------FAFVQYEVQEDA 198
           + +  + V N  P+    R++   F  +G++ +VR+ +          F FV +  ++DA
Sbjct: 6   QTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 199 TRALDA-TNMSKLTDRVISVEYAVRDD 224
            +A +A  + + L  R + +E+A  + 
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 4e-11
 Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDAT 199
           + S TL+V N   ++T    +   F   G I  + +  +        F FV+Y  + DA 
Sbjct: 5   KKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDRR 228
            A+   N ++L DR+I  ++     + R+
Sbjct: 64  NAMRYINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 55.3 bits (133), Expect = 2e-10
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 13/94 (13%)

Query: 51  EAMMRP---IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDER 99
           E +++    ++ GN  +   +  +  LF + G + ++ M          GF F+      
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 100 DAEDAIRGLDRTEFGRKGRRLRVEWTKHERGIRR 133
           DAE+A+R ++ T      R +R +W    +  R+
Sbjct: 61  DAENAMRYINGTRLD--DRIIRTDWDAGFKEGRQ 92

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++         Q +LE+LF +YG++    +          G  FI  D   +AE+AI+GL
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 109 DRTEFGRKGRRLRVEW 124
           +  +       + V++
Sbjct: 69  NGQKPSGATEPITVKF 84

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALD 203
            L+V    P     ++LE+ F  YG+II+ RI         R   F++++ + +A  A+ 
Sbjct: 8   NLYVSGL-PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 204 ATNMSKL--TDRVISVEYA 220
             N  K       I+V++A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 5e-11
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----GFAFIYMDDERDAEDAIRGLD 109
           R ++  N  Y     ++  +F +YG + ++ + +     G A++  +D  DA++A   L 
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 110 RTEFGRKGRRLRVEWTKHERGIRR 133
                   R L V +    R  ++
Sbjct: 68  GFNVC--NRYLVVLYYNANRAFQK 89

>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 = 56.9 bits (137), Expect = 7e-11
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV-----RIRRNFAFVQYEVQEDATRAL 202
             ++ L++ N  PY     ++   F  YG I  +        R  A+V YE   DA  A 
Sbjct: 5   EVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAC 63

Query: 203 DATNMSKLTDRVISVEYAVRDDDDRR 228
           D  +   + +R + V Y   +   ++
Sbjct: 64  DHLSGFNVCNRYLVVLYYNANRAFQK 89

>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 = 56.6 bits (136), Expect = 7e-11
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 10/83 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRV----------DMKSGFAFIYMDDERDAEDAIR 106
           +F G      ++ ++     +  +                  GFAF+  +  R A  A R
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 107 GLDRTEFGRKGRRLRVEWTKHER 129
            L        G ++ V+W + E 
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEI 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 6e-07
 Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 17/92 (18%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----------RNFAFVQYEVQ 195
           N R    LF+    P   +  ++        + +   I           R FAFV+YE  
Sbjct: 1   NCR----LFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 55

Query: 196 EDATRALDATNMS--KLTDRVISVEYAVRDDD 225
             A  A         +L    I+V++A  + D
Sbjct: 56  RAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 87

>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 = 58.1 bits (139), Expect = 1e-10
 Identities = 32/185 (17%), Positives = 56/185 (30%), Gaps = 31/185 (16%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVD--------MKSGFAFIYMDDERDAEDAI 105
           +R +F G   ++     L   F ++G +               GF F+      + + A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRT 165
                   GR     R    +               +        K +FV       T  
Sbjct: 66  NARPHKVDGRVVEPKRAVSRED-------------SQRPGAHLTVKKIFVGGI-KEDTEE 111

Query: 166 RDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISV 217
             L  +FE YGKI  + I        +R FAFV ++  +   + +       +      V
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEV 170

Query: 218 EYAVR 222
             A+ 
Sbjct: 171 RKALS 175

>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 = 54.6 bits (131), Expect = 2e-10
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           +       D    +L  LFR  G ++   +          G+AF+    E D++ AI+ L
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +        +RL+V + +
Sbjct: 65  NGITVR--NKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRA 201
           +  L V    P     R+L   F   G I + RI           +AFV +  + D+ RA
Sbjct: 2   NTNLIVNYL-PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 202 LDATNMSKLTDRVISVEYA 220
           +   N   + ++ + V YA
Sbjct: 61  IKVLNGITVRNKRLKVSYA 79

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 10/87 (11%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERH----FEPYGKIISVRIR-----RNFAFVQYEVQEDA 198
           RP+ T+++ N      +  +L++     F  +G+I+ + +      R  AFV ++    A
Sbjct: 1   RPNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59

Query: 199 TRALDATNMSKLTDRVISVEYAVRDDD 225
           T AL +       D+ + ++YA  D D
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAKTDSD 86

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 14/84 (16%)

Query: 55  RP---IFCGNFEYDARQSDLER----LFRRYG-----KVDRVDMKSGFAFIYMDDERDAE 102
           RP   I+  N     ++ +L++    +F R+G      V R     G AF+   +   A 
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 103 DAIRGLDRTEFGRKGRRLRVEWTK 126
           +A+R +    F    + +R+++ K
Sbjct: 61  NALRSMQGFPFY--DKPMRIQYAK 82

>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 = 55.0 bits (132), Expect = 3e-10
 Identities = 19/98 (19%), Positives = 34/98 (34%), Gaps = 5/98 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTE 112
           I   N  Y      L ++F ++G V ++          A +   D   A+ A   LD   
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 69

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPS 150
                  LR++++K    +        +R  +    PS
Sbjct: 70  IYNACCTLRIDFSKLTS-LNVKYNNDKSRDYTRPDLPS 106

>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 = 42.7 bits (100), Expect = 6e-06
 Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 13/108 (12%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDA 204
           P   + V N   Y      L + F  +G ++ +       +  A +QY     A  A  +
Sbjct: 6   PVLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS 64

Query: 205 TNMSKLTD--RVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPS 250
            +   + +    + ++++     + +       N D+S D  R   PS
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVK------YNNDKSRDYTRPDLPS 106

>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 = 54.3 bits (130), Expect = 3e-10
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 55  RPIFCGNFEYDARQSDLERLFRR--YGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTE 112
           + ++  N      +  +E+ F     G V+RV     +AF++  +  DA +A++ L+   
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKV 68

Query: 113 FGRKGRRLRVEWTK 126
               G  + V   K
Sbjct: 69  LD--GSPIEVTLAK 80

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEP--YGKIISVRIRRNFAFVQYEVQEDATRALDATNM 207
            K L+V N     T    +E+ F     G +  V+  R++AFV +  +EDA  A+ A N 
Sbjct: 8   VKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 208 SKLTDRVISVEYA 220
             L    I V  A
Sbjct: 67  KVLDGSPIEVTLA 79

>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 = 53.9 bits (129), Expect = 4e-10
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 13/81 (16%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-----------GFAFIYMDDERDAEDAI 105
           +F  N  +   +  L+ +F + G +    +             GF F+       A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 106 RGLDRTEFGRKGRRLRVEWTK 126
           + L        G +L V  ++
Sbjct: 61  KQLQGHTVD--GHKLEVRISE 79

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIIS-----------VRIRRNFAFVQYEVQEDATRA 201
           LF+ N   + T    L+  F   G I S           V +   F FV+Y+  E A +A
Sbjct: 1   LFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

Query: 202 LDATNMSKLTDRVISVEYAVR 222
           L       +    + V  + R
Sbjct: 60  LKQLQGHTVDGHKLEVRISER 80

>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 = 54.3 bits (130), Expect = 5e-10
 Identities = 18/88 (20%), Positives = 39/88 (44%), Gaps = 4/88 (4%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI---RRNFAFVQYEVQEDAT 199
            S   R ++TL   N   ++    +L+  FE   +I  V      +  A+++++ + DA 
Sbjct: 9   TSKKVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDR 227
           + L+    +++  R +S+ Y       R
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 53.5 bits (128), Expect = 7e-10
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVD---MKSGFAFIYMDDERDAEDAIRGLDRT 111
           R +   N  ++  + +L+ +F    ++  V       G A+I    E DAE  +      
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 76

Query: 112 EFGRKGRRLRVEWTKHERGIR 132
           E    GR + + +T  + G R
Sbjct: 77  EID--GRSVSLYYTGEKGGTR 95

>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 = 53.5 bits (128), Expect = 7e-10
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 9/92 (9%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEV 194
           P +      T++V            L   F   G +++  +         + + FV++  
Sbjct: 2   PISERNQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 195 QEDATRALDATNMSKLTDRVISVEYAVRDDDD 226
           +EDA  A+   +M KL  + I V  A   + +
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKN 92

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRV--------DMKSGFAFIYMDDERDAEDAIR 106
             ++ G  +    +  L  LF + G V               G+ F+    E DA+ AI+
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 107 GLDRTEFGRKGRRLRVEWTK 126
            +D  +    G+ +RV    
Sbjct: 70  IMDMIKLY--GKPIRVNKAS 87

>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 = 53.6 bits (128), Expect = 8e-10
 Identities = 13/101 (12%), Positives = 28/101 (27%), Gaps = 8/101 (7%)

Query: 147 TRPSKTLFVINFDP----YHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATR 200
           +  S  L     +             E  F  Y K  + +         + +     A  
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAAD 61

Query: 201 ALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSP 241
           A    + ++   + + + +A        +   P  N D+S 
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPP--NPDKSG 100

>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 = 42.5 bits (99), Expect = 8e-06
 Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 9/90 (10%)

Query: 62  FEYDARQSDLERLFRRYGKVDRVDMKS--GFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
           F     ++  E LFR Y K              I   +   A DA   L +TEF   G+ 
Sbjct: 18  FSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF--LGKE 75

Query: 120 LRVEWTKHERGIRRPGGGSSARRPSTNTRP 149
           +++ + +         G S    P+ +   
Sbjct: 76  MKLYFAQ-----TLHIGSSHLAPPNPDKSG 100

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 13/85 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRG 107
           IF GN + +  +  L   F  +G + +              G+AFI       ++ AI  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 108 LDRTEFGRKGRRLRVEW--TKHERG 130
           ++        R + V +   K  +G
Sbjct: 61  MNGQYLC--NRPITVSYAFKKDSKG 83

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI---------RRNFAFVQYEVQEDATRALD 203
           +F+ N        + L   F  +G I+              + +AF+ +   + +  A++
Sbjct: 1   IFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 59

Query: 204 ATNMSKLTDRVISVEYAVRDDD 225
           A N   L +R I+V YA + D 
Sbjct: 60  AMNGQYLCNRPITVSYAFKKDS 81

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--FAFIYMDDERDAEDAIRGLDRTE 112
             ++ G    +   + L R F R+G +  +D   G  FA+I  +    A+ A   +    
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77

Query: 113 FGRKGRRLRVEWTKHERG 130
            G   RRLRV++ K    
Sbjct: 78  LGGPDRRLRVDFAKSGPS 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 7e-07
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISV--RIRRNFAFVQYEV 194
           GSS +       P+  L+V      +T    L R F+ +G I ++      +FA++QYE 
Sbjct: 4   GSSGKIGYGKANPTTRLWVGGL-GPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES 62

Query: 195 QEDATRALDATNMSKL--TDRVISVEYA 220
            + A  A        L   DR + V++A
Sbjct: 63  LDAAQAACAKMRGFPLGGPDRRLRVDFA 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 = 51.3 bits (122), Expect = 5e-09
 Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 3/71 (4%)

Query: 145 TNTRPSKTLFVINFD-PYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRA 201
           T +  +++L V N           L    E  G + ++ +   + ++F +Y   E++ RA
Sbjct: 13  TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRA 72

Query: 202 LDATNMSKLTD 212
               N  ++ D
Sbjct: 73  YVTLNGKEVVD 83

>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 = 47.0 bits (111), Expect = 2e-07
 Identities = 13/88 (14%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 42  HSQLSIAAFEAMMRP-----IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIY 94
           H+ L     E +        +  G       ++ L  +  + G VD + M     ++F  
Sbjct: 3   HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFAR 62

Query: 95  MDDERDAEDAIRGLDRTEFGRKGRRLRV 122
                +++ A   L+  E        ++
Sbjct: 63  YRTTEESKRAYVTLNGKEV-VDDLGQKI 89

>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 = 50.5 bits (120), Expect = 6e-09
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALD 203
                + + +++F         L +  EP+G I +  I  + N AF++    EDA  A+D
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 63

Query: 204 ATNM--SKLTDRVISVEYAVRD 223
                 + +  + + V  + + 
Sbjct: 64  YYTTTPALVFGKPVRVHLSQKY 85

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 55  RPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRT 111
           R +   +F+     +  L +L   +G +    +      AFI M    DA+ A+     T
Sbjct: 9   RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTT 68

Query: 112 EFGRKGRRLRVEWTKHERGIR 132
                G+ +RV  ++  + I+
Sbjct: 69  PALVFGKPVRVHLSQKYKRIK 89

>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 = 50.0 bits (119), Expect = 8e-09
 Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 11/76 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGL 108
           +F G   +   Q  L   F ++G+V    +          GF F+   D+   +  +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 109 DRTEFGRKGRRLRVEW 124
            R E     + +  + 
Sbjct: 62  SRHELD--SKTIDPKV 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 9e-08
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 10/76 (13%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDA 204
           +F+     + T    L  +F  +G++    + R+        F FV +  Q    + L  
Sbjct: 3   MFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 205 TNMSKLTDRVISVEYA 220
            +  +L  + I  + A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>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 = 50.1 bits (119), Expect = 8e-09
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGF--------AFIYMDDERDAEDAIRGL 108
           +       +  Q +   LF   G+++   +             F+   D +DAE AI  L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +        + ++V + +
Sbjct: 65  NGLRLQ--TKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 10/80 (12%)

Query: 150 SKT-LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQEDATR 200
           SKT L V    P +    +    F   G+I S ++ R+          FV Y   +DA +
Sbjct: 1   SKTNLIVNYL-PQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 59

Query: 201 ALDATNMSKLTDRVISVEYA 220
           A++  N  +L  + I V YA
Sbjct: 60  AINTLNGLRLQTKTIKVSYA 79

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 8e-09
 Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDAT 205
           R   TL+V   D        L   F P+G II + +   RN AFV YE  E A +A+   
Sbjct: 3   RKGNTLYVYGED---MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 59

Query: 206 NMSKLTDRVISVEYA 220
           N +++    + V  A
Sbjct: 60  NGTQVESVQLKVNIA 74

>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 = 44.6 bits (105), Expect = 6e-07
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFG 114
           ++      D   + L   F  +G +  + M      AF+  +    A+ A+  L+ T+  
Sbjct: 8   LYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 65

Query: 115 RKGRRLRVEWTK 126
               +L+V   +
Sbjct: 66  --SVQLKVNIAR 75

>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 = 50.1 bits (119), Expect = 1e-08
 Identities = 32/79 (40%), Positives = 46/79 (58%), Gaps = 7/79 (8%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRT 111
           I+ GN   D R  D+E +F +YG +  +D+K       FAF+  +D RDAEDA+ G D  
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 112 EFGRKGRRLRVEWTKHERG 130
           ++   G RLRVE+ +  RG
Sbjct: 77  DYD--GYRLRVEFPRSGRG 93

>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 = 49.8 bits (118), Expect = 2e-08
 Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 2/86 (2%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGF--AFIYMDDERDAEDAIRGLDRTEFG 114
           +          ++DL     ++G +  V M      A +  ++   A++ +         
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77

Query: 115 RKGRRLRVEWTKHERGIRRPGGGSSA 140
             G++    ++  +R  R    G S+
Sbjct: 78  IAGQQAFFNYSTSKRITRPGNSGPSS 103

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (115), Expect = 5e-08
 Identities = 17/104 (16%), Positives = 28/104 (26%), Gaps = 5/104 (4%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--AFVQYE 193
           G S +         S  + V           DL    E +G I  V +      A V++E
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFE 59

Query: 194 VQEDATRALDATNMSKLT--DRVISVEYAVRDDDDRRNGHSPDR 235
             + A   +       +    +     Y+      R     P  
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 7/88 (7%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAFVQYEVQEDAT 199
           +    +TL+V N          + + F   G   S ++         + FV++    DA 
Sbjct: 4   DDGQPRTLYVGNL-SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 62

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDR 227
            AL A N  K+  + + V +A      +
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRV------DMKSGFAFIYMDDERDAEDAIRGL 108
           R ++ GN   D  +  + +LF + G                + F+   + RDA  A+  +
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  +    G+ ++V W  
Sbjct: 69  NGRKIL--GKEVKVNWAT 84

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 6/89 (6%)

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR---NFAFVQYEVQEDATRALD 203
           +  S  +FV           +L   F  YG ++ V I +    FAFV +   + A     
Sbjct: 2   SSGSSGVFVGRC-TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 204 ATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
                 +    + +  A    +      S
Sbjct: 61  --EDLIIKGISVHISNAEPKHNSNSGPSS 87

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVD---MKSGFAFIYMDDERDAEDAIRGLDRTEF 113
           +F G    D  + +L   F +YG V  V        FAF+   D++ A+      +    
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLII 65

Query: 114 GRKGRRLRVEWTKHERGIRRPGGGS 138
             KG  + +   +  +     G  S
Sbjct: 66  --KGISVHISNAE-PKHNSNSGPSS 87

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV--DRVDMKSGFAFIYMDDERDAEDAIRGLDRT 111
           M  ++ GN        DL +LF         +V +KSG+AF+   D+  A  AI  L   
Sbjct: 1   MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGK 60

Query: 112 EFGRKGRRLRVEWTKHER 129
                G+ + V+++  ++
Sbjct: 61  -VELHGKIMEVDYSVSKK 77

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 3e-08
 Identities = 26/80 (32%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQED 197
           N  P+  L V      +T  RDL   F  YG I  V I  +         AFV +E  +D
Sbjct: 5   NPDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 198 ATRALDATNMSKLTDRVISV 217
           A  A +  N  +L  R I V
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 10/76 (13%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIR 106
             +          + DL  +F +YG +  V +          GFAF+Y ++  DA++A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 107 GLDRTEFGRKGRRLRV 122
             +  E    GRR+RV
Sbjct: 70  RANGMELD--GRRIRV 83

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--------FAFIYMDDERDAEDAIRGL 108
           +F G          ++ L   +G +   ++           +AF    D    + AI GL
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 109 DRTEFGRKGRRLRVEW 124
           +  + G   ++L V+ 
Sbjct: 64  NGMQLG--DKKLLVQR 77

>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 = 47.7 bits (113), Expect = 6e-08
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 9/79 (11%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRA 201
           +  LF+    P +     ++     +G + +  +         + +AF +Y       +A
Sbjct: 1   AHKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 59

Query: 202 LDATNMSKLTDRVISVEYA 220
           +   N  +L D+ + V+ A
Sbjct: 60  IAGLNGMQLGDKKLLVQRA 78

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIR 106
           R ++ G    +     L   F  +G +  + +          GFAF+  +   DA  AI 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 107 GLDRTEFGRKGRRLRVEWTKHER 129
            ++ +E    GR +RV   K  R
Sbjct: 66  NMNESELF--GRTIRVNLAKPMR 86

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQEDATR 200
             + L+V          + L   F P+G I  ++I  ++        AFV++E+ EDA  
Sbjct: 4   TKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 201 ALDATNMSKLTDRVISVEYA 220
           A+D  N S+L  R I V  A
Sbjct: 63  AIDNMNESELFGRTIRVNLA 82

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 14/91 (15%)

Query: 144 STNTRPSKTLFVIN-FDP---------YHTRTRDLERHFEPYGKIISVRIRRN----FAF 189
            +  R  + + + N F P          +    DL      +G+I  + +        A 
Sbjct: 2   PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVAS 61

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           V +   E+A   +   +      R I+ +  
Sbjct: 62  VSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 1e-06
 Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 64  YDARQSDLERLFRRYGKVDRVDMKS----GFAFIYMDDERDAEDAIRGLDRTEFGRKGRR 119
            +  + DL     ++G++ ++ +      G A +   D  +A+  I+ LD   FG  GR+
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG--GRQ 86

Query: 120 LRVEW 124
           +  + 
Sbjct: 87  ITAQA 91

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 10/76 (13%), Positives = 29/76 (38%), Gaps = 10/76 (13%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDA 204
           +FV       T    +  +F  +G++ S+ +  +        F F+ ++ +E   + ++ 
Sbjct: 2   IFVGGL-SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 205 TNMSKLTDRVISVEYA 220
                +      ++ A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>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 = 46.1 bits (109), Expect = 2e-07
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 11/75 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGL 108
           IF G    D  +  +   F  +G+V+ +++          GF FI   +E   +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60

Query: 109 DRTEFGRKGRRLRVE 123
                G    +  ++
Sbjct: 61  KYHNVG--LSKCEIK 73

>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 = 47.8 bits (113), Expect = 5e-08
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGR 115
           I   N   D+   ++  L + Y        ++   AF+ + +   A++AI+   +  F  
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF-- 65

Query: 116 KGRRLRVEWTKHERGIRRPGGGSS 139
           +G+ L V+    +       G SS
Sbjct: 66  RGKDLIVQLQPTDA--LLCSGPSS 87

>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 = 39.7 bits (92), Expect = 5e-05
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 2/77 (2%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRNFAFVQYEVQEDATRALDATN 206
             S  + V N  P  +  +++    + Y  K   V   +  AFV     E A  A+   +
Sbjct: 3   SGSSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 207 MSKLTDRVISVEYAVRD 223
                 + + V+    D
Sbjct: 62  QYSFRGKDLIVQLQPTD 78

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 5e-08
 Identities = 23/110 (20%), Positives = 36/110 (32%), Gaps = 9/110 (8%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATN 206
           +  L V N +P     + L   F  YG +  V+I    +  A VQ      A  A+   N
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 207 MSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGRRRSPSPYRRER 256
             KL  + I +  +      +       R         +    SP  R +
Sbjct: 62  GHKLHGKPIRITLS------KHQNVQLPREGQEDQGLTKDYGNSPLHRFK 105

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 7/99 (7%)

Query: 57  IFCGNF-EYDARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTE 112
           +   N          L  LF  YG V RV +       A + M D   A+ A+  L+  +
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 64

Query: 113 FGRKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSK 151
               G+ +R+  +KH+  ++ P  G   +  + +   S 
Sbjct: 65  LH--GKPIRITLSKHQN-VQLPREGQEDQGLTKDYGNSP 100

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 7/89 (7%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------FAFVQYEVQE 196
           PS        +F+ N        + L   F  +G I+S ++  +      + FV +E QE
Sbjct: 1   PSLRKSGVGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 59

Query: 197 DATRALDATNMSKLTDRVISVEYAVRDDD 225
            A RA++  N   L DR + V       +
Sbjct: 60  AAERAIEKMNGMLLNDRKVFVGRFKSRKE 88

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 10/81 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG------FAFIYMDDERDAEDAIRGLDR 110
           IF  N +       L   F  +G +    +         + F++ + +  AE AI  ++ 
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 70

Query: 111 TEFGRKGRRLRVEW--TKHER 129
                  R++ V    ++ ER
Sbjct: 71  MLLN--DRKVFVGRFKSRKER 89

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           +F  +   +A++ +++  F  YG++  + +          G+A +  +  + A  A   L
Sbjct: 10  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  E    G+ ++V+W  
Sbjct: 70  NGAEIM--GQTIQVDWCF 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 42.0 bits (98), Expect = 8e-06
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 9/81 (11%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
               LFV +      +  +++  F  YG+I ++ +  +        +A V+YE  + A  
Sbjct: 6   EGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 64

Query: 201 ALDATNMSKLTDRVISVEYAV 221
           A +A N +++  + I V++  
Sbjct: 65  AKEALNGAEIMGQTIQVDWCF 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 11/87 (12%)

Query: 147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDA 198
            + +  L V+   P+ T  +DL+ +F  +G+++ V+++++        F FV++   E  
Sbjct: 5   VQKTSDLIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 199 TRALDATNMSKLTDRVISVEYAVRDDD 225
            + +       +  R    +       
Sbjct: 64  VKVMS--QRHMIDGRWCDCKLPNSKQS 88

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 12/78 (15%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAIRGL 108
           +      +   + DL+  F  +G+V       D     S GF F+   +       +   
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 109 DRTEFGRKGRRLRVEWTK 126
              +    GR    +   
Sbjct: 71  HMID----GRWCDCKLPN 84

>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 = 46.7 bits (110), Expect = 1e-07
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
           ++  NF     Q ++  L +    V                FA+I +  + DA   +  L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  +    G  L  + + 
Sbjct: 64  NGLKIE--GYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.5 bits (99), Expect = 5e-06
 Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 9/77 (11%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQEDATRALD 203
           TL++ NF P     R++    +    +       +         A++    +EDA   ++
Sbjct: 3   TLWMTNF-PPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 204 ATNMSKLTDRVISVEYA 220
             N  K+    +  + +
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 19/100 (19%)

Query: 149 PSKTLFVIN-FDP--------YHTRTRDLERHFEPYGKIISVRIRRN----------FAF 189
           P++ L ++N   P        Y     D+      YG + S+ I R             F
Sbjct: 3   PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
           V++    D  +A+      K  +RV+  +Y   D   RR+
Sbjct: 63  VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRD 102

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 12/77 (15%)

Query: 63  EYDARQSDLERLFRRYGKV----------DRVDMKSGFAFIYMDDERDAEDAIRGLDRTE 112
           EY+    D+     +YG V                 G  F+      D + A++GL   +
Sbjct: 23  EYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK 82

Query: 113 FGRKGRRLRVEWTKHER 129
           F    R +  ++   + 
Sbjct: 83  FA--NRVVVTKYCDPDS 97

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 9/86 (10%)

Query: 143 PSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEV 194
           P+     + T+ V N     TR  DL+  F P+G I  + + ++        FAF+ +  
Sbjct: 1   PNRRADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 59

Query: 195 QEDATRALDATNMSKLTDRVISVEYA 220
           +EDA RA+   +       +++VE+A
Sbjct: 60  REDAARAIAGVSGFGYDHLILNVEWA 85

>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 = 45.0 bits (106), Expect = 7e-07
 Identities = 26/78 (33%), Positives = 35/78 (44%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGL 108
           I   N   D R++DL+ LFR +G + R+ +          GFAFI      DA  AI G+
Sbjct: 11  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 70

Query: 109 DRTEFGRKGRRLRVEWTK 126
               +      L VEW K
Sbjct: 71  SGFGYD--HLILNVEWAK 86

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQ 195
           S+ +  S  LFV N   Y +   DLE+ F  YG +  +    +        FAFV +   
Sbjct: 2   SSGSSGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 196 EDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
           E A +A    +      R++ V  +    +  ++G S
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.9 bits (108), Expect = 4e-07
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 10/90 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSG--------FAFIYMDDERDAEDAIRGL 108
           +F  N  Y + + DLE+LF  YG +  +             FAF+       A  A   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGS 138
           D   F   GR L V  +  ++   + G  S
Sbjct: 71  DGQVFQ--GRMLHVLPSTIKKEASQSGPSS 98

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRV------DMKSGFAFIYMDDERDAEDAIRGL 108
           + +   N  +  R  DL ++F ++GK+  V          GF F+  ++  DA+ A   L
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 71

Query: 109 DRTEFGRKGRRLRVEWTK 126
             T     GR++ V    
Sbjct: 72  HGTVVE--GRKIEVNNAT 87

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 4e-07
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 144 STNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQED 197
           S +    K L V N  P+  R  DL + F  +GKI+ V I       + F FV +E   D
Sbjct: 5   SESKSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 198 ATRALDATNMSKLTDRVISVEYA 220
           A RA +  + + +  R I V  A
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNA 86

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRAL 202
           + LF+     + T    L  HFE +G +    +         R F FV Y   E+   A+
Sbjct: 7   RKLFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 203 DATNMSKLTDRVISVEYAV 221
           +A    K+  RV+  + AV
Sbjct: 66  NARPH-KVDGRVVEPKRAV 83

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 11/79 (13%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAI 105
           +R +F G   ++     L   F ++G +    +          GF F+      + + A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 106 RGLDRTEFGRKGRRLRVEW 124
                 +    GR +  + 
Sbjct: 66  N-ARPHKVD--GRVVEPKR 81

>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 = 45.5 bits (107), Expect = 6e-07
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 9/99 (9%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFA 188
              A            LF+ +  P     +DL + F P+G ++S ++         + F 
Sbjct: 5   SIGAAGSQKEGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 63

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDR 227
           FV Y+    A  A+ + N  ++  + + V+     +D +
Sbjct: 64  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGL 108
           +F  +   +    DL ++F  +G V    +           F F+  D+   A+ AI+ +
Sbjct: 21  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 80

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +  + G   +RL+V+  +
Sbjct: 81  NGFQIG--MKRLKVQLKR 96

>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 = 44.6 bits (105), Expect = 7e-07
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 10/76 (13%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATRALDA 204
           +F+     + T  +DL+ +F  +G+++   ++ +        F FV ++  E   + +D 
Sbjct: 2   MFIGGL-SWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 205 TNMSKLTDRVISVEYA 220
               KL  +VI  + A
Sbjct: 61  -KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 5e-06
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 11/75 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSG-FAFIYMDDERDAEDAIRGL 108
           +F G   +D  + DL+  F ++G+V       D +  +S  F F+   +    +  +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 109 DRTEFGRKGRRLRVE 123
              +    G+ +  +
Sbjct: 61  KEHKLN--GKVIDPK 73

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 11/76 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG--------KVDRVDMKSGFAFIYMDDERDAEDAIRGL 108
           IF G    +    D++  F ++G             +   GF F+  + E   E     +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 109 DRTEFGRKGRRLRVEW 124
              E     + +  + 
Sbjct: 61  HFHEIN--NKMVECKK 74

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 8e-06
 Identities = 12/76 (15%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQEDATRALDA 204
           +FV      +T   D++ +FE +GK+    +  +          FV +E ++   +  + 
Sbjct: 2   IFVGGL-SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 205 TNMSKLTDRVISVEYA 220
            +  ++ ++++  + A
Sbjct: 61  -HFHEINNKMVECKKA 75

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 10/94 (10%)

Query: 140 ARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQ 191
             R        + LF+     + T    L  ++E +GK+    +         R F FV 
Sbjct: 10  LERKKREKEQFRKLFIGGL-SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 68

Query: 192 YEVQEDATRALDATNMSKLTDRVISVEYAVRDDD 225
           +    +   A+ A     +  RV+  + AV  ++
Sbjct: 69  FSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE 101

>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 = 43.1 bits (101), Expect = 3e-06
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 13/87 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAI 105
            R +F G   ++  +  L   + ++GK+    +          GF F+      + + A+
Sbjct: 20  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 106 RGLDRTEFGRKGRRLRVEWT--KHERG 130
                      GR +  +    + E G
Sbjct: 80  A-ARPHSID--GRVVEPKRAVAREESG 103

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 12/101 (11%)

Query: 49  AFEAMMRPIFCGNFEYDARQSDLERLFR--------RYGKVDRVDMKSGFAFIYMDDERD 100
           A +  +R +F GN  Y+A +  L+ +F         R           G+ F    D+  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 101 AEDAIRGLDRTEFGRKGRRLRVEW--TKHERGIRRPGGGSS 139
           A  A+R L+  EF   GR LRV+   ++  +   +  G  +
Sbjct: 63  ALSAMRNLNGREFS--GRALRVDNAASEKNKEELKSLGTGA 101

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 23/106 (21%), Positives = 43/106 (40%), Gaps = 20/106 (18%)

Query: 148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNF--------AFVQYEVQEDAT 199
           R  +++FV N  PY      L+  F   G ++S R+  +          F +Y+ QE A 
Sbjct: 6   RSLRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 200 RALDATNMSKLTDRVISVEYAVRDDDDRRNGHSPDRNRDRSPDRGR 245
            A+   N  + + R + V+ A           + ++N++     G 
Sbjct: 65  SAMRNLNGREFSGRALRVDNA-----------ASEKNKEELKSLGT 99

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 7e-06
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDA 204
           PS TL + N  P      DL+  F   G ++         R  A +Q    E+A +AL  
Sbjct: 9   PSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 205 TNMSKLTD-RVISVEYA 220
            +   L +   + V ++
Sbjct: 68  LHNHDLGENHHLRVSFS 84

>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 = 41.7 bits (97), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV----DRVDMKSGFAFIYMDDERDAEDAIRGLDR 110
             +   N      + DL+ LF   G V             A I M    +A  A+  L  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 70

Query: 111 TEFGRKGRRLRVEWTK 126
            + G +   LRV ++K
Sbjct: 71  HDLG-ENHHLRVSFSK 85

>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 = 41.8 bits (97), Expect = 9e-06
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTE 112
           R +       +  ++++  L   +GKV  + M      AF+ +  E  A   +       
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 68

Query: 113 FGRKGRRLRVEWTKHER 129
              + + + ++++ H+ 
Sbjct: 69  PHLRNQPIYIQYSNHKE 85

>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 = 40.2 bits (93), Expect = 3e-05
 Identities = 15/81 (18%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKI--ISVRIRRNFAFVQYEVQEDATRALD 203
           +  PS+ L +    P      ++     P+GK+  I +   +N AF++   +E A   ++
Sbjct: 4   DGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVN 62

Query: 204 ATNMSKLT--DRVISVEYAVR 222
             +       ++ I ++Y+  
Sbjct: 63  YYSAVTPHLRNQPIYIQYSNH 83

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 9e-06
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 52  AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDA 104
           + +  +       +  +     +  +YG+V+ +++         G  ++    E DAE A
Sbjct: 25  SAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKA 84

Query: 105 IRGLDRTEFGRKGRRLRVEWT 125
           +  L+   F   G+ +  E +
Sbjct: 85  VIDLNNRWFN--GQPIHAELS 103

>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 = 41.9 bits (98), Expect = 1e-05
 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 7/60 (11%)

Query: 167 DLERHFEPYGKIISVRIRRNF-------AFVQYEVQEDATRALDATNMSKLTDRVISVEY 219
                 E YG++  + +  N         +V++  +EDA +A+   N      + I  E 
Sbjct: 43  VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 4/75 (5%)

Query: 152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--NFAFVQYEVQEDATRALDATNMSK 209
            + V  F         +   F  YG I+   +    N+  ++Y+ +  A +AL       
Sbjct: 6   WVTVFGFPQ--ASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIF 63

Query: 210 LTDRVISVEYAVRDD 224
               +I V+  +  +
Sbjct: 64  GESIMIGVKPCIDKN 78

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 10/105 (9%)

Query: 136 GGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNF 187
           G S +        P  T F+ N  PY      ++  F           R        + F
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNL-PYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGF 59

Query: 188 AFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRNGHS 232
            + ++E  +    AL + N   L ++ I V+ A +  D      S
Sbjct: 60  GYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 36.2 bits (83), Expect = 0.001
 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 13/91 (14%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGL 108
            F GN  YD  +  ++  FR                    GF +   +D      A+  L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 76

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSS 139
           +    G   +R+RV+     +   +  G SS
Sbjct: 77  NEESLG--NKRIRVDVADQAQ--DKDSGPSS 103

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 11/91 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIRGL 108
           IF G   Y    + L + F  +G ++   + +        G+ F+ M D   AE A +  
Sbjct: 13  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 72

Query: 109 DRTEFGRKGRRLRVEWTKHERGIRRPGGGSS 139
           +       GR+  V         R    G +
Sbjct: 73  NPI---IDGRKANVNLAYLGAKPRSLQTGFA 100

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 7e-04
 Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 14/99 (14%)

Query: 139 SARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRR--------NFAFV 190
            +++ +T T+    +FV    PYHT    L ++FE +G I    +           + FV
Sbjct: 3   GSQKDTTFTK----IFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 57

Query: 191 QYEVQEDATRALDATNMSKLTDRVISVEYAVRDDDDRRN 229
               +  A RA    N   +  R  +V  A      R  
Sbjct: 58  TMADRAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSL 95

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 10/73 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG--------KVDRVDMKSGFAFIYMDDERDAEDAIRGL 108
           ++    +      DL +L + YG             +   G+ F+  D    A+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 109 DRTEFGRKGRRLR 121
             +    + +  +
Sbjct: 61  KASGV--QAQMAK 71

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 4/75 (5%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKV---DRVDMKSGFAFIYMDDERDAEDAIRGLDRT 111
           + +F  N   +  +  L  LF ++        V  +   AF+    E  +  A   L   
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGF 68

Query: 112 EFGRKGRRLRVEWTK 126
           +       +++ + K
Sbjct: 69  KIT-PTHAMKITFAK 82

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.8 bits (92), Expect = 4e-05
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKII---SVRIRRNFAFVQYEVQEDATRALDAT 205
           P++ LF+ N  P  T    L   F  +        V  R + AFV++  +  +  A +A 
Sbjct: 7   PNQILFLTNL-PEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 206 NMSKLTD-RVISVEYA 220
              K+T    + + +A
Sbjct: 66  QGFKITPTHAMKITFA 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 = 40.4 bits (94), Expect = 2e-05
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 14/92 (15%)

Query: 137 GSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHF-EPYGKIISVRIRRN-------FA 188
           G+S+ +P         + V N  P+     ++   F        SV ++ N        A
Sbjct: 1   GASSGKPGPTI-----IKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 54

Query: 189 FVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
            V +E +++AT A+   N   +  R + +   
Sbjct: 55  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 40.4 bits (94), Expect = 3e-05
 Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 10/76 (13%)

Query: 57  IFCGNFEYDARQSDLERLFRRYG--------KVDRVDMKSGFAFIYMDDERDAEDAIRGL 108
           I   N  +     ++   F  Y         K +   M +G A +  +   +A  A+  L
Sbjct: 12  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 71

Query: 109 DRTEFGRKGRRLRVEW 124
           +    G   R++++  
Sbjct: 72  NDRPIG--SRKVKLVL 85

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 9/86 (10%)

Query: 150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRA 201
              LFV     + T  + LE+ F  YG+I  V +         R F FV +E  +DA  A
Sbjct: 5   EGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 202 LDATNMSKLTDRVISVEYAVRDDDDR 227
           + A N   +  R I V+ A +  D+R
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSSDNR 89

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 10/78 (12%)

Query: 57  IFCGNFEYDARQSDLERLFR--------RYGKVDRVDMKSGFAFIYMDDERDAEDAIRGL 108
           +F G   +D  +  LE++F            K        GF F+  ++  DA+DA+  +
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 109 DRTEFGRKGRRLRVEWTK 126
           +       GR++RV+   
Sbjct: 68  NGKSVD--GRQIRVDQAG 83

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 7e-05
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 10/79 (12%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRG 107
           R ++   F  DA   D++      G+V  + M+        G  F+  D    A+  +  
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE- 65

Query: 108 LDRTEFGRKGRRLRVEWTK 126
               ++  K   L + +  
Sbjct: 66  TPGQKY--KETDLLILFKD 82

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 7e-05
 Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 11/78 (14%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKS-GFAFIYMDDERDAEDAI 105
           ++ IF G  + D  +  L   F +YGK+       DR   K  GFAF+  DD  D+ D I
Sbjct: 2   VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 60

Query: 106 RGLDRTEFGRKGRRLRVE 123
                      G    V 
Sbjct: 61  VIQKYHTVN--GHNCEVR 76

>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 = 39.2 bits (91), Expect = 7e-05
 Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 14/95 (14%)

Query: 138 SSARRPSTNT----RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN------- 186
           S  R P  N     R ++T+F +       R RDLE  F   GK+  VRI  +       
Sbjct: 2   SPVREPVDNLSPEERDARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 187 -FAFVQYEVQEDATRALDATNMSKLTDRVISVEYA 220
             A+V++   +    A+      +L    I V+ +
Sbjct: 61  GIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS 94

>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 = 36.9 bits (85), Expect = 6e-04
 Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS--------GFAFIYMDDERDAEDAIR 106
           R +FC       R  DLE  F   GKV  V + S        G A++   + +       
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAI 77

Query: 107 GLDRTEFGRKGRRLRVEWTKHER 129
           GL        G  + V+ ++ E+
Sbjct: 78  GLTGQRLL--GVPIIVQASQAEK 98

>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 = 8e-05
 Identities = 13/91 (14%), Positives = 23/91 (25%), Gaps = 17/91 (18%)

Query: 146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN----------------FAF 189
               +  ++V           DL   F+  G +   +                     A 
Sbjct: 4   EDSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 190 VQYEVQEDATRALDATNMSKLTDRVISVEYA 220
           V YE    A  A++  +        + V  A
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 8e-05
 Identities = 14/86 (16%), Positives = 23/86 (26%), Gaps = 18/86 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDD----------------ERD 100
           I+           DL   F++ G V               D                   
Sbjct: 11  IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 70

Query: 101 AEDAIRGLDRTEFGRKGRRLRVEWTK 126
           A+ A+   D  +F   G +L+V   +
Sbjct: 71  AKAAVEWFDGKDFQ--GSKLKVSLAR 94

>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 = 38.6 bits (89), Expect = 1e-04
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 15/95 (15%)

Query: 145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQE 196
           ++    KT+F+ N   + +    L    + +G +  VR+  +         AF Q+  QE
Sbjct: 3   SDVTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 197 DATRALDATNMS------KLTDRVISVEYAVRDDD 225
            A + L A ++       KL  R + V+ AV  D+
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (87), Expect = 3e-04
 Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 12/84 (14%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRV--------DMKSGFAFIYMDDERDAEDAIR 106
           + +F  N  +D+ +  L  + +++G +  V        +   G AF     +  A+  + 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 107 GLDRTEFGRK----GRRLRVEWTK 126
                  G      GR+L+V+   
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 14/94 (14%), Positives = 29/94 (30%), Gaps = 18/94 (19%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-------------GFAFIYMDDERDA 101
           R ++ GN  +   +  +   F    ++  +                  FAF+      + 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 102 EDAIRGLDRTEFGRKGRRLRVEWTKHERGIRRPG 135
             A+   D   F   G+ L++      +    PG
Sbjct: 62  TQAMA-FDGIIFQ--GQSLKIRRPHDYQP--LPG 90

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.5 bits (91), Expect = 2e-04
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 12/97 (12%)

Query: 54  MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGF--------AFIYMDDERDAEDAI 105
           +R +          +  L +LF RYG ++ V +             F+       A+ AI
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 106 RGLDRTEFGRKGRRLRVEWTKHERGIRRPGGGSSARR 142
            GL+        +RL+V         +RPG   +   
Sbjct: 102 AGLNGFNIL--NKRLKVALAASGH--QRPGIAGAVGD 134

>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 = 37.6 bits (86), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDR-VDMKSGFAFIYMDDERDAEDAIRGLDRTEFGR 115
           I       D    ++  L   Y      VD   G AF+ + +   AE AI    ++    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL-- 58

Query: 116 KGRRLRVEWTKHE 128
           + R L V+    +
Sbjct: 59  RERELSVQLQPTD 71

>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 = 33.7 bits (76), Expect = 0.004
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 153 LFVINFDPYHTRTRDLERHFEPYGKI-ISVRIRRNFAFVQYEVQEDATRALDATNMSKLT 211
           + +    P     +++      Y      V   +  AFV     E A  A++  + S+L 
Sbjct: 1   ILIRGL-PGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLR 59

Query: 212 DRVISVEYAVRD 223
           +R +SV+    D
Sbjct: 60  ERELSVQLQPTD 71

>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 = 38.2 bits (88), Expect = 2e-04
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN--------FAFVQYEVQEDATR 200
           P+K L++ N        RDL   F  + +     I+           AF+ +  +E A +
Sbjct: 17  PNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 201 ALDATNMSKLTDRVISVEYAVRDDD 225
           AL   N  KL  +++ +E+      
Sbjct: 76  ALHLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 55  RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIR 106
           + ++  N      + DL  LF R+ +     ++         G AFI   ++  A  A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 107 GLDRTEFGRKGRRLRVEWTKHER 129
            ++  +    G+ L +E+ K+++
Sbjct: 79  LVNGYKLY--GKILVIEFGKNKK 99

>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 = 36.8 bits (84), Expect = 4e-04
 Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 9/73 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDR 110
           +   N      Q+ + + F+  G +  VD+         FA I       A  AI    +
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 62

Query: 111 TEFGRKGRRLRVE 123
                    + V 
Sbjct: 63  V---VGQNEIIVS 72

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.6 bits (84), Expect = 5e-04
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 13/82 (15%)

Query: 55  RPIFCGNFEYDARQSD-LERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDA 104
           R I   N   +    + L   F  +G ++++++          +  AF+  +++  AE A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 105 IRGLDRTEFGRKGRRLRVEWTK 126
           ++ ++R+  G   R + V    
Sbjct: 65  LQ-MNRSLLG--NREISVSLAD 83

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 6e-04
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 9/77 (11%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLD 109
           ++  N      + +LE + + +G+V    +         G  F  M+     E  I   +
Sbjct: 21  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 80

Query: 110 RTEFGRKGRRLRVEWTK 126
                 K        T+
Sbjct: 81  GKFI--KTPPGVSAPTE 95

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 7e-04
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 3/86 (3%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIY-MDDERDAEDAIRGLDRTEFGR 115
           +            DL+   R  G V   D+      +     + D   A+R LD T+F  
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF-- 60

Query: 116 KGRRLRVEWTKHERGIRRPGGGSSAR 141
           +       + + +    R      +R
Sbjct: 61  RSHEGETAYIRVKVDGPRSPSYGRSR 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 8e-04
 Identities = 12/80 (15%), Positives = 23/80 (28%), Gaps = 16/80 (20%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV--------------DRVDMKSGFAFIYMDDERDAE 102
           +F           ++ +    +GK                     S  A++      DA 
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 103 DAIRGLDRTEFGRKGRRLRV 122
            AI+ ++       GR L+ 
Sbjct: 71  RAIQCVNNVVVD--GRTLKA 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 0.001
 Identities = 19/84 (22%), Positives = 30/84 (35%), Gaps = 5/84 (5%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMKS-GFAFIYMDDERDAEDAIRGLDRTEFGR 115
           +            DL+   R  G V   D++  G   +    + D E A+R LD T+F  
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKF-- 75

Query: 116 KGRRLRVEWTKHERGIRRPGGGSS 139
           +       + +      R  G SS
Sbjct: 76  RSHEGETSYIRVYP--ERSSGPSS 97

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 4/97 (4%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFG 114
           I   N       ++++  F R+G + RV +      A +   +  +A  A R L  ++F 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF- 71

Query: 115 RKGRRLRVEWTKHERGIRRPGGGSSARRPSTNTRPSK 151
                L +EW         P    S          S 
Sbjct: 72  -HHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESG 107

>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 = 35.3 bits (80), Expect = 0.002
 Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 10/77 (12%)

Query: 57  IFCGNFEYDARQSDLERLFRRYGKV-------DRVDMKSGFAFIYMDDERDAEDAIRGLD 109
           +F GN   +   ++L+                 R      F ++  +   D E A+  L 
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LT 74

Query: 110 RTEFGRKGRRLRVEWTK 126
             +    G  +++E  K
Sbjct: 75  GLKVF--GNEIKLEKPK 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	425
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.76
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.75
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.74
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.73
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.73
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.73
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.72
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.71
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.7
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.7
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.7
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.7
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.7
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.7
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.69
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.68
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.68
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.67
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.67
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.66
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.66
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.65
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.65
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.64
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.64
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.64
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.64
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.63
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.63
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.62
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.62
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.62
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.61
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.61
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.6
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.6
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.6
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.6
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.6
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.59
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.59
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.59
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.59
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.58
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.56
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.56
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.55
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.55
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.54
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.54
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.54
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.54
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.54
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.54
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.53
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.53
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.52
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.51
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.51
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.51
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.51
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.5
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.49
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.49
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.48
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.47
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.45
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.44
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.44
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	99.43
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.43
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.39
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.38
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.35
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.29
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.29
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.28
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.22
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	99.17
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.16
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.12
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.1
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.64
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.61
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.57
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.22
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.17
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.49
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.24
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.12

>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=99.95  E-value=6.3e-28  Score=212.57  Aligned_cols=157  Identities=20%  Similarity=0.380  Sum_probs=132.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      +.+++|||+|||+.+|+++|.++|++||.|..|.+.        +|||||+|.+.++|.+|+. +++..+  .+..+.+.
T Consensus         4 ~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~--~~~~~~~~   80 (183)
T d1u1qa_           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKV--DGRVVEPK   80 (183)
T ss_dssp             HHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEE--TTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcc--cccchhhh
Confidence            456899999999999999999999999999999872        7899999999999999995 455556  57777777


Q ss_pred             EeccccCCCCCCCCCCCCCCCCCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCH
Q 014384          124 WTKHERGIRRPGGGSSARRPSTNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQ  195 (425)
Q Consensus       124 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~  195 (425)
                      +.......          ..........+|||+|| |..+++++|.++|..||.|..+.+.        +|||||+|.+.
T Consensus        81 ~~~~~~~~----------~~~~~~~~~~~i~V~~l-p~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~  149 (183)
T d1u1qa_          81 RAVSREDS----------QRPGAHLTVKKIFVGGI-KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  149 (183)
T ss_dssp             ECCCTTGG----------GSTTTTCCCSEEEEECC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCH
T ss_pred             hhhhcccc----------cccccccccceeEEccC-CCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCH
Confidence            65433311          11223456689999999 8899999999999999999999885        56999999999


Q ss_pred             HHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          196 EDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       196 ~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ++|.+|++ +++..|+|+.|.|.+|..+
T Consensus       150 e~A~~Al~-~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         150 DSVDKIVI-QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             HHHHHHHT-SSCEEETTEEEEEEECCCH
T ss_pred             HHHHHHHH-hCCCeECCEEEEEEecCCc
Confidence            99999997 7888999999999998654

>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=99.78  E-value=3.3e-19  Score=134.93  Aligned_cols=72  Identities=24%  Similarity=0.479  Sum_probs=68.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+++|+++|.++|++||.|..|.|        ++|||||+|.+.++|+.|+..|||..|  .|+.|.|+||
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~--~g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEc
Confidence            468999999999999999999999999999998        379999999999999999999999999  8999999998


Q ss_pred             cc
Q 014384          126 KH  127 (425)
Q Consensus       126 ~~  127 (425)
                      ++
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.77  E-value=4.4e-19  Score=134.27  Aligned_cols=71  Identities=20%  Similarity=0.469  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ++|||+|||+.+|+++|.++|++||+|..|.|        .+|||||+|.+.++|+.|+..|||..|  +|+.|.|+||+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~--~g~~l~v~~Ak   80 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL--QTKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEee
Confidence            57999999999999999999999999999998        278999999999999999999999999  89999999987


Q ss_pred             c
Q 014384          127 H  127 (425)
Q Consensus       127 ~  127 (425)
                      +
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=7.2e-19  Score=136.27  Aligned_cols=76  Identities=24%  Similarity=0.527  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|..|+..|||..|  +|+.|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~gr~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL--DDRIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEE--TTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEE
Confidence            45789999999999999999999999999999998        268999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      |+....
T Consensus        83 ~a~~~~   88 (93)
T d1h2vz_          83 WDAGFK   88 (93)
T ss_dssp             EESCCC
T ss_pred             EcCCCC
Confidence            987543

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=2.1e-19  Score=145.00  Aligned_cols=77  Identities=22%  Similarity=0.404  Sum_probs=71.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +..+++|||+|||..+|+++|.++|++||+|..|.|.     +|||||+|.+.++|..|++.|||..|  .|+.|.|.|+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~--~gr~l~V~~a   81 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNV--CNRYLVVLYY   81 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEEEC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEc
Confidence            4557899999999999999999999999999999994     79999999999999999999999999  8999999998


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      ....
T Consensus        82 ~~~~   85 (114)
T d2f9da1          82 NANR   85 (114)
T ss_dssp             CHHH
T ss_pred             CCCc
Confidence            7543

>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=99.77  E-value=3.2e-19  Score=139.51  Aligned_cols=77  Identities=30%  Similarity=0.576  Sum_probs=70.4

Q ss_pred             cCCCceEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           51 EAMMRPIFCGNFE-YDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        51 ~~~~~~l~V~nL~-~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .....+|||+||+ ..+++++|+++|.+||+|..|.|++|||||+|.+.++|++||+.|||+.|  +|+.|.|+|+....
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~rg~aFV~f~~~~~A~~Ai~~lng~~~--~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMI--AGQVLDINLAAEPK   89 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEETEEEEEEESSHHHHHHHHHTTTTCEE--TTEECEEEETTSCC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEeCCeEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECCCCC
Confidence            3455789999997 57888999999999999999999999999999999999999999999999  89999999997543

>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=6.5e-19  Score=135.73  Aligned_cols=78  Identities=21%  Similarity=0.466  Sum_probs=71.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||.++|+++|.++|+.||+|..|.|.      +|||||+|.+.++|..|+..|||..|  .|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~--~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKI--LGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            34567899999999999999999999999999999883      78999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ||....
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            997643

>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=99.76  E-value=6.5e-19  Score=135.42  Aligned_cols=75  Identities=25%  Similarity=0.508  Sum_probs=69.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|++|+..|||..|  +|+.|.|.
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i--~g~~l~v~   80 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--FGRTIRVN   80 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE--TTEEEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            34689999999999999999999999999999998        379999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      ||.+.
T Consensus        81 ~a~p~   85 (89)
T d2cqba1          81 LAKPM   85 (89)
T ss_dssp             ECCCC
T ss_pred             EeCCC
Confidence            99754

>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=99.76  E-value=1e-18  Score=133.99  Aligned_cols=75  Identities=19%  Similarity=0.463  Sum_probs=69.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....+|||+|||..+|+++|.++|++||+|..|.|        ++|||||+|.+.++|+.|+..|||..|  +|+.|.|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l--~g~~l~V~   82 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI--MGQTIQVD   82 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            34679999999999999999999999999999988        278999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      ||..+
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            99753

>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=99.76  E-value=2.1e-18  Score=135.34  Aligned_cols=76  Identities=29%  Similarity=0.475  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+.+|+++|+++|.+||+|..|.|.        +|||||+|.+.++|.+||+.|||..|  +|+.|+|.
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~--~gr~i~V~   83 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF--QGRMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEES--SSCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            456789999999999999999999999999999982        78999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ++....
T Consensus        84 ~a~~~~   89 (99)
T d1whwa_          84 PSTIKK   89 (99)
T ss_dssp             ECCCCS
T ss_pred             ECCCCC
Confidence            998765

>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=99.76  E-value=1.1e-18  Score=135.30  Aligned_cols=77  Identities=23%  Similarity=0.385  Sum_probs=70.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||..+|+++|+++|++||.|..|.|        ++|||||+|.+.++|++|+..|||..|  +|+.|+|
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V   83 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL--YGKPIRV   83 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC--SSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEE--CCEEEEE
Confidence            345679999999999999999999999999999988        378999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .||....
T Consensus        84 ~~A~~~~   90 (93)
T d1x5ua1          84 NKASAHN   90 (93)
T ss_dssp             EETTTTS
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.75  E-value=1e-18  Score=132.42  Aligned_cols=76  Identities=16%  Similarity=0.286  Sum_probs=69.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ...++++|||+|||..+|+++|.++|++||+|..|.+   .+|||||+|.+.++|..|+..|||..|+ .|+.|+|.||+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKIT-PTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSS-TTCBCEEEECC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeC-CCcEEEEEEec
Confidence            3456789999999999999999999999999999998   3799999999999999999999999884 57899999986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.7e-18  Score=134.81  Aligned_cols=78  Identities=17%  Similarity=0.431  Sum_probs=71.7

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .....++|||+|||..+|+++|.++|++||+|..|.|.  +|||||+|.+.++|..|+..|||..|  .|+.|+|.|++.
T Consensus        14 ~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i--~g~~l~v~~ak~   91 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTI--EGHVVKCYWGKE   91 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEE--TTEECEEECCCC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCC
Confidence            34456799999999999999999999999999999994  89999999999999999999999999  899999999976


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.75  E-value=1.1e-18  Score=131.20  Aligned_cols=70  Identities=21%  Similarity=0.495  Sum_probs=66.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      +|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.++++|..|++.|||..|  .|+.|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~--~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI--KGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEE--TTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEeCC
Confidence            69999999999999999999999999999983        68999999999999999999999999  899999999853

>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=99.75  E-value=1.9e-18  Score=133.93  Aligned_cols=78  Identities=24%  Similarity=0.488  Sum_probs=71.6

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .....++|||+|||+.+|+++|.++|++||+|..|.|.      +|||||+|.+.++|.+|+..|||..|  +|+.|.|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~--~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVV--EGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            34556789999999999999999999999999999983      79999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ||....
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998643

>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=99.75  E-value=9.9e-19  Score=134.66  Aligned_cols=76  Identities=34%  Similarity=0.581  Sum_probs=70.3

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||.++|+++|.++|++||+|..|.|        ++|||||+|.+.++|.+||+.|||..|  +|+.|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~v   82 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY--DHLILNV   82 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEE--TTEECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            345689999999999999999999999999999988        278999999999999999999999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      +||++.
T Consensus        83 ~~akp~   88 (90)
T d2cq0a1          83 EWAKPS   88 (90)
T ss_dssp             EESSCC
T ss_pred             EeeeCC
Confidence            999754

>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=1.1e-18  Score=134.19  Aligned_cols=74  Identities=20%  Similarity=0.355  Sum_probs=69.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      ...+|||+|||+.+|+++|.++|.+||.|..|.|.      +|||||+|.+.++|++||+.|||..|  +|+.|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEE--TTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEECC
Confidence            45689999999999999999999999999999983      79999999999999999999999999  89999999997


Q ss_pred             cc
Q 014384          127 HE  128 (425)
Q Consensus       127 ~~  128 (425)
                      ..
T Consensus        85 ~~   86 (89)
T d1cvja2          85 SR   86 (89)
T ss_dssp             CT
T ss_pred             CC
Confidence            64

>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=99.75  E-value=2e-18  Score=129.16  Aligned_cols=69  Identities=17%  Similarity=0.471  Sum_probs=65.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .|||+|||+.+|+++|.++|++||+|..|.|.       +|||||+|.+.++|..|++.|||..|  +|++|.|+++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPL--DGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEE--TTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEee
Confidence            59999999999999999999999999999993       78999999999999999999999999  89999999985

>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=6.4e-19  Score=132.57  Aligned_cols=74  Identities=27%  Similarity=0.426  Sum_probs=67.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCC-eecCCCcEEEEEEecccc
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRT-EFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~-~ig~~gr~l~V~~a~~~~  129 (425)
                      |.+|||+|||+++|+++|.++|++||.|..+.+  .+|||||+|.+.++|.+|++.|||. .|  +|+.|.|+|+.+..
T Consensus         1 mn~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~--~G~~i~V~~a~~k~   77 (80)
T d2cqha1           1 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL--HGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEE--TTEECEEEECCCCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEE--CCEEEEEEEcCCcC
Confidence            468999999999999999999999999866444  6999999999999999999999996 58  89999999998654

>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=99.75  E-value=2.1e-18  Score=133.82  Aligned_cols=76  Identities=30%  Similarity=0.608  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---------eCCEEEEEEcCHHHHHHHHHhc-CCCeecCCCcEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRGL-DRTEFGRKGRRLR  121 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---------~kg~aFV~F~~~~~A~~A~~~l-ng~~ig~~gr~l~  121 (425)
                      ...++|||+|||+.+|+++|.++|++||.|..|.|         ++|||||+|.+.++|.+||..| ||..|  +|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~--~Gr~l~   83 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL--YGRRLV   83 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS--SSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEE--CCEEEE
Confidence            46689999999999999999999999999999998         2789999999999999999988 89988  899999


Q ss_pred             EEEecccc
Q 014384          122 VEWTKHER  129 (425)
Q Consensus       122 V~~a~~~~  129 (425)
                      |+||+...
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99998654

>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=1.9e-18  Score=131.56  Aligned_cols=70  Identities=20%  Similarity=0.504  Sum_probs=65.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      |||+|||+++|+++|.++|++||+|..|.|.           +|||||+|.+.++|.+|+..|||..|  +|+.|.|+|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~--~g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV--DGHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE--TTEECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEC
Confidence            8999999999999999999999999999882           68999999999999999999999999  8999999998


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        79 ~~~   81 (85)
T d2cpfa1          79 ERA   81 (85)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            643

>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=99.74  E-value=2e-18  Score=138.46  Aligned_cols=76  Identities=21%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ...++|||+|||+.+|+++|.+||++||+|..|.|.  +|||||+|.+.++|.+||+.|||..|  .|+.|.|+|+....
T Consensus         8 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_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF--HHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBS--SSSBCEEEEEETTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCcc--CCCeEEEEECCCCc
Confidence            345799999999999999999999999999999994  79999999999999999999999999  89999999997654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2.5e-18  Score=133.76  Aligned_cols=76  Identities=39%  Similarity=0.706  Sum_probs=70.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ....++|||+|||+.+|+++|+++|+.||.|..|.+.     ++||||+|.+.++|+.||+.|||+.|  +|+.|+|+|+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~--~g~~l~V~~a   88 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY--DGYRLRVEFP   88 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEE--TTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEec
Confidence            3556789999999999999999999999999999883     79999999999999999999999999  8999999998


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>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=2.1e-18  Score=132.83  Aligned_cols=76  Identities=26%  Similarity=0.615  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....+|||+|||+++|+++|.++|++||+|..|.+        ++|||||+|.++++|+.|+..|||..|  .|+.|.|+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~--~g~~l~V~   80 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV--DGRQIRVD   80 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT--TSCCCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            35678999999999999999999999999999887        389999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ||....
T Consensus        81 ~a~~~~   86 (90)
T d1x5sa1          81 QAGKSS   86 (90)
T ss_dssp             EEECCC
T ss_pred             EcCCCC
Confidence            997654

>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=99.74  E-value=1.9e-18  Score=130.34  Aligned_cols=71  Identities=18%  Similarity=0.257  Sum_probs=66.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      +||||+|||+.+|+++|.++|+.||+|..+.+        ++|||||+|.+.++|.+|++.|||..|  +|+.|.|.+++
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 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI--EGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcc
Confidence            69999999999999999999999999977665        389999999999999999999999999  89999999987


Q ss_pred             c
Q 014384          127 H  127 (425)
Q Consensus       127 ~  127 (425)
                      +
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=2.7e-18  Score=130.63  Aligned_cols=71  Identities=27%  Similarity=0.535  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCC--cEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKG--RRLRV  122 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~g--r~l~V  122 (425)
                      ..++|||+|||+.+|+++|+++|++||+|..|.|        ++|||||+|.+.++|.+|++.|||..|  .|  ++|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~--~G~~~~i~V   82 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP--SGATEPITV   82 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC--TTCSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEe--CCCCEEEEE
Confidence            4578999999999999999999999999999988        378999999999999999999999999  55  66999


Q ss_pred             EEe
Q 014384          123 EWT  125 (425)
Q Consensus       123 ~~a  125 (425)
                      .||
T Consensus        83 ~~A   85 (85)
T d1fxla2          83 KFA   85 (85)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2e-18  Score=129.53  Aligned_cols=74  Identities=16%  Similarity=0.308  Sum_probs=68.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      +...++|||+||+  +|+++|.++|++||.|..|.+.  +|||||+|.+.++|..|+..|||..|  +|+.|+|.|++.+
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--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV--ESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBC--SSCBCEEEECCSS
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEE--CCEEEEEEEecCC
Confidence            4567899999996  9999999999999999999994  79999999999999999999999999  8999999999754

>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=3.9e-18  Score=130.16  Aligned_cols=75  Identities=16%  Similarity=0.304  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..++|||+|||+.+|+++|.++|++||.|..+.+  .+|||||+|.+.++|..|+..|||..|  .|+.|.|.|+++..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i--~g~~i~V~~akP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL--DGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEE--TTEEEEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEE--CCEEEEEEeccCCC
Confidence            4579999999999999999999999998776666  699999999999999999999999999  89999999997543

>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=99.74  E-value=2.9e-18  Score=131.31  Aligned_cols=75  Identities=23%  Similarity=0.351  Sum_probs=67.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYG-KVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G-~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..++|||+|||+++|+++|+++|.+|| .+..+...+|||||+|.+.++|++|+..|||+.|  +|+.|.|+|++...
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~--~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF--RGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEE--TTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEEcCCCC
Confidence            467999999999999999999999999 4555555799999999999999999999999999  89999999996543

>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=99.74  E-value=3.1e-18  Score=130.40  Aligned_cols=74  Identities=19%  Similarity=0.381  Sum_probs=66.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+.+|+++|.++|++||+|..|.|        ++|||||+|.+.++|..|++.|||..+...+++|.|.
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            45678999999999999999999999999999988        3689999999999999999999999883223889999


Q ss_pred             Ee
Q 014384          124 WT  125 (425)
Q Consensus       124 ~a  125 (425)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.74  E-value=2.4e-18  Score=130.90  Aligned_cols=73  Identities=19%  Similarity=0.390  Sum_probs=68.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .+|||+|||+.+|+++|.++|++||+|..|.|.        +|||||+|.++++|..|+..|||..|  .|+.|.|+||.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l--~g~~l~V~~A~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCC--SSSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECC
Confidence            479999999999999999999999999999983        79999999999999999999999999  79999999997


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        80 ~~~   82 (85)
T d2u2fa_          80 VGA   82 (85)
T ss_dssp             CCC
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=99.73  E-value=3.2e-18  Score=129.70  Aligned_cols=70  Identities=29%  Similarity=0.507  Sum_probs=65.2

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +.+.++|||+|||+.+|+++|+++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|  +|+.|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEE--TTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEE--CCEEeEC
Confidence            3456899999999999999999999999999999882        68999999999999999999999999  8999987

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4e-18  Score=130.67  Aligned_cols=75  Identities=24%  Similarity=0.332  Sum_probs=68.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      .++++|||+|||+++|+++|.++|+.||.|..+.+    .+|||||+|.+.++|.+|+..|||..|+ +|+.|+|.|++.
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 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSS-SSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEec-CCCEEEEEeCCC
Confidence            45789999999999999999999999999987766    3789999999999999999999999885 689999999875

>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=99.73  E-value=3.4e-18  Score=134.78  Aligned_cols=75  Identities=20%  Similarity=0.366  Sum_probs=69.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      +.++|||+|||+++|+++|.++|+.||.|..|.+        ++|||||+|.+.++|+.||..|||..|  .|+.|.|+|
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~--~g~~i~V~~   94 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI--GMKRLKVQL   94 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEE--CCEEEEEEE
Confidence            4578999999999999999999999999999887        268999999999999999999999999  799999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +..+.
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             eCCCC
Confidence            98754

>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=99.73  E-value=3.1e-18  Score=130.57  Aligned_cols=75  Identities=32%  Similarity=0.583  Sum_probs=70.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ..++|||+|||.++|+++|.++|++||+|.+|.|.  +|||||+|.+.++|..|+..|||..|  +|+.|.|+||....
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i--~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL--RGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCB--TTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCcC
Confidence            34679999999999999999999999999999995  79999999999999999999999999  89999999997653

>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=99.73  E-value=9.3e-18  Score=131.07  Aligned_cols=78  Identities=24%  Similarity=0.472  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +.....+|||+||++..+++++|+++|.+||.|+.|.|.+|||||+|.+.++|.+||+.|||..|.|+.|.|+|+..+
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEeCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            344567899999966788899999999999999999999999999999999999999999999999999999998764

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=4.9e-18  Score=128.85  Aligned_cols=73  Identities=16%  Similarity=0.427  Sum_probs=66.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +...++|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|++|++ +++..|  +|+.|.|
T Consensus         3 pe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i--~Gr~i~V   79 (84)
T d1l3ka1           3 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKV--DGRVVEP   79 (84)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEE--TTEECEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEE--CCEEEEE
Confidence            345689999999999999999999999999999988        38999999999999999995 688999  8999999


Q ss_pred             EEec
Q 014384          123 EWTK  126 (425)
Q Consensus       123 ~~a~  126 (425)
                      ..|.
T Consensus        80 ~~A~   83 (84)
T d1l3ka1          80 KRAV   83 (84)
T ss_dssp             EECC
T ss_pred             Eeee
Confidence            8874

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=5.9e-18  Score=135.18  Aligned_cols=74  Identities=26%  Similarity=0.419  Sum_probs=68.2

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEe---CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           54 MRPIFCGNFEY-DARQSDLERLFRRYGKVDRVDMK---SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        54 ~~~l~V~nL~~-~~t~~~L~~lF~~~G~V~~v~i~---kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      +++|||+||++ .+|+++|.++|+.||+|..|.|.   +|||||+|.+.++|.+|++.|||..|  .|+.|.|+|++...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l--~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKL--HGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBC--SSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEE--CCEEEEEEECCCCC
Confidence            57999999965 59999999999999999999983   79999999999999999999999999  89999999987543

>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=99.72  E-value=1.3e-17  Score=139.19  Aligned_cols=77  Identities=23%  Similarity=0.513  Sum_probs=70.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +...++|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|..||+.|||..|  +|+.|.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~--~gr~l~V  116 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI--LNKRLKV  116 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEEC--SSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEE--CCEEEEE
Confidence            345578999999999999999999999999999988        378999999999999999999999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus       117 ~~a~~~~  123 (139)
T d1u6fa1         117 ALAASGH  123 (139)
T ss_dssp             EESSCCC
T ss_pred             EEcCCCC
Confidence            9997544

>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=99.72  E-value=1.2e-17  Score=131.91  Aligned_cols=76  Identities=22%  Similarity=0.496  Sum_probs=68.5

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      +...++|||+|||+.+|+++|.++|++||+|..|.|        ++|||||+|.+.++|++||+.+|+ .|  +|+.|.|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l--~Gr~l~V   83 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-II--DGRKANV   83 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EE--TTEECEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cC--CCEEEEE
Confidence            345678999999999999999999999999999998        379999999999999999988876 67  7999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        84 ~~a~~~~   90 (103)
T d2cqda1          84 NLAYLGA   90 (103)
T ss_dssp             EESTTTC
T ss_pred             EEcCCCC
Confidence            9987654

>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=4.3e-18  Score=134.79  Aligned_cols=73  Identities=34%  Similarity=0.638  Sum_probs=68.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+++|+++|.++|++||+|..|.|.        +|||||+|.+.++|++|+..|||..|  .|+.|.|+|+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~--~g~~i~V~~a   85 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF--SGRALRVDNA   85 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSC--SSSCBEEEET
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEE--CCEEEEEEEC
Confidence            5789999999999999999999999999999882        68999999999999999999999999  8999999998


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        86 ~~~   88 (104)
T d1p1ta_          86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCC
Confidence            653

>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=99.72  E-value=4.4e-18  Score=129.78  Aligned_cols=73  Identities=19%  Similarity=0.422  Sum_probs=66.1

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHHhhcCCeeEEEE---------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           53 MMRPIFCGNFEYDAR-QSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t-~~~L~~lF~~~G~V~~v~i---------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ..++|||+|||+++| +++|+++|++||+|..|.|         ++|||||+|.+.++|++|+ .|||..|  +|+.|.|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~~n~~~~--~gr~l~V   79 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLL--GNREISV   79 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEE--TTEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCCCEE--CCEEEEE
Confidence            468999999999986 5669999999999999988         2789999999999999999 5999999  8999999


Q ss_pred             EEeccc
Q 014384          123 EWTKHE  128 (425)
Q Consensus       123 ~~a~~~  128 (425)
                      .|++.+
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999754

>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=99.71  E-value=1.9e-18  Score=132.13  Aligned_cols=73  Identities=19%  Similarity=0.282  Sum_probs=67.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .+|||+|||+++|+++|+++|++||+|..|.|. .|||||+|.+.++|++||..|||..|  +|+.|.|.++....
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~--~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF--RSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBC--CCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccccceeeEEeCCHHHHHHHHHHhCCCEE--CCcEeEEeEEecCc
Confidence            369999999999999999999999999999984 78999999999999999999999999  89999998876544

>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=99.71  E-value=5.6e-18  Score=132.02  Aligned_cols=78  Identities=21%  Similarity=0.379  Sum_probs=71.4

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .....++|||+|||+++|+++|.++|++||.|..+..   .+|||||+|.+.++|++|+..|||..|  +|+.|.|.|+.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~--~gr~i~V~~a~   89 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTG   89 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEE--TTEEEEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEE--CCEEEEEEEeC
Confidence            3455689999999999999999999999999988776   489999999999999999999999999  89999999998


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        90 ~k~   92 (96)
T d1fjca_          90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            754

>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=99.71  E-value=1.2e-17  Score=130.24  Aligned_cols=78  Identities=24%  Similarity=0.436  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      .++++|||+|||+++|+++|+++|++||+|..|.+.  ++||||+|.+.++|++|+..|||..|...++.|+|+|++..+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~   94 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCC
Confidence            457899999999999999999999999999999994  789999999999999999999999994344689999998643

>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=99.71  E-value=7.2e-18  Score=132.43  Aligned_cols=73  Identities=29%  Similarity=0.456  Sum_probs=67.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ..++|||+|||+++|+++|.++|+.||+|..|.|        ++|||||+|.+.++|.+|+ .|||..|  +|+.|.|.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~--~G~~l~V~~   93 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRL--LGVPIIVQA   93 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEE--TTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEE--CCEEEEEEE
Confidence            3479999999999999999999999999999999        3789999999999999999 5999999  899999999


Q ss_pred             eccc
Q 014384          125 TKHE  128 (425)
Q Consensus       125 a~~~  128 (425)
                      +...
T Consensus        94 a~~~   97 (101)
T d2cq4a1          94 SQAE   97 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            8653

>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=99.71  E-value=1.7e-17  Score=124.42  Aligned_cols=69  Identities=26%  Similarity=0.562  Sum_probs=64.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+++|+++|+++|++||.|..+.+        ++|||||+|.++++|.+|+ .|||..|  +|+.|.|..|
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 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTV--NGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEE--TTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEE--CCEEEEEEEC
Confidence            579999999999999999999999999999888        3799999999999999999 6899999  8999999876

>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=99.70  E-value=1.8e-17  Score=127.77  Aligned_cols=74  Identities=20%  Similarity=0.498  Sum_probs=68.2

Q ss_pred             CCceEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           53 MMRPIFCGNFEYDARQSDLE----RLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~----~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ++++|||+|||+.+|+++|+    ++|++||+|..|.+.     +|||||+|.+.++|..|+..|||..|  .|+.|.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~--~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPF--YDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEE--TTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEE--CCEEEEEE
Confidence            56899999999999999886    468999999999994     79999999999999999999999999  89999999


Q ss_pred             Eeccc
Q 014384          124 WTKHE  128 (425)
Q Consensus       124 ~a~~~  128 (425)
                      ||+..
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99764

>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=99.70  E-value=1e-17  Score=126.83  Aligned_cols=71  Identities=21%  Similarity=0.408  Sum_probs=64.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEE-EE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRV-DM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v-~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      |||+|||+++|+++|.++|++||.|..+ .|        ++|||||+|.+.++|+.|+..|||..|  +|+.|.|.||..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~--~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL--CNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE--TTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEE--CCEEEEEEEecC
Confidence            8999999999999999999999998654 44        279999999999999999999999999  899999999875


Q ss_pred             cc
Q 014384          128 ER  129 (425)
Q Consensus       128 ~~  129 (425)
                      ..
T Consensus        79 k~   80 (83)
T d1x5ta1          79 KD   80 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.70  E-value=1.5e-17  Score=131.05  Aligned_cols=72  Identities=17%  Similarity=0.462  Sum_probs=67.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .++|||+|||+++|+++|+++|.+||+|..|.|        ++|||||+|.+.++|.+|| .++|..|  +|+.|.|.+|
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al-~~~~~~l--~G~~i~V~~a   96 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSI--DGRVVEPKRA   96 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEE--TTEEEEEECC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeE--CCEEEEEEEC
Confidence            478999999999999999999999999999998        3799999999999999999 6899999  8999999998


Q ss_pred             ccc
Q 014384          126 KHE  128 (425)
Q Consensus       126 ~~~  128 (425)
                      ...
T Consensus        97 ~~k   99 (103)
T d1x4ba1          97 VAR   99 (103)
T ss_dssp             SSC
T ss_pred             ccc
Confidence            764

>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=99.70  E-value=2.2e-17  Score=129.12  Aligned_cols=75  Identities=19%  Similarity=0.438  Sum_probs=67.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcC------CCeecCCC
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLD------RTEFGRKG  117 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~ln------g~~ig~~g  117 (425)
                      ...++|||+|||+++|+++|.++|++||.|..+.+        ++|||||+|.+.++|.+||+.||      |..|  +|
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~--~g   83 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--DG   83 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--SS
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE--CC
Confidence            45689999999999999999999999999998888        37999999999999999999887      5566  89


Q ss_pred             cEEEEEEeccc
Q 014384          118 RRLRVEWTKHE  128 (425)
Q Consensus       118 r~l~V~~a~~~  128 (425)
                      +.|.|.|+...
T Consensus        84 r~l~v~~a~~k   94 (98)
T d1x4ha1          84 RQLKVDLAVTR   94 (98)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999999764

>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=99.70  E-value=2.5e-17  Score=126.41  Aligned_cols=75  Identities=15%  Similarity=0.312  Sum_probs=66.9

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ....++|||+|||+++|+++|+++|+.||.|..|.|        ++|||||+|.++++|++||..+  ..|  +|+.|.|
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l--~Gr~i~v   80 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMI--DGRWCDC   80 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEE--TTEEEEE
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--Ccc--CCEEeEE
Confidence            356789999999999999999999999999999998        3799999999999999999754  467  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        81 ~~a~~k~   87 (90)
T d2cqga1          81 KLPNSKQ   87 (90)
T ss_dssp             ECCCTTC
T ss_pred             EeCCCCC
Confidence            9987654

>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=99.70  E-value=2.8e-17  Score=121.77  Aligned_cols=69  Identities=20%  Similarity=0.352  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      |||+|||+++|+++|+++|++|| +..+.+  .+|||||+|.+.++|.+|+..|||..|  .|+.|.|+|+...
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-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL--RERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEES--SSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccC--CCCEEEEEEeCCC
Confidence            79999999999999999999999 555555  599999999999999999999999999  8999999999754

>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=99.70  E-value=1.5e-17  Score=129.96  Aligned_cols=76  Identities=20%  Similarity=0.269  Sum_probs=70.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHER  129 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~~  129 (425)
                      ....+|||+|||+.+|+++|.++|.+||+|+.|.|. +|||||+|.+.++|++||+.|||..|  +|+.|.|.++....
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~lng~~~--~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKF--RSHEGETSYIRVYP   89 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETTTEEEEEESSHHHHHHHHHHHSSEEE--ECTTSCEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccccceEEEEECCHHHHHHHHHHhCCCEe--CCeEEEEEEEecCC
Confidence            345689999999999999999999999999999995 89999999999999999999999999  89999999987654

>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=99.70  E-value=1.5e-17  Score=132.53  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=71.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      +.+..+|||+||++.+|+++|.++|++||.|..|.|    .+|||||+|.++++|+.|+..|||..|...+..|.|.|++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            456788999999999999999999999999999988    3789999999999999999999999985568999999987


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            654

>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=99.70  E-value=1.1e-17  Score=131.63  Aligned_cols=77  Identities=21%  Similarity=0.371  Sum_probs=68.4

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE----------------eCCEEEEEEcCHHHHHHHHHhcCCCeec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM----------------KSGFAFIYMDDERDAEDAIRGLDRTEFG  114 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i----------------~kg~aFV~F~~~~~A~~A~~~lng~~ig  114 (425)
                      ....++|||+|||..+|+++|.++|..||.|..+.+                .+|||||+|.+.++|..||..|||..| 
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~-   83 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF-   83 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE-
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE-
Confidence            456789999999999999999999999998854322                268999999999999999999999999 


Q ss_pred             CCCcEEEEEEecccc
Q 014384          115 RKGRRLRVEWTKHER  129 (425)
Q Consensus       115 ~~gr~l~V~~a~~~~  129 (425)
                       +|+.|.|.||+...
T Consensus        84 -~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 -QGSKLKVSLARKKP   97 (101)
T ss_dssp             -TTEECEEECSSCCC
T ss_pred             -CCEEEEEEEcCCCC
Confidence             89999999998643

>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=99.69  E-value=3.4e-17  Score=124.39  Aligned_cols=72  Identities=19%  Similarity=0.365  Sum_probs=66.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ..++|||+|||.++|+++|.++|+.||.|..|.|.       +|||||+|.++++|.+|| .++|..|  .|+.|.|.|+
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 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKY--KETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHH-TCCCCEE--TTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHH-HHCCCEE--CCEEEEEEEc
Confidence            45799999999999999999999999999999993       789999999999999999 6899999  8999999997


Q ss_pred             cc
Q 014384          126 KH  127 (425)
Q Consensus       126 ~~  127 (425)
                      ..
T Consensus        82 ~d   83 (85)
T d1zh5a2          82 DD   83 (85)
T ss_dssp             GG
T ss_pred             CC
Confidence            54

>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=99.69  E-value=7.9e-18  Score=125.38  Aligned_cols=68  Identities=19%  Similarity=0.466  Sum_probs=63.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ++|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|++|+. +|+..|  +|+.|.|.+|
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-QSRHEL--DSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCC--SSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEE--CCeEEEEEEC
Confidence            57999999999999999999999999999988        37999999999999999995 799999  8999999876

>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=99.69  E-value=2.7e-17  Score=121.84  Aligned_cols=68  Identities=19%  Similarity=0.199  Sum_probs=63.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      ++|||+|||+++|+++|+++|..||+|..|.|.      ++||||+|.++++|.+|+ .||+..|  +|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVV--GQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEE--TTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEE--CCEEEEEEEC
Confidence            589999999999999999999999999999993      679999999999999999 7999999  8999999864

>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=99.69  E-value=2.2e-17  Score=122.34  Aligned_cols=67  Identities=18%  Similarity=0.546  Sum_probs=61.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.++++|++||. +++..|  +|+.|.|..|
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-QKEHKL--NGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCB--TTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEE--CCCEEEeeEC
Confidence            4899999999999999999999999999998        37999999999999999995 788888  8999998643

>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=99.69  E-value=5.2e-18  Score=130.67  Aligned_cols=75  Identities=16%  Similarity=0.266  Sum_probs=67.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .+....+|||+|||+.+|+++|+++|+.||.|..|.|       ++|||||+|.+.++|++|| .|||..|  +|+.|.|
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al-~~~g~~~--~g~~i~V   85 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKV--FGNEIKL   85 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEE--TTEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHH-hcCCcEE--CCEEEEE
Confidence            3455679999999999999999999999999887766       3899999999999999999 5999999  8999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      ++|+.
T Consensus        86 ~~ak~   90 (91)
T d1fjeb1          86 EKPKG   90 (91)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99875

>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=99.68  E-value=2.2e-17  Score=122.51  Aligned_cols=67  Identities=22%  Similarity=0.485  Sum_probs=62.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .|||+|||+++|+++|.++|++||.|..+.+        .+|||||+|.+.++|.+|++ |||..|  +|+.|.|.+|
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-IHFHEI--NNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCB--TTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEE--CCeEEEEEEC
Confidence            4999999999999999999999999999888        27999999999999999994 999999  8999999876

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.5e-17  Score=127.38  Aligned_cols=74  Identities=22%  Similarity=0.363  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ...++|||+|||+++|+++|+++|++||+|..|.+   +++||||+|.+.++|++|+.  ++..|  +|+.|.|.++...
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--EDLII--KGISVHISNAEPK   78 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEE--TTEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEE--CCEEeEEEeCCCC
Confidence            45789999999999999999999999999999988   48999999999999999983  77888  8999999999764


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        79 ~   79 (88)
T d1wf0a_          79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=9.3e-18  Score=131.99  Aligned_cols=75  Identities=17%  Similarity=0.264  Sum_probs=67.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....++|||+|||+++|+++|.++|+.||+|..+.+       ++|||||+|.+.++|.+||..|||..|  .|++|.|.
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i--~gr~~~v~   92 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFI--KTPPGVSA   92 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCC--CCCTTSCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEE--CCcCCccC
Confidence            345679999999999999999999999999998887       378999999999999999999999999  89998887


Q ss_pred             Eecc
Q 014384          124 WTKH  127 (425)
Q Consensus       124 ~a~~  127 (425)
                      ++++
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            6653

>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=99.68  E-value=3.3e-17  Score=125.44  Aligned_cols=77  Identities=16%  Similarity=0.249  Sum_probs=69.8

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhc--CCCeecCCCcEEEEEEec
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGL--DRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~l--ng~~ig~~gr~l~V~~a~  126 (425)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.+.  ++||||+|.+.++|++|+..|  ++..|  .|+.|.|.|++
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~--~g~~l~v~~sk   82 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHL--RNQPIYIQYSN   82 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCcc--CCCEEEEEECC
Confidence            4678999999999999999999999999999999994  899999999999999999866  45677  89999999997


Q ss_pred             ccc
Q 014384          127 HER  129 (425)
Q Consensus       127 ~~~  129 (425)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            643

>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=99.68  E-value=6.8e-17  Score=127.65  Aligned_cols=79  Identities=11%  Similarity=0.169  Sum_probs=69.6

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      ..+..+|||+|||+.+|+++|.++|+.||.|..|.|.  +++|||+|.+.++|+.|+..|++..+.+.|+.|.|.|++.+
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            4568899999999999999999999999999999994  89999999999999999998854433227999999999765


Q ss_pred             c
Q 014384          129 R  129 (425)
Q Consensus       129 ~  129 (425)
                      .
T Consensus        92 ~   92 (104)
T d1wexa_          92 R   92 (104)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.68  E-value=9.9e-18  Score=132.17  Aligned_cols=76  Identities=21%  Similarity=0.327  Sum_probs=69.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      .+.++|||+|||.++|+++|.++|.+||.|..+.+        .+|||||+|.+.++|..||+.|||..|  .|+.|.|.
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~   93 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL--YGKILVIE   93 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC--SSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEE--CCEEEEEE
Confidence            45789999999999999999999999999887666        379999999999999999999999999  89999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ||+...
T Consensus        94 ~ak~k~   99 (102)
T d2cpxa1          94 FGKNKK   99 (102)
T ss_dssp             ECCCCS
T ss_pred             eCCCcc
Confidence            998654

>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=99.68  E-value=5.3e-17  Score=126.40  Aligned_cols=76  Identities=22%  Similarity=0.314  Sum_probs=67.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEe---------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGK-VDRVDMK---------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~-V~~v~i~---------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ++.|||+|||..+|+++|.++|+.||+ |..|.|.         +|||||+|.+.++|..|+..|++..+.+.|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 8889882         689999999999999999999765543379999999


Q ss_pred             Eecccc
Q 014384          124 WTKHER  129 (425)
Q Consensus       124 ~a~~~~  129 (425)
                      ||++..
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            997654

>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=99.67  E-value=7.8e-17  Score=127.38  Aligned_cols=74  Identities=22%  Similarity=0.473  Sum_probs=65.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE---------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM---------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i---------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .+.++|||+|||+++|+++|+++|+.|| |..+.+         .+|||||+|.+.++|++|+ .||+..|  +|+.|.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~--~gr~l~V   88 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL--GNKRIRV   88 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEE--TTEECEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEE--CCEEEEE
Confidence            4568999999999999999999999999 666655         2689999999999998877 7999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .|+....
T Consensus        89 ~~a~~~~   95 (104)
T d1wi8a_          89 DVADQAQ   95 (104)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998654

>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=99.67  E-value=2.9e-17  Score=121.52  Aligned_cols=67  Identities=18%  Similarity=0.455  Sum_probs=61.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           56 PIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        56 ~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .|||+|||+++|+++|.++|++||+|..|.|        ++|||||+|.+.++|++|| .+++..|  +|+.|.|..|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNV--GLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHT-TCSSCCB--TTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHH-hhCCCEE--CCEEeEEEEC
Confidence            5999999999999999999999999999998        3899999999999999999 5677788  7999998764

>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=99.66  E-value=2.4e-16  Score=121.81  Aligned_cols=76  Identities=28%  Similarity=0.425  Sum_probs=70.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...+++|||+|| |..+++++|+++|++||+|..|.++        +|||||+|.+.++|..|++.|||..|+|+.|.|+
T Consensus         4 ~~~s~tlfV~nl-p~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~   82 (93)
T d1h2vz_           4 LKKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD   82 (93)
T ss_dssp             TTTCCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCEEEEeCC-CCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            456789999999 8899999999999999999999985        5699999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      |+...
T Consensus        83 ~a~~~   87 (93)
T d1h2vz_          83 WDAGF   87 (93)
T ss_dssp             EESCC
T ss_pred             EcCCC
Confidence            98654

>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=99.66  E-value=3.3e-17  Score=125.58  Aligned_cols=69  Identities=20%  Similarity=0.370  Sum_probs=63.5

Q ss_pred             CCceEEEcCCCCCCCHHHH---HHHHhhcCCeeEEEEe-----------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCc
Q 014384           53 MMRPIFCGNFEYDARQSDL---ERLFRRYGKVDRVDMK-----------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGR  118 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L---~~lF~~~G~V~~v~i~-----------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr  118 (425)
                      ..++|||+|||+++|+++|   .++|++||+|..|.|.           .|||||+|.+.++|.+|++.|||..|  +|+
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~--~gr   84 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV--DGR   84 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE--TTE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEE--CCE
Confidence            4568999999999999999   7789999999999983           38999999999999999999999999  899


Q ss_pred             EEEEE
Q 014384          119 RLRVE  123 (425)
Q Consensus       119 ~l~V~  123 (425)
                      .|+|.
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99983

>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=99.65  E-value=4.4e-16  Score=121.82  Aligned_cols=77  Identities=27%  Similarity=0.468  Sum_probs=70.9

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ...++|||+|| |..+++++|+++|.+||.|..|.|+        +|||||+|.+.++|..|++.||+..|+|+.|.|.+
T Consensus         6 ~~~~~lfV~nL-~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           6 SGSGRLFVRNL-SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CSCEEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCEEEEECC-CCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44678999999 8899999999999999999999985        57999999999999999999999999999999999


Q ss_pred             eeeCCC
Q 014384          220 AVRDDD  225 (425)
Q Consensus       220 a~~~~~  225 (425)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987643

>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=99.65  E-value=1.7e-16  Score=121.43  Aligned_cols=77  Identities=21%  Similarity=0.257  Sum_probs=68.9

Q ss_pred             cCCCceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHHhc--CCCeecCCCcEEEEEEe
Q 014384           51 EAMMRPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIRGL--DRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~-~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~~l--ng~~ig~~gr~l~V~~a  125 (425)
                      ....++|||+|||.. +|++||.+||+.||+|..|.|  .+++|||+|++.++|..|+..|  ++..|  .|++|.|.|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~--~gr~l~V~~s   82 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALV--FGKPVRVHLS   82 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCcc--CCceEEEEEC
Confidence            466889999999986 889999999999999999999  4789999999999999999966  56677  8999999999


Q ss_pred             cccc
Q 014384          126 KHER  129 (425)
Q Consensus       126 ~~~~  129 (425)
                      +...
T Consensus        83 ~~~~   86 (89)
T d1x4da1          83 QKYK   86 (89)
T ss_dssp             CCCT
T ss_pred             CCcc
Confidence            7544

>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=99.65  E-value=3.9e-16  Score=117.91  Aligned_cols=76  Identities=24%  Similarity=0.419  Sum_probs=69.6

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccC-CeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLT-DRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~i~v~~a~  221 (425)
                      ..+|+++|||+|| |..+++++|.++|++||.|..|.+.   +|||||+|.+.++|..|++.|||..|. |+.|.|.||+
T Consensus         4 ~~pP~~tl~V~nL-p~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           4 EQPPNQILFLTNL-PEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSCCSEEEEESC-CTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4567899999999 8899999999999999999999995   589999999999999999999999985 6899999986


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus        83 k   83 (83)
T d2b0ga1          83 K   83 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.65  E-value=3.8e-16  Score=119.36  Aligned_cols=75  Identities=23%  Similarity=0.452  Sum_probs=69.3

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ....+|||+|| |..+++++|.++|++||.|..|.+.        +|||||+|.+.++|..|+..|||..|+|+.|.|+|
T Consensus         5 ~~~~~l~V~nL-~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           5 VEGWILFVTSI-HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             C-CEEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45689999999 7889999999999999999999885        57999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      |..+
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9875

>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=99.64  E-value=2.5e-16  Score=118.73  Aligned_cols=72  Identities=28%  Similarity=0.441  Sum_probs=67.5

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|..|++.|||..|+|+.|.|.||+
T Consensus         2 ~t~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~   80 (82)
T d1b7fa1           2 NTNLIVNYL-PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   80 (82)
T ss_dssp             CSEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            468999999 8889999999999999999999884        6799999999999999999999999999999999986


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      +
T Consensus        81 p   81 (82)
T d1b7fa1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=4.5e-16  Score=119.46  Aligned_cols=76  Identities=29%  Similarity=0.510  Sum_probs=70.0

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ..+.++|||+|| |..+++++|.++|++||.|..|.|+        +|||||+|.+.++|..|++.|||..|+|+.|.|+
T Consensus         5 ~~~~~~i~V~nL-p~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           5 ADDNATIRVTNL-SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CSSSEEEEEESC-CTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345689999999 8899999999999999999999985        5699999999999999999999999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      ||++.
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99764

>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=99.64  E-value=2.8e-16  Score=123.60  Aligned_cols=79  Identities=23%  Similarity=0.455  Sum_probs=71.7

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ..++.++|||+|| |..+++++|+++|+.||.|..+.+.        +|||||+|.+.++|..|++.|||..|+|+.|.|
T Consensus        14 ~~p~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V   92 (102)
T d2cpza1          14 EGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   92 (102)
T ss_dssp             CCSTTCCEEEESC-CSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456788999999 8999999999999999999988874        579999999999999999999999999999999


Q ss_pred             EEeeeCCC
Q 014384          218 EYAVRDDD  225 (425)
Q Consensus       218 ~~a~~~~~  225 (425)
                      +|+..+.+
T Consensus        93 ~~a~~k~~  100 (102)
T d2cpza1          93 QLKRSKND  100 (102)
T ss_dssp             ECCCCSCC
T ss_pred             EEeCCCCC
Confidence            99987643

>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=99.64  E-value=4.8e-16  Score=119.32  Aligned_cols=75  Identities=24%  Similarity=0.344  Sum_probs=69.7

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .+..+|||+|| |..+++++|+++|++||+|..|.+.      ++||||+|.+.++|..|+..|||..|.|+.|.|.||.
T Consensus         6 ~~~~tl~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNL-SRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESC-CTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            44579999999 8899999999999999999999985      5799999999999999999999999999999999997


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      .+
T Consensus        85 ~~   86 (90)
T d2cqia1          85 TP   86 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            65

>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=99.64  E-value=6.7e-16  Score=119.77  Aligned_cols=77  Identities=27%  Similarity=0.433  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ...+.++|||+|| |..+++++|+++|.+||.|..+.+.     ++||||+|.+.++|..|++.||+..|.|+.|.|+||
T Consensus        10 ~~~~~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          10 AGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCCSSEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            4566789999999 8889999999999999999999985     679999999999999999999999999999999998


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            763

>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=99.64  E-value=3.7e-16  Score=120.67  Aligned_cols=76  Identities=22%  Similarity=0.328  Sum_probs=70.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ....+|||+|| |..+++++|+++|++||.|..|.++        +|||||+|.+.++|..|++.|||..|+|+.|.|.+
T Consensus         7 ~~~~tlfV~nL-p~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           7 NQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CTTTEEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCEEEEeCC-CCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34579999999 8999999999999999999999884        57999999999999999999999999999999999


Q ss_pred             eeeCC
Q 014384          220 AVRDD  224 (425)
Q Consensus       220 a~~~~  224 (425)
                      |..+.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97753

>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=99.64  E-value=1.4e-16  Score=124.55  Aligned_cols=78  Identities=23%  Similarity=0.302  Sum_probs=69.3

Q ss_pred             hcCCCceEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEE--eCCEEEEEEcCHHHHHHHHH--hcCCCeecCCCcEEEEEE
Q 014384           50 FEAMMRPIFCGNFEYD-ARQSDLERLFRRYGKVDRVDM--KSGFAFIYMDDERDAEDAIR--GLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~-~t~~~L~~lF~~~G~V~~v~i--~kg~aFV~F~~~~~A~~A~~--~lng~~ig~~gr~l~V~~  124 (425)
                      .+...++|||+|||.. +|+++|.++|+.||.|..|.|  .+|+|||+|.+.++|..|+.  .+++..|  +|+.|.|.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~--~gr~l~V~~   91 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF--QGRCVKVDL   91 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS--SSSCCEEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceE--CCEEEEEEE
Confidence            3456789999999985 899999999999999999999  48999999999999999997  4677788  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      ++...
T Consensus        92 s~~~~   96 (99)
T d1x4fa1          92 SEKYK   96 (99)
T ss_dssp             ECSCS
T ss_pred             cCCcc
Confidence            97654

>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=99.64  E-value=4.1e-16  Score=117.58  Aligned_cols=72  Identities=26%  Similarity=0.438  Sum_probs=67.3

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .++|||+|| |..+++++|+++|++||.|..|.+.        +|||||+|.+.++|..|++.|||..|+|+.|.|.||+
T Consensus         2 ~t~l~V~nL-p~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           2 KTNLIVNYL-PQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             CSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEECC-CCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            357999999 8899999999999999999999985        5799999999999999999999999999999999986


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      +
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.63  E-value=1e-15  Score=118.20  Aligned_cols=76  Identities=34%  Similarity=0.541  Sum_probs=70.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .....+|||+|| |..+++++|+++|.+||+|..|.+.      +|||||+|.+.++|.+|+..|||..|+|+.|.|++|
T Consensus         8 ~~~~~~l~v~nL-p~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESC-CTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            344678999999 8899999999999999999999985      679999999999999999999999999999999999


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      ..+
T Consensus        87 ~~r   89 (93)
T d2cq3a1          87 TAR   89 (93)
T ss_dssp             CSS
T ss_pred             CcC
Confidence            875

>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=99.63  E-value=4e-16  Score=121.15  Aligned_cols=75  Identities=17%  Similarity=0.421  Sum_probs=70.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +..++|||+|| |..+++++|+++|++||.|..|.+.  +|||||+|.+.++|..|+..|||..|+|+.|.|.|++..
T Consensus        16 ~~~~~l~v~nL-~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          16 PKNCTVYCGGI-ASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SSCCEEEEECC-SSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEcCC-CCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            34578999999 7889999999999999999999996  789999999999999999999999999999999998764

>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=99.63  E-value=2.4e-16  Score=119.99  Aligned_cols=72  Identities=15%  Similarity=0.255  Sum_probs=64.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ...++|||+|||+++|+++|.++|..||.|.. +.+       ++|+|||+|.+.++|.+|+..|||..|  .|+.|.|.
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l--~gr~i~v~   84 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI--GSRKVKLV   84 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE--TTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEE--CCEEEEEE
Confidence            34578999999999999999999999999864 344       379999999999999999999999999  79999998


Q ss_pred             Ee
Q 014384          124 WT  125 (425)
Q Consensus       124 ~a  125 (425)
                      ++
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            75

>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=99.63  E-value=6.3e-16  Score=124.18  Aligned_cols=76  Identities=28%  Similarity=0.443  Sum_probs=70.5

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ...+.+|||+|| |..+++++|.++|++||.|..|.+.     +|||||+|.+.++|..|++.|||..|+|+.|.|.++.
T Consensus         4 p~~~r~l~V~nL-p~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           4 PEVNRILYIRNL-PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TTCCSEEEEESC-CTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cCCCCEEEEECC-CCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            345689999999 8999999999999999999999996     6899999999999999999999999999999999986


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.63  E-value=5.8e-17  Score=119.12  Aligned_cols=63  Identities=19%  Similarity=0.425  Sum_probs=58.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEE
Q 014384           57 IFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLR  121 (425)
Q Consensus        57 l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~  121 (425)
                      |||+|||+++|+++|.++|++||.|..+.+        .+|||||+|.+.++|++|+..|||..|  +|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~--~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV--QAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTC--CEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEE--CCEECc
Confidence            899999999999999999999999999888        379999999999999999999999999  787653

>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=99.62  E-value=1.7e-16  Score=121.10  Aligned_cols=72  Identities=18%  Similarity=0.244  Sum_probs=67.2

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ++|||+|| |..+++++|+++|++||.|..+.+. .|||||+|.+.++|.+||+.|||..|.|+.|.|.++..+
T Consensus         1 nrvfV~nl-p~~~~~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEEC-CSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECC-CCcCCHHHHHHHHhhhcccccccccccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            46999999 8899999999999999999999996 579999999999999999999999999999999887664

>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=99.62  E-value=3.1e-16  Score=120.17  Aligned_cols=74  Identities=27%  Similarity=0.463  Sum_probs=69.0

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..+|||+|| |..+++++|+++|.+||.|..+.|.      +|||||+|.+.++|.+|++.|||..|+|+.|.|.++..+
T Consensus         8 ~~~l~V~nL-p~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESC-CSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            357999999 8889999999999999999999995      689999999999999999999999999999999999875


Q ss_pred             C
Q 014384          224 D  224 (425)
Q Consensus       224 ~  224 (425)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.62  E-value=4.1e-16  Score=122.82  Aligned_cols=76  Identities=21%  Similarity=0.258  Sum_probs=68.2

Q ss_pred             CCCceEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEE
Q 014384           52 AMMRPIFCGNFEYDA-R----QSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEW  124 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~-t----~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~  124 (425)
                      ....+|||+||+..+ +    +++|+++|+.||.|..|.+.  ++||||+|.+.++|.+|+..|||..|  .|+.|+|.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~--~g~~l~v~~   80 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF--LGKEMKLYF   80 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEE--TTEECEEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhccccc--CCCEeEEee
Confidence            356899999999986 3    35799999999999999994  78999999999999999999999999  899999999


Q ss_pred             ecccc
Q 014384          125 TKHER  129 (425)
Q Consensus       125 a~~~~  129 (425)
                      +....
T Consensus        81 a~~~~   85 (104)
T d1weya_          81 AQTLH   85 (104)
T ss_dssp             CCCSS
T ss_pred             cccCC
Confidence            97654

>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=99.62  E-value=9.2e-16  Score=118.68  Aligned_cols=76  Identities=26%  Similarity=0.590  Sum_probs=70.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHc-CCCccCCeEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDAT-NMSKLTDRVISV  217 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~i~v  217 (425)
                      .+..+|||+|| |..+++++|+++|.+||.|..|.|+         +|||||+|.+.++|..|++.| |+..|+|+.|.|
T Consensus         6 ~~~~~l~V~nL-p~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           6 QTTSKILVRNI-PFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            45678999999 8899999999999999999999984         579999999999999999998 899999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      +||..+.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998754

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.4e-15  Score=118.54  Aligned_cols=78  Identities=19%  Similarity=0.264  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ......+|||+|| |..+++++|+++|.+||.|+.+.|. +|||||+|.+.++|..||+.|||..|.|+.|.|.++....
T Consensus        11 ~~~~~~~i~V~Nl-p~~~~~~~L~~~F~~~G~v~~~~i~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          11 TRRSDFRVLVSGL-PPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             CCSCSCEEEEECC-CSSCCHHHHHHHHTTSSCEEEEEEETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCCCCCEEEEECC-CCCCCHHHHHHHHHhhcccccccccccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            3445678999999 8999999999999999999999996 7899999999999999999999999999999999998754

>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=99.61  E-value=4e-16  Score=119.51  Aligned_cols=75  Identities=35%  Similarity=0.546  Sum_probs=69.6

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ....+|||+|| |..+++++|+++|++||+|..|.++        +|||||+|.+.++|..|++.|||..|+|+.|.|.+
T Consensus         3 ~~~~tlfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           3 TTKRVLYVGGL-AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCCSCEEEESC-CSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCcEEEEeCC-CCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34679999999 8899999999999999999999884        67999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      |.+.
T Consensus        82 a~p~   85 (89)
T d2cqba1          82 AKPM   85 (89)
T ss_dssp             CCCC
T ss_pred             eCCC
Confidence            9764

>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=99.61  E-value=6.3e-16  Score=115.91  Aligned_cols=70  Identities=27%  Similarity=0.515  Sum_probs=66.1

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .|||+|| |..+++++|.++|++||+|..|.|+        +|||||+|.+.++|..|++.|||..++|+.|.|.||+.
T Consensus         2 slfV~nL-~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDL-HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCC-CCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            6999999 7889999999999999999999995        57999999999999999999999999999999999864

>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=99.61  E-value=9.8e-16  Score=115.70  Aligned_cols=70  Identities=39%  Similarity=0.516  Sum_probs=65.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      ..+.++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|..|+..|||..|+|+.|+|
T Consensus         6 p~~~~~l~V~nL-~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGL-SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESC-CSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCC-CCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            356789999999 8999999999999999999999885        569999999999999999999999999999987

>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=99.61  E-value=1.1e-15  Score=117.40  Aligned_cols=75  Identities=33%  Similarity=0.506  Sum_probs=69.4

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ...+|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.++|..|++.|||..|+|+.|.|++|
T Consensus         4 ~~~kifV~nL-p~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           4 DEGKLFVGGL-SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCSEEEEESC-CTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCEEEEECC-CCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3567999999 8999999999999999999999874        679999999999999999999999999999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8764

>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=99.61  E-value=9.3e-16  Score=116.56  Aligned_cols=74  Identities=27%  Similarity=0.411  Sum_probs=69.4

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..++|||+|| |..+++++|+++|++||.|..|.+.  ++||||+|.+.++|..|+..|||..|+|+.|.|+||...
T Consensus         7 ~~~~l~V~nL-p~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           7 QRSRLFVGNL-PPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             CTTEEEEESC-CTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCEEEEECC-CCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            4568999999 7899999999999999999999996  689999999999999999999999999999999999764

>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=99.60  E-value=1.1e-15  Score=116.75  Aligned_cols=74  Identities=20%  Similarity=0.276  Sum_probs=67.4

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCC-cEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYG-KIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G-~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ...+|||+|| |..+++++|+++|++|| .+..+...++||||+|.+.++|.+|++.||+..|+|+.|.|+++..+
T Consensus         4 ~s~~i~V~nL-p~~~t~~~l~~lF~~~G~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           4 GSSGILVKNL-PQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESC-CSSCCHHHHHHHTCSSCCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCC-CCccChHHHHHHHHhcCceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3578999999 88999999999999999 56666667999999999999999999999999999999999999664

>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=99.60  E-value=8.1e-16  Score=122.88  Aligned_cols=74  Identities=19%  Similarity=0.279  Sum_probs=69.6

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..++|||+|| |..+++++|+++|.+||+|..|.|.  ++||||+|.+.++|.+|++.|||..|.|+.|.|+|+...
T Consensus         9 ~~~~l~V~nL-p~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNL-PAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECC-CCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            4579999999 8889999999999999999999996  679999999999999999999999999999999999775

>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=99.60  E-value=1e-15  Score=114.13  Aligned_cols=69  Identities=22%  Similarity=0.380  Sum_probs=65.6

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      .|||+|| |..+++++|+++|.+||.|..|.+.       +|||||+|.+.++|..|++.|||..++|+.|.|+++.
T Consensus         2 rl~V~nL-p~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNL-DFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESC-CTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECC-CCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            6999999 7889999999999999999999995       5799999999999999999999999999999999985

>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=99.60  E-value=1.1e-15  Score=116.08  Aligned_cols=70  Identities=29%  Similarity=0.449  Sum_probs=65.4

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      |||+|| |..+++++|+++|++||.|..|.|+           +|||||+|.+.++|..|++.|||..|+|+.|.|.++.
T Consensus         1 LfV~nL-p~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1           1 LFIKNL-NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             EEEESC-CTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CEEcCC-CCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            799999 8899999999999999999999884           5799999999999999999999999999999999986


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      ..
T Consensus        80 ~~   81 (85)
T d2cpfa1          80 RA   81 (85)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>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=4.8e-16  Score=122.23  Aligned_cols=76  Identities=17%  Similarity=0.246  Sum_probs=66.2

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ......+|||+|||+++|+++|+++|..||.| .|.+       .+|||||+|.+.++|++|+ .||+..|  .|+.|.|
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al-~~~~~~i--~gR~I~V   86 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANM--QHRYVEL   86 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCS--SSSCCEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHH-HcCCCEE--CCEEEEE
Confidence            34556799999999999999999999999855 4444       3799999999999999999 5899999  7999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        87 ~~s~~~~   93 (102)
T d1weza_          87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            9988654

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.2e-15  Score=120.37  Aligned_cols=76  Identities=13%  Similarity=0.155  Sum_probs=67.0

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....+|||+|||+++|+++|+++|..||.|..+.+        ++|||||+|.++++|++|+ .||+..|  .|+.|.|
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~~i--~gR~i~V   88 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERI--GHRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCS--SSSCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEE--cceEEEE
Confidence            345568999999999999999999999998876444        3799999999999999999 6999999  8999999


Q ss_pred             EEecccc
Q 014384          123 EWTKHER  129 (425)
Q Consensus       123 ~~a~~~~  129 (425)
                      .++....
T Consensus        89 ~~~~~~~   95 (104)
T d1wg5a_          89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9987654

>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=99.60  E-value=1.1e-15  Score=114.31  Aligned_cols=73  Identities=32%  Similarity=0.480  Sum_probs=67.4

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      ..+++|||+|| +  +++++|+++|++||.|..|.+.  ++||||+|.+.++|..|+..|||..|+|+.|.|.|++++
T Consensus         3 ~~~~ti~V~~~-~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGE-D--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECS-S--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECC-C--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            34679999999 4  7799999999999999999995  689999999999999999999999999999999999764

>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=99.60  E-value=1.5e-15  Score=115.51  Aligned_cols=77  Identities=30%  Similarity=0.364  Sum_probs=68.3

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ....++|||+|| |..+++++|+++|++||.|..+.+  .+|||||+|.+.++|..|+..|||..|+|+.|.|.||++..
T Consensus         5 ~~~~k~l~V~nL-p~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           5 MSSVKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             SSCCCEEEEESC-CTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             ccCCCEEEEcCC-CCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            344579999999 889999999999999987655554  68999999999999999999999999999999999997643

>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=99.60  E-value=1.1e-15  Score=115.86  Aligned_cols=72  Identities=18%  Similarity=0.331  Sum_probs=67.9

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ++|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.++++|..|++.|||..|+|+.|.|++|..
T Consensus         2 ~rlfV~nl-p~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETC-CSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            57999999 8999999999999999999999995        58999999999999999999999999999999999976


Q ss_pred             C
Q 014384          223 D  223 (425)
Q Consensus       223 ~  223 (425)
                      .
T Consensus        81 ~   81 (85)
T d2u2fa_          81 G   81 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.59  E-value=3.4e-15  Score=116.14  Aligned_cols=78  Identities=26%  Similarity=0.402  Sum_probs=70.9

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCC--eEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTD--RVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~a~  221 (425)
                      ...|.++|||+|| |..+++++|+++|++||.|..|.+.  ++||||+|.+.++|..|++.||+..|.|  ..|.|+|++
T Consensus        13 ~~~Ps~tl~V~nL-p~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          13 KANPTTRLWVGGL-GPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECC-CSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEcCC-CCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            4567899999999 7889999999999999999999996  5799999999999999999999999986  589999998


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      ..+
T Consensus        92 ~~~   94 (97)
T d1whya_          92 SGP   94 (97)
T ss_dssp             CCC
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=99.59  E-value=8.6e-16  Score=122.33  Aligned_cols=74  Identities=26%  Similarity=0.345  Sum_probs=68.9

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      +.+|||+||+|..+++++|.++|+.||.|..|.|.   +|||||+|.+.++|.+|++.|||..|.|+.|.|.|++..
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            57999999977779999999999999999999996   579999999999999999999999999999999998653

>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=99.59  E-value=2.9e-15  Score=113.60  Aligned_cols=71  Identities=32%  Similarity=0.501  Sum_probs=65.6

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCC--eEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTD--RVISVE  218 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~  218 (425)
                      ..++|||+|| |..+++++|+++|++||.|..+.++        +|||||+|.+.++|..|++.|||..+.|  ++|.|.
T Consensus         5 ~~t~lfV~nl-p~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           5 KDTNLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTCEEEEESC-CTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            4568999999 8999999999999999999999985        5799999999999999999999999987  789999


Q ss_pred             Ee
Q 014384          219 YA  220 (425)
Q Consensus       219 ~a  220 (425)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.59  E-value=2.1e-15  Score=114.32  Aligned_cols=70  Identities=30%  Similarity=0.579  Sum_probs=64.4

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCC--eEEEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTD--RVISVEY  219 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~i~v~~  219 (425)
                      .++|||+|| |..+++++|+++|++||+|..+.++        +|||||+|.+.++|..|++.|||..+.|  .+|.|.|
T Consensus         6 ~~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           6 DANLYVSGL-PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TCEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCEEEEeCC-CCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            468999999 7889999999999999999999985        5699999999999999999999999998  5599988


Q ss_pred             e
Q 014384          220 A  220 (425)
Q Consensus       220 a  220 (425)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.59  E-value=8.1e-15  Score=121.86  Aligned_cols=75  Identities=27%  Similarity=0.425  Sum_probs=69.1

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ...++|||+|| |..+++++|+++|++||.|..|.|.        +|||||+|.+.++|..||+.|||..|+|+.|.|.+
T Consensus        40 ~~~~~l~V~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          40 DVLRNLMVNYI-PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTSEEEEESC-STTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999 7889999999999999999999884        57999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      |...
T Consensus       119 a~~~  122 (139)
T d1u6fa1         119 AASG  122 (139)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            9764

>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=99.58  E-value=2.3e-15  Score=114.94  Aligned_cols=75  Identities=25%  Similarity=0.329  Sum_probs=68.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCcc-CCeEEEEEEee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKL-TDRVISVEYAV  221 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~-~g~~i~v~~a~  221 (425)
                      .+|+.+|||+|| |..+++++|+++|+.||.|..+.+.    ++||||+|.+.++|.+|+..|||..| +|+.|.|.|++
T Consensus         7 ~pPs~tL~V~NL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           7 FPPSATLHLSNI-PPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CCSCSEEEEECC-CTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCCEEEEECC-CCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            467889999999 8899999999999999999887764    67999999999999999999999988 58999999986


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.58  E-value=1.1e-15  Score=114.80  Aligned_cols=71  Identities=20%  Similarity=0.281  Sum_probs=65.9

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ++|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|++.|||..|+|+.|.|.++.+
T Consensus         2 ~tl~v~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNF-PPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECC-CTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECC-CCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            68999999 8999999999999999999877663        68999999999999999999999999999999999864

>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=99.58  E-value=1.7e-15  Score=117.72  Aligned_cols=78  Identities=21%  Similarity=0.407  Sum_probs=71.1

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ...+..+|||+|| |..+++++|+++|.+||.|..+...   ++||||+|.+.++|..|++.|||..|+|+.|.|.|+..
T Consensus        12 ~~~~~~~l~V~nL-~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          12 KVRAARTLLAKNL-SFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TTTGGGEEEEESC-CSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             cCCCCCEEEEeCC-CCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3456789999999 8899999999999999999887763   78999999999999999999999999999999999988


Q ss_pred             CC
Q 014384          223 DD  224 (425)
Q Consensus       223 ~~  224 (425)
                      +.
T Consensus        91 k~   92 (96)
T d1fjca_          91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=8e-16  Score=121.20  Aligned_cols=73  Identities=18%  Similarity=0.227  Sum_probs=65.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEE
Q 014384           52 AMMRPIFCGNFEYDARQSDLERLFRRYGKVDR-VDM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVE  123 (425)
Q Consensus        52 ~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~-v~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~  123 (425)
                      ....+|||+|||+.+|+++|.++|..||.|.. +.+       ++|||||+|.++++|++|| .|||..|  +|+.|.|.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al-~~n~~~i--~gr~i~V~   82 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRKKL--NGREAFVH   82 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHG-GGCSEEE--TTEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHH-hcCCCeE--CCcEEEEE
Confidence            34568999999999999999999999998865 444       3899999999999999999 5999999  89999999


Q ss_pred             Eecc
Q 014384          124 WTKH  127 (425)
Q Consensus       124 ~a~~  127 (425)
                      ++..
T Consensus        83 ~~~~   86 (103)
T d2cpya1          83 VVTL   86 (103)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>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=99.57  E-value=4.5e-15  Score=129.21  Aligned_cols=115  Identities=17%  Similarity=0.261  Sum_probs=87.3

Q ss_pred             eeeEEEEeCCCCcccccccCCccee------ecccccccchhhhhhhcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeE
Q 014384           10 CHYLLIVYSHSVWPVQKKYLPRRLY------VLGFRRSHSQLSIAAFEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDR   83 (425)
Q Consensus        10 ~~y~~i~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~   83 (425)
                      ..||||.|.....+..+........      ........ ...........++|||+|||..+|+++|.++|+.||.|..
T Consensus        48 ~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~  126 (183)
T d1u1qa_          48 RGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE-DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV  126 (183)
T ss_dssp             EEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTT-GGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             cCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcc-cccccccccccceeEEccCCCcCCHHHHhhhhccCCceee
Confidence            4599999998777665544433221      11111111 1222234556789999999999999999999999999999


Q ss_pred             EEE--------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEeccc
Q 014384           84 VDM--------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKHE  128 (425)
Q Consensus        84 v~i--------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~~  128 (425)
                      |.|        ++|||||+|.+.++|.+|| .+++..|  +|+.|.|.+|..+
T Consensus       127 ~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al-~~~~~~~--~G~~i~V~~A~~k  176 (183)
T d1u1qa_         127 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTV--NGHNCEVRKALSK  176 (183)
T ss_dssp             EEEEECTTTCCEEEEEEEEESCHHHHHHHH-TSSCEEE--TTEEEEEEECCCH
T ss_pred             eeeecccccCccceeEEEEECCHHHHHHHH-HhCCCeE--CCEEEEEEecCCc
Confidence            987        3689999999999999999 5889888  8999999998654

>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=99.56  E-value=1.1e-15  Score=114.53  Aligned_cols=73  Identities=23%  Similarity=0.418  Sum_probs=65.8

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--eccEEEEEEcCHHHHHHHHHHcCCC-ccCCeEEEEEEeeeCC
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMS-KLTDRVISVEYAVRDD  224 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~i~v~~a~~~~  224 (425)
                      ++|||+|| |..+++++|+++|.+||.|..+.+  .+|||||+|.+.++|..|++.|||. .|+|+.|.|+||.++.
T Consensus         2 n~l~V~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           2 NKLYIGNL-SPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECC-CTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            47999999 889999999999999999866544  5899999999999999999999996 6999999999998753

>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=99.56  E-value=4.5e-15  Score=114.03  Aligned_cols=74  Identities=26%  Similarity=0.490  Sum_probs=67.9

Q ss_pred             CCcEEEEEcCCCCCCCHHHHH----hhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          149 PSKTLFVINFDPYHTRTRDLE----RHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~----~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      |+++|||+|| |..+++++|+    .+|++||+|..|.+.     +|||||+|.+.++|..|+..|||..|+|+.|.|.|
T Consensus         2 P~~tl~V~nL-p~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           2 PNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCSEEEEESC-CTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCC-CCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5789999999 7888898886    468999999999985     68999999999999999999999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      |+.+
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9765

>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=99.56  E-value=1.2e-14  Score=114.49  Aligned_cols=76  Identities=25%  Similarity=0.454  Sum_probs=65.8

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      +..|..+|||+|| |..+++++|+++|++|| |..+.+.         +|||||+|.+.++|++|+ .||+..|+|+.|.
T Consensus        11 p~~p~~~v~V~nL-p~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~   87 (104)
T d1wi8a_          11 PKSPPYTAFLGNL-PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             CSSSCEEEEEESC-CSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCCCEEEEeCC-CCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEE
Confidence            3456789999999 89999999999999999 6666653         579999999999998666 5999999999999


Q ss_pred             EEEeeeCC
Q 014384          217 VEYAVRDD  224 (425)
Q Consensus       217 v~~a~~~~  224 (425)
                      |.+|..+.
T Consensus        88 V~~a~~~~   95 (104)
T d1wi8a_          88 VDVADQAQ   95 (104)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998754

>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=99.55  E-value=1.3e-14  Score=110.58  Aligned_cols=77  Identities=19%  Similarity=0.363  Sum_probs=70.2

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc--CCCccCCeEEEEEEee
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT--NMSKLTDRVISVEYAV  221 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~a~  221 (425)
                      ..+|+.+|||+|| |..+++++|+++|++||.|..+.+.  +++|||+|.+.++|..|++.+  ++..++|+.|.|.|++
T Consensus         4 ~~~Ps~~l~V~nL-p~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           4 DGAPSRVLHIRKL-PGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             CSSCCSEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            4678999999999 7889999999999999999999996  789999999999999999865  6788999999999997


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      .+
T Consensus        83 ~~   84 (88)
T d2cq1a1          83 HK   84 (88)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.55  E-value=4.3e-15  Score=112.87  Aligned_cols=73  Identities=30%  Similarity=0.434  Sum_probs=64.6

Q ss_pred             CCcEEEEEcCCCCCC-CHHHHHhhhccCCcEEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          149 PSKTLFVINFDPYHT-RTRDLERHFEPYGKIISVRIR---------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~-~~~~L~~~f~~~G~v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ...+|||+|| |..+ ++++|+++|++||.|..|.|+         +|||||+|.+.++|.+|++ ||+..|+|+.|.|.
T Consensus         3 e~~~l~V~nL-p~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNL-STELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEE-CTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCEEEEECC-CCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            3579999999 6655 466799999999999999984         5699999999999999995 99999999999999


Q ss_pred             EeeeC
Q 014384          219 YAVRD  223 (425)
Q Consensus       219 ~a~~~  223 (425)
                      +|..+
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99764

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=7.3e-17  Score=124.04  Aligned_cols=71  Identities=17%  Similarity=0.429  Sum_probs=62.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEE-------------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEE
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDM-------------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRL  120 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i-------------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l  120 (425)
                      .++|||+|||+.+|+++|.++|+.||.|..+.+             .+|||||+|.+.++|++|+ .|||..|  +|+.|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~--~Gr~l   77 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIF--QGQSL   77 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCS--SSSCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEE--CCEEE
Confidence            368999999999999999999999998765544             3899999999999999999 6999999  89999


Q ss_pred             EEEEecc
Q 014384          121 RVEWTKH  127 (425)
Q Consensus       121 ~V~~a~~  127 (425)
                      +|..++.
T Consensus        78 ~V~r~k~   84 (90)
T d1u2fa_          78 KIRRPHD   84 (90)
T ss_dssp             CCBCTTC
T ss_pred             EECCCCC
Confidence            9975543

>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=99.55  E-value=3.8e-14  Score=111.56  Aligned_cols=79  Identities=16%  Similarity=0.198  Sum_probs=71.1

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc--CCCccCCeEEEEEEe
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT--NMSKLTDRVISVEYA  220 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~a  220 (425)
                      ....++.+|||+|| |..+++++|.++|.+||.|..|.+.  +++|||+|.+.++|..|+..|  ++..++|+.|.|.|+
T Consensus        10 ~~~~ps~~l~v~nl-p~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          10 HKVSVSPVVHVRGL-CESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCSEEEEESC-CSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CcCCCCCEEEEeCC-CCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            34567899999999 7889999999999999999999996  789999999999999999977  567789999999999


Q ss_pred             eeCC
Q 014384          221 VRDD  224 (425)
Q Consensus       221 ~~~~  224 (425)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T d1wexa_          89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             CCCc
Confidence            7754

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=8.5e-15  Score=114.08  Aligned_cols=77  Identities=30%  Similarity=0.497  Sum_probs=68.6

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcC------CCccCC
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATN------MSKLTD  212 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~------g~~~~g  212 (425)
                      ....++|||+|| |..+++++|+++|.+||.|..+.+.        +|||||+|.+.++|..|++.||      |..|.|
T Consensus         5 ~~~~~tlfV~nL-p~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           5 VTEGKTVFIRNL-SFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCEEEESC-CTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCEEEEcCC-CCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            445679999999 8999999999999999999999884        6899999999999999999887      567889


Q ss_pred             eEEEEEEeeeCC
Q 014384          213 RVISVEYAVRDD  224 (425)
Q Consensus       213 ~~i~v~~a~~~~  224 (425)
                      +.|.|.+|..+.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999998753

>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=99.54  E-value=1.3e-14  Score=114.11  Aligned_cols=73  Identities=29%  Similarity=0.434  Sum_probs=66.7

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ..++|||+|| |..+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+|++.+|+ .|+|+.|.|.+|
T Consensus         9 ~~~~lfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           9 TFTKIFVGGL-PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             SSSEEEEECC-CSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCcEEEEeCC-CCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3468999999 8899999999999999999999995        67999999999999999998876 799999999998


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      ..+
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            764

>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=99.54  E-value=9.8e-15  Score=110.25  Aligned_cols=71  Identities=28%  Similarity=0.544  Sum_probs=65.3

Q ss_pred             CCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          149 PSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ...+|||+|| |..+++++|+++|++||.|..+.|+        +|||||+|.+.++|.+|++ +++..|+|+.|.|..|
T Consensus         5 ~~~~lfV~nl-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           5 QLRKLFIGGL-SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGEEEEESC-CTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCcEEEEECC-CCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            3468999999 8999999999999999999999984        6799999999999999997 6899999999999887


Q ss_pred             e
Q 014384          221 V  221 (425)
Q Consensus       221 ~  221 (425)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.54  E-value=3.3e-15  Score=112.76  Aligned_cols=71  Identities=27%  Similarity=0.510  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEE-EEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISV-RIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v-~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      |||+|| |..+++++|+++|.+||.|..+ .++        +|||||+|.+.++|..|++.|||..|+|+.|.|.+|..+
T Consensus         1 lfV~nL-p~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNL-DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECC-CTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCC-CCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            799999 8899999999999999998654 443        579999999999999999999999999999999999865


Q ss_pred             C
Q 014384          224 D  224 (425)
Q Consensus       224 ~  224 (425)
                      .
T Consensus        80 ~   80 (83)
T d1x5ta1          80 D   80 (83)
T ss_dssp             C
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=99.54  E-value=3.4e-15  Score=117.78  Aligned_cols=73  Identities=27%  Similarity=0.534  Sum_probs=67.6

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| |..+++++|+++|++||+|..|.|+        +|||||+|.+.++|..|++.|||..|.|+.|.|.++.
T Consensus         8 ~rtl~V~nL-p~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           8 LRSVFVGNI-PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HSCEEEESC-CTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCEEEEECC-CCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            358999999 7889999999999999999999885        5699999999999999999999999999999999986


Q ss_pred             eC
Q 014384          222 RD  223 (425)
Q Consensus       222 ~~  223 (425)
                      .+
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            64

>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=99.54  E-value=9.1e-15  Score=111.87  Aligned_cols=75  Identities=19%  Similarity=0.498  Sum_probs=66.7

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+|||+|| |..+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+||+.+  ..|+|+.|.|.
T Consensus         5 ~~~~~~lfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~   81 (90)
T d2cqga1           5 VQKTSDLIVLGL-PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCEEEESC-CSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEE
T ss_pred             CcCCCeEEEECC-CCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEE
Confidence            345678999999 8999999999999999999999985        579999999999999999854  47999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      ++..+.
T Consensus        82 ~a~~k~   87 (90)
T d2cqga1          82 LPNSKQ   87 (90)
T ss_dssp             CCCTTC
T ss_pred             eCCCCC
Confidence            987753

>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=99.54  E-value=6.1e-15  Score=115.54  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=66.0

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ....++|||+|| |..+++++|+++|++||.|..+.+.       +|||||+|.+.++|.+|++.|||..|.|+++.|.+
T Consensus        15 ~~~~~~lfV~nL-p~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESC-CTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCC-CCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            344579999999 8889999999999999999988875       57999999999999999999999999998887765


Q ss_pred             ee
Q 014384          220 AV  221 (425)
Q Consensus       220 a~  221 (425)
                      +.
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.54  E-value=2.5e-15  Score=118.08  Aligned_cols=78  Identities=26%  Similarity=0.386  Sum_probs=70.1

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      +..|+++|||+|| |..+++++|+++|.+||.|..+.+.        +|||||+|.+.++|..|++.|||..|.|+.|.|
T Consensus        14 ~~~ps~tl~V~nL-p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   92 (102)
T d2cpxa1          14 PGEPNKVLYLKNL-SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   92 (102)
T ss_dssp             CCSCCSEEEEECC-CTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEeCC-CCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEE
Confidence            3457889999999 8899999999999999988766553        579999999999999999999999999999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      +||+.+.
T Consensus        93 ~~ak~k~   99 (102)
T d2cpxa1          93 EFGKNKK   99 (102)
T ss_dssp             EECCCCS
T ss_pred             EeCCCcc
Confidence            9998753

>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=99.54  E-value=6.5e-15  Score=115.64  Aligned_cols=73  Identities=22%  Similarity=0.454  Sum_probs=67.2

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| |..+++++|+++|.+||.|..+.|+        +|||||+|.+.++|.+|++ +++..|+|+.|.|.+|.
T Consensus        20 ~~~lfVgnL-p~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          20 FRKLFIGGL-SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HTEEEEECC-TTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCEEEEeCC-CCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            368999999 8999999999999999999999984        6899999999999999996 79999999999999988


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      .+.
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            753

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=4e-15  Score=116.39  Aligned_cols=72  Identities=13%  Similarity=0.212  Sum_probs=61.4

Q ss_pred             hcCCCceEEEc--CCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           50 FEAMMRPIFCG--NFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        50 ~~~~~~~l~V~--nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      ...++.+|+|+  ||+..+|+++|+++|++||.|..|.+.  ++||||+|.+.++|.+|+..|||..|. ++..+.|
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~-~~~~~~i   89 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV-DDLGQKI   89 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE-CTTSCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC-CCCCcEE
Confidence            34567788885  499999999999999999999999984  899999999999999999999998874 4433333

>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=99.53  E-value=3.3e-15  Score=114.03  Aligned_cols=74  Identities=22%  Similarity=0.290  Sum_probs=67.0

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe---ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeCC
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR---RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRDD  224 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~~  224 (425)
                      ...++|||+|| |..+++++|+++|++||.|..|.++   ++||||+|.+.++|+.|+.  ++..|+|+.|.|.++..+.
T Consensus         3 ~~s~~lfV~nL-p~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           3 SGSSGVFVGRC-TGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCCEEEEESC-CSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCCCEEEEeCC-CCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            35689999999 8889999999999999999999885   7899999999999999985  7889999999999997653

>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=99.53  E-value=1.8e-14  Score=106.32  Aligned_cols=69  Identities=20%  Similarity=0.332  Sum_probs=62.6

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeeeC
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISVRI--RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVRD  223 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~~  223 (425)
                      |||+|| |..+++++|+++|.+|| +..+.+  .+|||||+|.+.++|.+|++.|||..+.|+.|.|+++..+
T Consensus         1 i~V~nL-p~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGL-PGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECC-CTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCC-CCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            799999 88999999999999999 444444  4899999999999999999999999999999999999664

>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=99.53  E-value=5.3e-15  Score=115.95  Aligned_cols=76  Identities=18%  Similarity=0.232  Sum_probs=67.1

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEE--------Ee--------ccEEEEEEcCHHHHHHHHHHcCCCcc
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVR--------IR--------RNFAFVQYEVQEDATRALDATNMSKL  210 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~--------~~--------~g~afV~f~~~~~A~~A~~~l~g~~~  210 (425)
                      .....+|||+|| |..+++++|+++|.+||.|..+.        +.        ++||||+|.+.++|..|++.|||..|
T Consensus         5 ~~~~~~i~V~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           5 DSDNSAIYVQGL-NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCEEEEECC-CTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECC-CCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345689999999 89999999999999999875332        21        47999999999999999999999999


Q ss_pred             CCeEEEEEEeeeC
Q 014384          211 TDRVISVEYAVRD  223 (425)
Q Consensus       211 ~g~~i~v~~a~~~  223 (425)
                      +|+.|.|.+|+.+
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999999874

>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=99.53  E-value=1.8e-14  Score=107.51  Aligned_cols=69  Identities=28%  Similarity=0.426  Sum_probs=63.5

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ..+|||+|| |..+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|++ |+|..|+|+.|.|..|
T Consensus         2 ~r~lfV~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGI-KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECC-TTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCC-CCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            468999999 8899999999999999999999885        5799999999999888885 8999999999999876

>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=99.53  E-value=3.5e-15  Score=110.75  Aligned_cols=68  Identities=21%  Similarity=0.411  Sum_probs=63.4

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ++|||+|| |..+++++|+++|++||.|..+.|+        +|||||+|.+.++|.+|++ +++..|+|+.|.|..|
T Consensus         1 cklfV~nL-p~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGL-SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESC-CSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCC-CCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            47999999 8899999999999999999999885        6899999999999999997 7999999999999876

>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=99.52  E-value=9.5e-15  Score=107.86  Aligned_cols=66  Identities=24%  Similarity=0.581  Sum_probs=61.1

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      .|||+|| |..+++++|.++|++||+|..|.++        +|||||+|.+.++|.+|++ +++..|+|+.|.|..
T Consensus         1 klfV~nl-~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGL-SWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECC-CTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCC-CCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            4899999 8999999999999999999999985        6899999999999999997 799999999999854

>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=99.51  E-value=1.9e-14  Score=106.17  Aligned_cols=68  Identities=22%  Similarity=0.304  Sum_probs=63.0

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      ++|||+|| |..+++++|+++|..||.|..|.+.      ++||||+|.+.++|.+|+. ||+..|+|+.|.|+.+
T Consensus         1 Ttv~V~nl-p~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNL-PKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECC-CCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999 8999999999999999999999995      4699999999999999985 8999999999999865

>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=99.51  E-value=3.3e-15  Score=119.43  Aligned_cols=74  Identities=14%  Similarity=0.243  Sum_probs=64.7

Q ss_pred             cCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EE-------eCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEE
Q 014384           51 EAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRV-DM-------KSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRV  122 (425)
Q Consensus        51 ~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v-~i-------~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V  122 (425)
                      .....+|||+|||+++|+++|.++|+.||.|..+ .+       .+|||||+|.+.++|.+|+ .|||..|  .|+.|.|
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~~i--~gR~i~V   91 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYM--GNRFIQV   91 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCS--TTSCBEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcC--CCEEEEE
Confidence            4456799999999999999999999999988643 22       3799999999999999999 6999999  7999999


Q ss_pred             EEecc
Q 014384          123 EWTKH  127 (425)
Q Consensus       123 ~~a~~  127 (425)
                      .++..
T Consensus        92 ~~~~~   96 (112)
T d1wela1          92 HPITK   96 (112)
T ss_dssp             EEECH
T ss_pred             EEcCh
Confidence            88754

>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=99.51  E-value=1.1e-14  Score=113.91  Aligned_cols=71  Identities=27%  Similarity=0.419  Sum_probs=66.1

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| |..+++++|+++|+.||.|..|.|+        +|||||+|.+.++|.+|+. |||..|+|+.|.|.++.
T Consensus        18 ~~tifV~nL-~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQL-AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESC-CTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECC-CCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            468999999 8999999999999999999999995        6799999999999999995 99999999999999976


Q ss_pred             e
Q 014384          222 R  222 (425)
Q Consensus       222 ~  222 (425)
                      .
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=4.3e-14  Score=110.13  Aligned_cols=77  Identities=22%  Similarity=0.359  Sum_probs=69.2

Q ss_pred             CCCCCcEEEEEcCCCC-CCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHH--HcCCCccCCeEEEEEEe
Q 014384          146 NTRPSKTLFVINFDPY-HTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALD--ATNMSKLTDRVISVEYA  220 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~-~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~--~l~g~~~~g~~i~v~~a  220 (425)
                      ...++.+|||+|| |. .+++++|.++|+.||.|..|.+.  +|+|||+|.+.++|..|++  .+++..|+|+.|.|.|+
T Consensus        14 ~~~~~~~l~v~nL-p~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          14 KQELGRVIHLSNL-PHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SSCCCCEEEEESC-CCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCC-cCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            4456789999999 65 58899999999999999999995  7899999999999999997  57889999999999999


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      +..
T Consensus        93 ~~~   95 (99)
T d1x4fa1          93 EKY   95 (99)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            764

>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=99.51  E-value=2.2e-14  Score=109.55  Aligned_cols=69  Identities=26%  Similarity=0.408  Sum_probs=62.8

Q ss_pred             CCcEEEEEcCCCCCCCHHHH---HhhhccCCcEEEEEEe-----------ccEEEEEEcCHHHHHHHHHHcCCCccCCeE
Q 014384          149 PSKTLFVINFDPYHTRTRDL---ERHFEPYGKIISVRIR-----------RNFAFVQYEVQEDATRALDATNMSKLTDRV  214 (425)
Q Consensus       149 ~~~~l~V~nl~p~~~~~~~L---~~~f~~~G~v~~v~~~-----------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  214 (425)
                      ..++|||+|| |..+++++|   .++|.+||+|..|.++           .|||||+|.+.++|.+|++.|||..|+|+.
T Consensus         7 q~n~vyV~nL-p~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           7 QKNLVFVVGL-SQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CSSCEEEEEE-CTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             ecCEEEEECC-CCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            3568999999 788889999   7899999999999995           269999999999999999999999999999


Q ss_pred             EEEE
Q 014384          215 ISVE  218 (425)
Q Consensus       215 i~v~  218 (425)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9874

>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=99.51  E-value=2.5e-15  Score=115.35  Aligned_cols=75  Identities=20%  Similarity=0.262  Sum_probs=66.7

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ......+|||+|| |..+++++|+++|++||.|..+.+.       +|||||+|.+.++|.+||+ |||..|+|+.|.|+
T Consensus         9 ~~~~~~~ifV~nL-~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECC-CTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCc-cCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445679999999 8999999999999999987766653       6899999999999999996 99999999999999


Q ss_pred             Eeee
Q 014384          219 YAVR  222 (425)
Q Consensus       219 ~a~~  222 (425)
                      +|+.
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9875

>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=99.50  E-value=9.8e-15  Score=107.82  Aligned_cols=67  Identities=21%  Similarity=0.489  Sum_probs=62.3

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .|||+|| |..+++++|+++|++||.|..+.+.        ++||||+|.+.++|.+|++ |||..|+|+.|.|.+|
T Consensus         1 rlfV~nL-p~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGL-SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECC-CSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCC-CCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            4899999 8899999999999999999998874        6799999999999999996 9999999999999876

>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=99.50  E-value=4.6e-14  Score=107.65  Aligned_cols=77  Identities=21%  Similarity=0.289  Sum_probs=68.4

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHc--CCCccCCeEEEEEEeee
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDAT--NMSKLTDRVISVEYAVR  222 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~i~v~~a~~  222 (425)
                      ..+..+|||+||+...+|++||.++|+.||.|..|.+.  +++|||+|++.++|..|++.|  ++..++|++|.|.|++.
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            56788999999943357899999999999999999996  679999999999999999966  67889999999999976


Q ss_pred             C
Q 014384          223 D  223 (425)
Q Consensus       223 ~  223 (425)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.49  E-value=3.8e-14  Score=107.23  Aligned_cols=70  Identities=17%  Similarity=0.439  Sum_probs=64.9

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ..+|||+|| |..+++++|+++|+.||+|..|.|.       +|||||+|.+.++|.+||+ +++..|.|+.|.|.++.
T Consensus         6 ~rtvfV~nl-p~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECC-CTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECC-CCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            468999999 8999999999999999999999995       5799999999999999996 79999999999999864

>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=99.49  E-value=2.2e-14  Score=113.73  Aligned_cols=76  Identities=16%  Similarity=0.235  Sum_probs=67.8

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCcc--CCeEEEEEEe
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKL--TDRVISVEYA  220 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~i~v~~a  220 (425)
                      ..+..+|||+|| ++.+|+++|+++|++||.|..|.+.    +|||||+|.+.++|+.|+..|||..|  .|..|.|.|+
T Consensus         4 ~s~~~~v~V~NL-~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           4 QSPVLRIIVENL-FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCCEEEEESCSC-CSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCCeEEEEEeCc-CCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            345678999999 8999999999999999999999885    67999999999999999999999998  4788888888


Q ss_pred             eeC
Q 014384          221 VRD  223 (425)
Q Consensus       221 ~~~  223 (425)
                      +..
T Consensus        83 ~~~   85 (108)
T d2adba1          83 KLT   85 (108)
T ss_dssp             SSC
T ss_pred             CCc
Confidence            664

>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=99.48  E-value=8.7e-14  Score=109.02  Aligned_cols=76  Identities=18%  Similarity=0.363  Sum_probs=66.1

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      ......+|||.|| |+.+|+++|+++|..||.+ .|.+.       +|||||+|.+.++|++|++ ||+..|+|+.|.|.
T Consensus        11 ~~~~~~~v~v~nL-p~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGL-PYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESC-CTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCC-CCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            4456689999999 8999999999999999855 44442       6799999999999999986 89999999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      ++....
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            988754

>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=99.48  E-value=1.9e-13  Score=107.51  Aligned_cols=76  Identities=20%  Similarity=0.257  Sum_probs=67.2

Q ss_pred             CCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEE
Q 014384          147 TRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVE  218 (425)
Q Consensus       147 ~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  218 (425)
                      .....+|||.|| |+.+++++|+++|..||.|..+.+.        +|||||+|.+.++|.+|++ +|+..|+|+.|.|.
T Consensus        12 ~~~~~~v~v~nL-P~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          12 TANDGFVRLRGL-PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESC-CTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCcEEEEeCC-CCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            445568999999 9999999999999999988775552        6899999999999999986 89999999999999


Q ss_pred             EeeeCC
Q 014384          219 YAVRDD  224 (425)
Q Consensus       219 ~a~~~~  224 (425)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            998764

>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=99.48  E-value=2.7e-14  Score=114.15  Aligned_cols=75  Identities=17%  Similarity=0.317  Sum_probs=63.8

Q ss_pred             hcCCCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCH-HHHHHHHHhcCCCeecCCCcEEEEEEec
Q 014384           50 FEAMMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDE-RDAEDAIRGLDRTEFGRKGRRLRVEWTK  126 (425)
Q Consensus        50 ~~~~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~-~~A~~A~~~lng~~ig~~gr~l~V~~a~  126 (425)
                      .+.....+||||||+.+|+++|.++|++||+|..|.|.  +|||||.|.+. ++|.+|+..||+..|  .++.+.|.|+.
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l--~~~~~~v~~~~   84 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNL--QLRNKEVTWEV   84 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCB--CTTSSSEEEEE
T ss_pred             CCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCce--ecCceEEEEee
Confidence            34556778999999999999999999999999999996  89999999996 689999999999988  45555555543

>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=99.47  E-value=1.5e-14  Score=106.65  Aligned_cols=67  Identities=16%  Similarity=0.391  Sum_probs=61.4

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .|||+|| |..+++++|+++|++||.|..|.|+        +|||||+|.+.++|.+||+ +++..|+|+.|.|..|
T Consensus         1 klfVgnL-p~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGL-SPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESC-CSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCC-CCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            5899999 8999999999999999999999985        6899999999999999997 5778899999998764

>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=99.45  E-value=4.5e-14  Score=107.13  Aligned_cols=72  Identities=21%  Similarity=0.280  Sum_probs=63.5

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE-EEE-------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS-VRI-------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~-v~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      +...+|||+|| |..+++++|+++|..||.|.. +.+       .+|+|||+|.+.++|.+|++.||+..|+|+.|.|.+
T Consensus         7 p~~~~l~v~nL-p~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNM-PFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESC-CTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECC-CCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999 899999999999999998754 233       268999999999999999999999999999999987


Q ss_pred             e
Q 014384          220 A  220 (425)
Q Consensus       220 a  220 (425)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.44  E-value=3.6e-14  Score=103.80  Aligned_cols=63  Identities=25%  Similarity=0.508  Sum_probs=58.9

Q ss_pred             EEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          153 LFVINFDPYHTRTRDLERHFEPYGKIISVRIR--------RNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       153 l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      |||+|| |..+++++|.++|.+||.|..+.+.        +|+|||+|.+.++|..|++.|||..|+|+.|+
T Consensus         1 lyV~nL-p~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGL-QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESC-CTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCC-CCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999 8999999999999999999999884        68999999999999999999999999998763

>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=99.44  E-value=7.6e-14  Score=108.14  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=65.1

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCc-EEEEEEe---------ccEEEEEEcCHHHHHHHHHHcCC--CccCCeEEEE
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGK-IISVRIR---------RNFAFVQYEVQEDATRALDATNM--SKLTDRVISV  217 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~-v~~v~~~---------~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~i~v  217 (425)
                      ++.|||+|| |..+++++|+++|++||+ |..+.+.         +|||||+|.+.++|..|++.|++  ..++|+.|.|
T Consensus         1 n~rLyV~nL-p~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGI-PKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             SEEEEEECC-CTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCEEEEcCC-CCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEE
Confidence            367999999 889999999999999996 8989884         46999999999999999999965  4557999999


Q ss_pred             EEeeeCC
Q 014384          218 EYAVRDD  224 (425)
Q Consensus       218 ~~a~~~~  224 (425)
                      .||.++.
T Consensus        80 ~~A~p~~   86 (96)
T d2disa1          80 DWAEPEI   86 (96)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9997653

>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=99.43  E-value=5.7e-15  Score=116.10  Aligned_cols=69  Identities=19%  Similarity=0.339  Sum_probs=64.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-------CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           55 RPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK-------SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        55 ~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~-------kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      +.|+|.++..++++++|+++|++||+|..|.|.       +|||||+|.+.++|.+|+..|||..|  +|++|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~--~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF--NGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEE--TTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEE--CCEEEEEEEC
Confidence            568888999999999999999999999999983       79999999999999999999999999  8999999985

>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=99.43  E-value=1.4e-13  Score=107.95  Aligned_cols=77  Identities=12%  Similarity=0.048  Sum_probs=66.6

Q ss_pred             CCCcEEEEEcCCCCCCCH----HHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEee
Q 014384          148 RPSKTLFVINFDPYHTRT----RDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAV  221 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~----~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  221 (425)
                      ....+|||+||++...++    ++|+++|++||.|+.+.+.  +++|||+|.+.++|.+|++.|||..|+|+.|.|.|++
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            346789999995433333    5699999999999999997  5699999999999999999999999999999999997


Q ss_pred             eCC
Q 014384          222 RDD  224 (425)
Q Consensus       222 ~~~  224 (425)
                      ...
T Consensus        83 ~~~   85 (104)
T d1weya_          83 TLH   85 (104)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            653

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=3.3e-13  Score=100.60  Aligned_cols=70  Identities=17%  Similarity=0.136  Sum_probs=60.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe--CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcE-EEEEEecc
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK--SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRR-LRVEWTKH  127 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~--kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~-l~V~~a~~  127 (425)
                      .+.|+|++||+++|++.| ++|++||+|.++.+.  ++||||+|.++++|++|| .|||..|  .|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al-~~nG~~~--~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIF--GESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHH-TTTTCEE--TTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHH-hcCCCeE--CCcEEEEEEeCCC
Confidence            467999999999987655 589999999999984  799999999999999999 6999999  6874 56877654

>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=99.39  E-value=3.3e-13  Score=104.90  Aligned_cols=77  Identities=21%  Similarity=0.301  Sum_probs=66.6

Q ss_pred             cCCCceEEEcCC--CCCC---------CHHHHHHHHhhcCCeeEEEEe----CCEEEEEEcCHHHHHHHHHhcCCCeecC
Q 014384           51 EAMMRPIFCGNF--EYDA---------RQSDLERLFRRYGKVDRVDMK----SGFAFIYMDDERDAEDAIRGLDRTEFGR  115 (425)
Q Consensus        51 ~~~~~~l~V~nL--~~~~---------t~~~L~~lF~~~G~V~~v~i~----kg~aFV~F~~~~~A~~A~~~lng~~ig~  115 (425)
                      ....++|+|.||  |.++         .+++|.+.|++||+|..|.+.    +|+|||+|.++++|.+|+..|||..|  
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~--   82 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWF--   82 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEE--
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEE--
Confidence            355789999999  4432         236899999999999999983    79999999999999999999999999  


Q ss_pred             CCcEEEEEEecccc
Q 014384          116 KGRRLRVEWTKHER  129 (425)
Q Consensus       116 ~gr~l~V~~a~~~~  129 (425)
                      +|+.|.|+|+.+..
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            89999999987654

>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=99.38  E-value=2.4e-13  Score=106.70  Aligned_cols=74  Identities=19%  Similarity=0.224  Sum_probs=65.1

Q ss_pred             CCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEE-EEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEE
Q 014384          148 RPSKTLFVINFDPYHTRTRDLERHFEPYGKIIS-VRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEY  219 (425)
Q Consensus       148 ~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~-v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  219 (425)
                      ....||||+|| |+.+++++|.++|..||.|.. +.+.       +|||||+|.+.++|.+||+ ||+..|+|+.|.|.+
T Consensus         6 ~~~~~v~v~nL-p~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           6 SAKVCAHITNI-PFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             SCCCEEEEESC-CTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCceEEEEeCC-CCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            44578999999 899999999999999998865 3442       7899999999999999996 999999999999999


Q ss_pred             eeeC
Q 014384          220 AVRD  223 (425)
Q Consensus       220 a~~~  223 (425)
                      +..+
T Consensus        84 ~~~~   87 (103)
T d2cpya1          84 VTLE   87 (103)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8653

>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=99.35  E-value=4.4e-13  Score=106.79  Aligned_cols=76  Identities=13%  Similarity=0.252  Sum_probs=65.4

Q ss_pred             CCCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE--------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          145 TNTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRI--------RRNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       145 ~~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      .+.....+|||+|| |+.+++++|+++|+.||.|..+.+        .+|+|||+|.+.++|.+|++ ||+..|+|+.|.
T Consensus        13 ~~~~~~~~i~v~nL-p~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~   90 (112)
T d1wela1          13 SPHEAGFCVYLKGL-PFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   90 (112)
T ss_dssp             SCCCCCCEEEEECC-CTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCCeEEEEecC-CCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEE
Confidence            34556779999999 899999999999999998754322        26899999999999999996 999999999999


Q ss_pred             EEEeee
Q 014384          217 VEYAVR  222 (425)
Q Consensus       217 v~~a~~  222 (425)
                      |..+..
T Consensus        91 V~~~~~   96 (112)
T d1wela1          91 VHPITK   96 (112)
T ss_dssp             EEEECH
T ss_pred             EEEcCh
Confidence            988754

>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=99.29  E-value=3e-12  Score=99.70  Aligned_cols=64  Identities=19%  Similarity=0.310  Sum_probs=58.3

Q ss_pred             CCCCCcEEEEEc--CCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCcc
Q 014384          146 NTRPSKTLFVIN--FDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKL  210 (425)
Q Consensus       146 ~~~~~~~l~V~n--l~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~  210 (425)
                      ...|..+|+|.|  | +..+++++|+++|++||.|..|.+.  ++||||+|.+.++|..|+..|||..+
T Consensus        14 ~~~pt~~l~V~ng~L-~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGL-GNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTG-GGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCC-CCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            346678999966  9 7899999999999999999999986  67999999999999999999999887

>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=1.3e-12  Score=102.39  Aligned_cols=74  Identities=18%  Similarity=0.299  Sum_probs=64.4

Q ss_pred             CCCceEEEcCC--CCCC--------CHHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCC
Q 014384           52 AMMRPIFCGNF--EYDA--------RQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRT  111 (425)
Q Consensus        52 ~~~~~l~V~nL--~~~~--------t~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~  111 (425)
                      .++++|+|.||  +..+        ..++|++.|++||.|+.|.|.          .|+|||+|.++++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            45788999999  4433        346789999999999999983          489999999999999999999999


Q ss_pred             eecCCCcEEEEEEecc
Q 014384          112 EFGRKGRRLRVEWTKH  127 (425)
Q Consensus       112 ~ig~~gr~l~V~~a~~  127 (425)
                      .|  +|+.|.|.|+..
T Consensus        82 ~f--~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KF--ANRVVVTKYCDP   95 (104)
T ss_dssp             CS--SSSCCEEEEECH
T ss_pred             EE--CCeEEEEEEcCH
Confidence            99  899999999864

>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=99.28  E-value=6.4e-12  Score=99.99  Aligned_cols=71  Identities=18%  Similarity=0.170  Sum_probs=62.4

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCH-HHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQ-EDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~-~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      ..+||+|| +..+|+++|+++|.+||+|..|.|+  ++||||.|.+. ++|..|+..|++..+.+..+.|.++..
T Consensus        12 ~~~fvgnL-~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDL-DDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESC-CSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCC-CCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999 7899999999999999999999998  67999999985 789999999999998887777777654

>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=99.22  E-value=6.8e-14  Score=107.05  Aligned_cols=67  Identities=16%  Similarity=0.370  Sum_probs=59.2

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEE-------------eccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEE
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRI-------------RRNFAFVQYEVQEDATRALDATNMSKLTDRVISV  217 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~-------------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  217 (425)
                      .+|||+|| |..+++++|+++|++||.|..+.+             .+|||||+|.+.++|..|+. |||..|.|+.|.|
T Consensus         2 RrlyVgNL-p~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNI-PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSC-CTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCC
T ss_pred             CEEEEcCC-CCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEE
Confidence            58999999 899999999999999997654443             26899999999999999985 9999999999999


Q ss_pred             EE
Q 014384          218 EY  219 (425)
Q Consensus       218 ~~  219 (425)
                      ..
T Consensus        80 ~r   81 (90)
T d1u2fa_          80 RR   81 (90)
T ss_dssp             BC
T ss_pred             CC
Confidence            63

>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=99.17  E-value=1.3e-12  Score=102.33  Aligned_cols=68  Identities=16%  Similarity=0.176  Sum_probs=61.3

Q ss_pred             EEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe-------ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEe
Q 014384          152 TLFVINFDPYHTRTRDLERHFEPYGKIISVRIR-------RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYA  220 (425)
Q Consensus       152 ~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  220 (425)
                      .++|.++ +..+++++|+++|++||+|..|.|+       +|+|||+|.+.++|.+|++.|||..|+|+.|.|+|.
T Consensus        29 ~~~v~~~-~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEH-YDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHH-HHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhh-hhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4666677 5667788999999999999999995       589999999999999999999999999999999985

>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=99.16  E-value=6.7e-11  Score=91.54  Aligned_cols=77  Identities=17%  Similarity=0.228  Sum_probs=65.1

Q ss_pred             CCCCcEEEEEcC-CCCCC---------CHHHHHhhhccCCcEEEEEEe----ccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 014384          147 TRPSKTLFVINF-DPYHT---------RTRDLERHFEPYGKIISVRIR----RNFAFVQYEVQEDATRALDATNMSKLTD  212 (425)
Q Consensus       147 ~~~~~~l~V~nl-~p~~~---------~~~~L~~~f~~~G~v~~v~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~g  212 (425)
                      .....+|+|.|| ++..+         ..++|+..|.+||.|..|.+.    +|+|||+|.+.++|.+|+..|||..|+|
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            456789999998 22111         136788999999999999885    6799999999999999999999999999


Q ss_pred             eEEEEEEeeeC
Q 014384          213 RVISVEYAVRD  223 (425)
Q Consensus       213 ~~i~v~~a~~~  223 (425)
                      +.|.|+++...
T Consensus        85 r~i~v~~~~g~   95 (99)
T d2dita1          85 RQITAQAWDGT   95 (99)
T ss_dssp             EECEEEECCSC
T ss_pred             EEEEEEEeCCc
Confidence            99999998664

>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=99.12  E-value=1.3e-10  Score=90.80  Aligned_cols=75  Identities=23%  Similarity=0.399  Sum_probs=64.0

Q ss_pred             CCCcEEEEEcCC-CCCC--------CHHHHHhhhccCCcEEEEEEe----------ccEEEEEEcCHHHHHHHHHHcCCC
Q 014384          148 RPSKTLFVINFD-PYHT--------RTRDLERHFEPYGKIISVRIR----------RNFAFVQYEVQEDATRALDATNMS  208 (425)
Q Consensus       148 ~~~~~l~V~nl~-p~~~--------~~~~L~~~f~~~G~v~~v~~~----------~g~afV~f~~~~~A~~A~~~l~g~  208 (425)
                      +|+.+|+|.||- +..+        ..++|++.|++||.|+.|.|+          .|++||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            578899999982 1221        125689999999999999985          379999999999999999999999


Q ss_pred             ccCCeEEEEEEeee
Q 014384          209 KLTDRVISVEYAVR  222 (425)
Q Consensus       209 ~~~g~~i~v~~a~~  222 (425)
                      .|+|+.|.|.|+..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>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=99.10  E-value=6.4e-11  Score=87.89  Aligned_cols=70  Identities=21%  Similarity=0.396  Sum_probs=58.4

Q ss_pred             CcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEe--ccEEEEEEcCHHHHHHHHHHcCCCccCCeE-EEEEEeee
Q 014384          150 SKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIR--RNFAFVQYEVQEDATRALDATNMSKLTDRV-ISVEYAVR  222 (425)
Q Consensus       150 ~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-i~v~~a~~  222 (425)
                      .+.|+|.|| |..++++.| ++|++||+|..+.+.  ++||||+|.+.++|.+||. +||..|+|+. |.|..+..
T Consensus         4 ~~wV~V~G~-p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGF-PQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECC-CGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECC-ChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999 666655555 689999999999996  6899999999999999996 9999999974 56766543

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.64  E-value=5.4e-05  Score=54.86  Aligned_cols=54  Identities=20%  Similarity=0.416  Sum_probs=49.9

Q ss_pred             HHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEe
Q 014384           69 SDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWT  125 (425)
Q Consensus        69 ~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a  125 (425)
                      .+|.+.|..||+|.-|++-.+..+|+|.+-+.|-+|+ .|+|++|  .|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d~mwVTF~dG~SAL~al-~l~g~~v--~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVL-DVDGMKV--KGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHH-HGGGSEE--TTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCCeEEEEECCcHHHHHHh-ccCCeEE--cceEEEEecC
Confidence            5688899999999999999999999999999999999 8999999  8999999753

>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=97.61  E-value=7.4e-05  Score=55.04  Aligned_cols=61  Identities=11%  Similarity=0.105  Sum_probs=54.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe----------CCEEEEEEcCHHHHHHHHHhcCCCeec
Q 014384           54 MRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMK----------SGFAFIYMDDERDAEDAIRGLDRTEFG  114 (425)
Q Consensus        54 ~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~----------kg~aFV~F~~~~~A~~A~~~lng~~ig  114 (425)
                      +++|.|..||+.+|++++.+.++..|++..+...          -.-|||.|.+.+++....+.++|..|-
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             CceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4689999999999999999999999988876662          358999999999999999999999883

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.57  E-value=6.3e-05  Score=54.50  Aligned_cols=72  Identities=21%  Similarity=0.264  Sum_probs=57.9

Q ss_pred             CCCCCcEEEEEcCCCCCC------C---HHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcCCCccCCeEEE
Q 014384          146 NTRPSKTLFVINFDPYHT------R---TRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATNMSKLTDRVIS  216 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~------~---~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  216 (425)
                      ..+|..||.|.=+. ...      .   -.+|.+.|..||+|.-+++..+..+|+|.+-+.|.+|+. |+|.++.|+.|+
T Consensus        11 qGPpDgTIvV~i~~-~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          11 QGPLDATVVVNLQS-PTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CCCTTCEEEEEESS-CCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             cCCCCcEEEEEecc-CCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCeEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            34566677774442 111      1   246888999999999999999999999999999999997 899999999999


Q ss_pred             EEE
Q 014384          217 VEY  219 (425)
Q Consensus       217 v~~  219 (425)
                      |..
T Consensus        89 It~   91 (95)
T d1ufwa_          89 ISG   91 (95)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            863

>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=97.22  E-value=0.00037  Score=47.86  Aligned_cols=58  Identities=29%  Similarity=0.311  Sum_probs=51.5

Q ss_pred             HHHHHhhhccCCcEEEEEEe-----ccEEEEEEcCHHHHHHHHHHcCCCccCCeEEEEEEeee
Q 014384          165 TRDLERHFEPYGKIISVRIR-----RNFAFVQYEVQEDATRALDATNMSKLTDRVISVEYAVR  222 (425)
Q Consensus       165 ~~~L~~~f~~~G~v~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  222 (425)
                      .+.|...|.++|.|..+.+.     .-.|-|...+.++|.-|+..|+..+|+++.|.|.++..
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            45677889999999999995     22899999999999999999999999999999998753

>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=97.17  E-value=0.00094  Score=45.76  Aligned_cols=57  Identities=26%  Similarity=0.378  Sum_probs=50.3

Q ss_pred             HHHHHHHhhcCCeeEEEEe-----CCEEEEEEcCHHHHHHHHHhcCCCeecCCCcEEEEEEecc
Q 014384           69 SDLERLFRRYGKVDRVDMK-----SGFAFIYMDDERDAEDAIRGLDRTEFGRKGRRLRVEWTKH  127 (425)
Q Consensus        69 ~~L~~lF~~~G~V~~v~i~-----kg~aFV~F~~~~~A~~A~~~lng~~ig~~gr~l~V~~a~~  127 (425)
                      +.|.+.|.++|.|..|.|.     .-.|-|...+..+|..|+..|+...|  .++.|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~Ki--G~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKI--GSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEE--TTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhc--CCeEEEEEEecC
Confidence            4567789999999999994     45899999999999999999999999  599999998753

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.49  E-value=0.0035  Score=45.90  Aligned_cols=57  Identities=18%  Similarity=0.275  Sum_probs=51.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeCCEEEEEEcCHHHHHHHHHhcC
Q 014384           53 MMRPIFCGNFEYDARQSDLERLFRRYGKVDRVDMKSGFAFIYMDDERDAEDAIRGLD  109 (425)
Q Consensus        53 ~~~~l~V~nL~~~~t~~~L~~lF~~~G~V~~v~i~kg~aFV~F~~~~~A~~A~~~ln  109 (425)
                      .-..||.-.+|..+...+|.+||+.||.|.--.|.-.-|||...+.++|+.++..++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEecCceEEEEecCHHHHHHHHHHhc
Confidence            345788889999999999999999999998888888999999999999999986554

>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=96.24  E-value=0.011  Score=43.07  Aligned_cols=70  Identities=20%  Similarity=0.250  Sum_probs=57.1

Q ss_pred             cEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEecc----------EEEEEEcCHHHHHHHHHHcCCCccCCe-----EE
Q 014384          151 KTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRN----------FAFVQYEVQEDATRALDATNMSKLTDR-----VI  215 (425)
Q Consensus       151 ~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g----------~afV~f~~~~~A~~A~~~l~g~~~~g~-----~i  215 (425)
                      ++|.|..| |-.+|++++.+.+...|.+.......|          -|||.|.+.+++..-.+.++|..|-+.     .-
T Consensus         2 tKvVvRrL-PP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a   80 (91)
T d1uw4a_           2 SKVVIRRL-PPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPA   80 (91)
T ss_dssp             CEEEEEEE-CTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEEC
T ss_pred             ceEEEecC-CCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeee
Confidence            57899999 677779999999999999888777532          899999999999999999999877542     34


Q ss_pred             EEEEee
Q 014384          216 SVEYAV  221 (425)
Q Consensus       216 ~v~~a~  221 (425)
                      .|++|.
T Consensus        81 ~VE~AP   86 (91)
T d1uw4a_          81 IVEFAP   86 (91)
T ss_dssp             EEEECS
T ss_pred             EEEEcC
Confidence            556553

>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=94.12  E-value=0.13  Score=37.26  Aligned_cols=60  Identities=23%  Similarity=0.350  Sum_probs=51.5

Q ss_pred             CCCCCcEEEEEcCCCCCCCHHHHHhhhccCCcEEEEEEeccEEEEEEcCHHHHHHHHHHcC
Q 014384          146 NTRPSKTLFVINFDPYHTRTRDLERHFEPYGKIISVRIRRNFAFVQYEVQEDATRALDATN  206 (425)
Q Consensus       146 ~~~~~~~l~V~nl~p~~~~~~~L~~~f~~~G~v~~v~~~~g~afV~f~~~~~A~~A~~~l~  206 (425)
                      +.+....||.-.+ |......+|.++|..||.|.-..|.-.-|||...+.++|..++..+.
T Consensus        11 ~~p~RdHVf~~tF-P~~Wk~~dI~~lFSpfG~V~VswIddTSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTF-PKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEEC-CTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeC-CcccchhHHHHHhcCCCceEEEEecCceEEEEecCHHHHHHHHHHhc
Confidence            4455677888899 77777999999999999999889988899999999999998887554