Citrus Sinensis ID: 010374

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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-------430-------440-------450-------460-------470-------480-------490-------500-------510--
Protein Sequence
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGRGLSGHRKNHGY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccEEEEEccccHHHHHHHHHccccEEEcccccccccEEEEEEccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEEccccccccccccccEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccHHHHHHHcccccccccccccccccEEEEccccccccccHHHHHHHHcccccccccccccccccEEEEEEEccccEEEEEccccccHHHHHHHHccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEccccccccccEEEEEcccHHHHHHHcccccccHHHHHHHHHHHHHccccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEccccccccccEEEEEccccccccHHHHHHHHHHHHHHccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
magqsninygkrthfqsdaatnggskrrnpgdeteqrgigsedtVYRYLCplrkigsiigkGGEIVKQLRSETksnirisetvpgcdeRIVTIYsssegtnlfedsgefvspaQDALFRVHDrivaedsladdefgeLTLITVRMlvpadqigcvigkggqVIQNIRTETRAQIRILkdehlplcaLSFDELLQVAGEPAVVRKALVQIASRlhenpsrsqhLLLSsssniyqssgvylsaplvgsygnysarrdeasAREFSLRlvcpagniggvigkggGIIKQIRQesgasikvdssgaegddciifistkeffedpsptiTAALrlqprcsekteresgdpvittrilvpsaqigcligrgGAIISEMRSATRASIRIltnenvpkvayedeeMVQITGSLDVASSALSQVTLRLRANTFeregalaahppvlpyvpmslditdgskygnrdnqsrgrgnsyatgnlpgrdsygsyggslsgggnaygaygdhssgrglsghrknhgy
Flexible Loop (DISEMBL)
magqsninygkrthfqsdaatnggskrrnpgdeteqrgigsedtvYRYLCPLRkigsiigkggeIVKQLrsetksnirisetvpgcderIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAedsladdefGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPagniggvigkGGGIIKQIRQESGAsikvdssgaegDDCIIFIStkeffedpsPTITAAlrlqprcsekteresgdpvittrilvpsaqiGCLIGRGGAIISEMRSATRasiriltnenvpkvaYEDEEMVQITGSLDVASSALSQVTLRLRANTFERegalaahppvlpyvpMSLDITDGSkygnrdnqsrgrgnsyatgnlpgRDSYGSYGGSLSGGGNAYGAYGDhssgrglsghrknhgy
Low Complexity Region (SEG)
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRkigsiigkggeivkQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPsrsqhlllssssNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAgniggvigkgggiikqiRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDsygsyggslsgggnaygaygDHSSGRGLSGHRKNHGY
Disordered region (IsUnstruct)
******************************************DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASR******************IYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQ*************EGDDCIIFISTKEFFEDP**TITAA******************VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDI******************************************************************
Disordered Region (DISOPRED)
*********************************************YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV**********************VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQ**********************************************CPAGNIGGV**************************************************************************ILVPSAQIGCLIGRGGAIISEMRSA*RA**************YEDEEMVQITGSLDVASSALSQVTLR**********************************************************************************************
Disordered Region (DISEMBL)
MAGQSNINYGKRTHFQSD*******************GIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE***********AEGDDCIIFISTKEFFEDPSPTITAALRLQP************PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGR***********
Disordered Region (DISPRO)
****************************************SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAE**********LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS***H********IYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF*******AHPPVLPYVPMSLDITDGSK*********GRG*SYATGNLPGRDSYGSYGGSL****************************
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGRGLSGHRKNHGY
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	512	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.886	0.749	0.301	7e-50
Q5RB68	556	Insulin-like growth facto	no	no	0.667	0.615	0.261	3e-16
Q9CPN8	579	Insulin-like growth facto	no	no	0.730	0.645	0.243	7e-15
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.466	0.593	0.292	1e-14
P57724	403	Poly(rC)-binding protein	no	no	0.470	0.598	0.290	1e-14
P57721	371	Poly(rC)-binding protein	no	no	0.292	0.404	0.312	1e-14
P57722	371	Poly(rC)-binding protein	no	no	0.292	0.404	0.312	1e-14
P57723	403	Poly(rC)-binding protein	no	no	0.453	0.575	0.292	1e-14
Q9Y6M1	599	Insulin-like growth facto	no	no	0.679	0.580	0.250	1e-14
O00425	579	Insulin-like growth facto	no	no	0.728	0.644	0.242	2e-14

>sp|P58223|Y4837_ARATH KH domain-containing protein At4g18375 OS=Arabidopsis thaliana GN=At4g18375 PE=2 SV=1

 Score =  198 bits (504), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 170/563 (30%), Positives = 271/563 (48%), Gaps = 109/563 (19%)

Query: 11  KRTHFQ-SDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQL 69
           KR   Q +++ +N   KRR   D+  +     E  VYR LCP+  +G +IGK G+++  +
Sbjct: 6   KRKQIQRNNSESNRNQKRRISHDKINR----DELVVYRILCPIDVVGGVIGKSGKVINAI 61

Query: 70  RSETKSNIRISETVPGCDERIVTIYSS----SEGTNLFEDSGEFVSPAQDALFRVHDRIV 125
           R  TK+ I++ + + GC +R++TIY S     E     +   E +  AQDAL +V+D IV
Sbjct: 62  RHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEIGFTKSENEPLCCAQDALLKVYDAIV 121

Query: 126 AEDSLADDEFGELTLI------TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL-K 178
           A    +D+E    T +        R+LVP  Q   +IGK G+ I+ IR  TRA ++++ K
Sbjct: 122 A----SDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSK 177

Query: 179 DEHLP--LCALSFDELLQVAGEPAVVRKALVQIASRLHE-NP-------SRSQHLLLSS- 227
           D   P  +CA+ +D ++ ++GEP  V++AL  +++ +++ NP       S SQ +  +S 
Sbjct: 178 DVSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINPRENIPLDSTSQDVPAASV 237

Query: 228 ------SSNIYQSSGVYLSAPL-------VGSYGNYSARRD------------------- 255
                 S+++Y  +G Y +          V SY N  +  D                   
Sbjct: 238 IVPSDLSNSVYPQTGFYSNQDHILQQGAGVPSYFNALSVSDFQGYAETAANPVPVFASSL 297

Query: 256 --------EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV-DSSGAEGDD 306
                    + + E   +++CP  NI  VIGKGG  IK+IR+ SG+ I+V DS    GDD
Sbjct: 298 PVTHGFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDD 357

Query: 307 -CIIFISTKEFFED-PSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGR 364
            C+I ++  E  +D  S  + A L LQ    E    E  + V   ++LV S  IGC+IG+
Sbjct: 358 ECVIIVTATESPDDMKSMAVEAVLLLQ----EYINDEDAENV-KMQLLVSSKVIGCVIGK 412

Query: 365 GGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF 424
            G++I+E+R  T A+I I   +         +++V+++G +     AL Q+ LRLR +  
Sbjct: 413 SGSVINEIRKRTNANICISKGKK--------DDLVEVSGEVSSVRDALIQIVLRLREDVL 464

Query: 425 EREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPG-----RDSYGS 479
             + ++A   P                    DN S   G+S A   LP        + G 
Sbjct: 465 GDKDSVATRKP----------------PARTDNCSFLSGSSNAGYTLPSFMSSMASTSGF 508

Query: 480 YG-GSLSGGGNAYGAYGDHSSGR 501
           +G GS   G N  G+ G +S GR
Sbjct: 509 HGYGSFPAGDNVLGSTGPYSYGR 531

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RB68|IF2B2_PONAB Insulin-like growth factor 2 mRNA-binding protein 2 OS=Pongo abelii GN=IGF2BP2 PE=2 SV=1

 Score = 87.4 bits (215), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 103/394 (26%), Positives = 185/394 (46%), Gaps = 52/394 (13%)

Query: 30  PGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETVPGCDE 88
           PG  ++ R I   D   R L P + +G+IIGK G  +K +  +T+S + I  +   G  E
Sbjct: 183 PGGTSQARQI---DFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAE 239

Query: 89  RIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVP 148
           + VTI+++ EGT          S A   +  +  +   E  LA++       I +++L  
Sbjct: 240 KPVTIHATPEGT----------SEACRMILEIMQKEADETKLAEE-------IPLKILAH 282

Query: 149 ADQIGCVIGKGGQVIQNIRTETRAQIRI--LKDEHLPLCALSFDELLQVAGEPAVVRKAL 206
              +G +IGK G+ ++ I  ET  +I I  L+D    L   + +  + V G       A 
Sbjct: 283 NGLVGRLIGKEGRNLKKIEHETGTKITISSLQD----LSIYNPERTITVKGTVEACASAE 338

Query: 207 VQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRL 266
           ++I  +L E     ++ +L+ +++    SG + S      +G +      +   +  + L
Sbjct: 339 IEIMKKLREA---FENDMLAVNTH----SGYFSSLYPHHQFGPFP--HHHSYPEQEIVNL 389

Query: 267 VCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDC---IIFISTKEFFEDPSPT 323
             P   +G +IGK G  IKQ+ + +GASIK+  + AEG D    ++ I+       P   
Sbjct: 390 FIPTQAVGAIIGKKGAHIKQLARFAGASIKI--APAEGPDVSERMVIITG-----PPEAQ 442

Query: 324 ITAALRLQPRCSEKTERESGDPV-ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI 382
             A  R+  +  E+      + V +   I VPS+  G +IG+GG  ++E+++ T A + I
Sbjct: 443 FKAQGRIFGKLKEENFFNPKEEVKLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEV-I 501

Query: 383 LTNENVPKVAYEDEE-MVQITGSLDVASSALSQV 415
           +  +  P    E+EE +V+I G    + +A  ++
Sbjct: 502 VPRDQTPD---ENEEVIVRIIGHFFASQTAQRKI 532

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Pongo abelii (taxid: 9601)

>sp|Q9CPN8|IF2B3_MOUSE Insulin-like growth factor 2 mRNA-binding protein 3 OS=Mus musculus GN=Igf2bp3 PE=1 SV=1

 Score = 82.4 bits (202), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 105/432 (24%), Positives = 194/432 (44%), Gaps = 58/432 (13%)

Query: 25  SKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETV 83
           S++ +PG  ++Q+     D   R L P + +G+IIGK G  ++ +  +T+S I +  +  
Sbjct: 180 SRQASPGSVSKQKPC---DLPLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKEN 236

Query: 84  PGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITV 143
            G  E+ +TI S+ EGT          S A  ++  +  +        D +F E   I +
Sbjct: 237 TGAAEKSITILSTPEGT----------SAACKSILEIMHK-----EAQDIKFTEE--IPL 279

Query: 144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVR 203
           ++L   + +G +IGK G+ ++ I  +T  +I I   + L L   + +  + V G      
Sbjct: 280 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELTL--YNPERTITVKGSVETCA 337

Query: 204 KALVQIASRL---HENPSRSQ----HLL---------LSSSSNIYQSSGVYLSAPLVGSY 247
           KA  +I  ++   +EN   S     HL+         L   ++          + L   Y
Sbjct: 338 KAEEEIMKKIRESYENDIASMNLQAHLIPGLNLNALGLFPPTSGMPPPTSGPPSTLTPPY 397

Query: 248 GNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDC 307
             +     E      ++ L  PA ++G +IGK G  IKQ+ + +GASIK+  + A     
Sbjct: 398 PQFEQSETE------TVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAKV 451

Query: 308 IIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPV-ITTRILVPSAQIGCLIGRGG 366
            + I T      P     A  R+  +  E+      + V +   I VPS   G +IG+GG
Sbjct: 452 RMVIITG----PPEAQFKAQGRIYGKIKEENFVSPKEEVKLEAHIRVPSFAAGRVIGKGG 507

Query: 367 AIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL---DVASSALSQVTLRLRANT 423
             ++E++S + A + ++  +  P     D+ +V+ITG      VA   + ++  +++ + 
Sbjct: 508 KTVNELQSLSSAEV-VVPRDQTPD--ENDQVVVKITGHFYACQVAQRKIQEILTQVKQH- 563

Query: 424 FEREGALAAHPP 435
            +++ AL + PP
Sbjct: 564 -QQQKALQSGPP 574

RNA-binding protein that act as a regulator of mRNA translation and stability. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binds to sequences in the 3'-UTR of CD44 mRNA.

Mus musculus (taxid: 10090)

>sp|Q0VCU0|PCBP4_BOVIN Poly(rC)-binding protein 4 OS=Bos taurus GN=PCBP4 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 83/284 (29%), Positives = 130/284 (45%), Gaps = 45/284 (15%)

Query: 46  YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFED 105
            R L   +++GSIIGK GE VK++R ++ + I ISE    C ERI TI  S+    +F  
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGSTAA--VFHA 75

Query: 106 SGEFVSPAQDALFRVHDRIVAEDSLADDEFGELT--LITVRMLVPADQIGCVIGKGGQVI 163
                       F++ + + A    A    G ++   +T+R+++PA Q G +IGK G  I
Sbjct: 76  VSMIA-------FKLDEDLCA----APANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKI 124

Query: 164 QNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHL 223
           + IR  T AQ+++  D    L   S +  + V+G P  +   + QI + + E+P +   +
Sbjct: 125 KEIRETTGAQVQVAGD----LLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 224 ----------LLSSSSNIYQSSGVY-------------LSAPLVGSYGNYSARRDEASAR 260
                     +L S++  +   G Y             LS   V           + S +
Sbjct: 181 PYHPSLSLGTVLLSTNQGFSVQGQYGTVTPAEVTKLQQLSGHAVPFASPSMVPGLDPSTQ 240

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG 304
             S   + P   IG VIG+ G  I +IRQ SGA IK+ +  AEG
Sbjct: 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ-AEG 283

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Bos taurus (taxid: 9913)

>sp|P57724|PCBP4_MOUSE Poly(rC)-binding protein 4 OS=Mus musculus GN=Pcbp4 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 128/282 (45%), Gaps = 41/282 (14%)

Query: 46  YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFED 105
            R L   +++GSIIGK GE VK++R ++ + I ISE    C ERI TI  S+    +F  
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGSTAA--VFHA 75

Query: 106 SGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQN 165
                       F++ + + A    A+        +T+R+++PA Q G +IGK G  I+ 
Sbjct: 76  VSMIA-------FKLDEDLCAAP--ANGGSVSRPPVTLRLVIPASQCGSLIGKAGTKIKE 126

Query: 166 IRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHL-- 223
           IR  T AQ+++  D    L   S +  + V+G P  +   + QI + + E+P +   +  
Sbjct: 127 IRETTGAQVQVAGD----LLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATIPY 182

Query: 224 --------LLSSSSNIYQSSGVY-------------LSAPLVGSYGNYSARRDEASAREF 262
                   +L S++  +   G Y             LS   V           + S +  
Sbjct: 183 HPSLSLGTVLLSANQGFSVQGQYGAVTPAEVTKLQQLSGHAVPFASPSVVPGMDPSTQTS 242

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG 304
           S   + P   IG VIG+ G  I +IRQ SGA IK+ +  AEG
Sbjct: 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ-AEG 283

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score = 81.6 bits (200), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 91/179 (50%), Gaps = 29/179 (16%)

Query: 47  RYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDS 106
           R L   +++GSIIGK GE VK++R E+ + I ISE    C ERIVTI   +         
Sbjct: 49  RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPT--------- 97

Query: 107 GEFVSPAQDALFRVHDRIVAE------DSLADDEFGELTLITVRMLVPADQIGCVIGKGG 160
                   DA+F+    I  +      +S+++        +T+R++VPA Q G +IGKGG
Sbjct: 98  --------DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGG 149

Query: 161 QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSR 219
             I+ IR  T AQ+++  D    +   S +  + ++G P  + + + QI   + E+P +
Sbjct: 150 SKIKEIRESTGAQVQVAGD----MLPNSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|P57722|PCBP3_MOUSE Poly(rC)-binding protein 3 OS=Mus musculus GN=Pcbp3 PE=2 SV=3

 Score = 81.6 bits (200), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 91/179 (50%), Gaps = 29/179 (16%)

Query: 47  RYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDS 106
           R L   +++GSIIGK GE VK++R E+ + I ISE    C ERIVTI   +         
Sbjct: 49  RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPT--------- 97

Query: 107 GEFVSPAQDALFRVHDRIVAE------DSLADDEFGELTLITVRMLVPADQIGCVIGKGG 160
                   DA+F+    I  +      +S+++        +T+R++VPA Q G +IGKGG
Sbjct: 98  --------DAIFKAFAMIAYKFEEDIINSMSNSPATSKPPVTLRLVVPASQCGSLIGKGG 149

Query: 161 QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSR 219
             I+ IR  T AQ+++  D    +   S +  + ++G P  + + + QI   + E+P +
Sbjct: 150 SKIKEIRESTGAQVQVAGD----MLPNSTERAVTISGTPDAIIQCVKQICVVMLESPPK 204

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Mus musculus (taxid: 10090)

>sp|P57723|PCBP4_HUMAN Poly(rC)-binding protein 4 OS=Homo sapiens GN=PCBP4 PE=2 SV=1

 Score = 81.3 bits (199), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 85/291 (29%), Positives = 133/291 (45%), Gaps = 59/291 (20%)

Query: 46  YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFED 105
            R L   +++GSIIGK GE VK++R ++ + I ISE    C ERI TI  S+    +F  
Sbjct: 20  LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGSTAA--VFHA 75

Query: 106 SGEFVSPAQDALFRVHDRIVAEDSLADDEFGELT--LITVRMLVPADQIGCVIGKGGQVI 163
                       F++ + + A    A    G ++   +T+R+++PA Q G +IGK G  I
Sbjct: 76  VSMIA-------FKLDEDLCA----APANGGNVSRPPVTLRLVIPASQCGSLIGKAGTKI 124

Query: 164 QNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHL 223
           + IR  T AQ+++  D    L   S +  + V+G P  +   + QI + + E+P +   +
Sbjct: 125 KEIRETTGAQVQVAGD----LLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 224 LLSSSSNIYQSSGVYLSA----PLVGSYGNYSARR------------------------- 254
               S ++     V LSA     + G YG  +                            
Sbjct: 181 PYHPSLSL---GTVLLSANQGFSVQGQYGAVTPAEVTKLQQLSSHAVPFATPSVVPGLDP 237

Query: 255 -DEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG 304
             + S++EF    + P   IG VIG+ G  I +IRQ SGA IK+ +  AEG
Sbjct: 238 GTQTSSQEF----LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ-AEG 283

Single-stranded nucleic acid binding protein that binds preferentially to oligo dC.

Homo sapiens (taxid: 9606)

>sp|Q9Y6M1|IF2B2_HUMAN Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2 PE=1 SV=2

 Score = 81.3 bits (199), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 108/431 (25%), Positives = 186/431 (43%), Gaps = 83/431 (19%)

Query: 30  PGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETVPGCDE 88
           PG  ++ R I   D   R L P + +G+IIGK G  +K +  +T+S + I  +   G  E
Sbjct: 183 PGGTSQARQI---DFPLRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDIHRKENSGAAE 239

Query: 89  RIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVP 148
           + VTI+++ EGT          S A   +  +  +   E  LA++       I +++L  
Sbjct: 240 KPVTIHATPEGT----------SEACRMILEIMQKEADETKLAEE-------IPLKILAH 282

Query: 149 ADQIGCVIGKGGQVIQNIRTETRAQIRI--LKDEHLPLCALSFDELLQVAGEPAVVRKAL 206
              +G +IGK G+ ++ I  ET  +I I  L+D    L   + +  + V G       A 
Sbjct: 283 NGLVGRLIGKEGRNLKKIEHETGTKITISSLQD----LSIYNPERTITVKGTVEACASAE 338

Query: 207 VQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSA------------------------- 241
           ++I  +L E    +  L ++  +N+    G+ LSA                         
Sbjct: 339 IEIMKKLREA-FENDMLAVNQQANLI--PGLNLSALGIFSTGLSVLSPPAGPRGAPPAAP 395

Query: 242 --PLVGSYGNYSARRDEASAREFS----------LRLVCPAGNIGGVIGKGGGIIKQIRQ 289
             P     G +S+         F           + L  P   +G +IGK G  IKQ+ +
Sbjct: 396 YHPFTTHSGYFSSLYPHHQFGPFPHHHSYPEQEIVNLFIPTQAVGAIIGKKGAHIKQLAR 455

Query: 290 ESGASIKVDSSGAEGDDC---IIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPV 346
            +GASIK+  + AEG D    ++ I+       P     A  R+  +  E+      + V
Sbjct: 456 FAGASIKI--APAEGPDVSERMVIITG-----PPEAQFKAQGRIFGKLKEENFFNPKEEV 508

Query: 347 -ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE-MVQITGS 404
            +   I VPS+  G +IG+GG  ++E+++ T A + I+  +  P    E+EE +V+I G 
Sbjct: 509 KLEAHIRVPSSTAGRVIGKGGKTVNELQNLTSAEV-IVPRDQTPD---ENEEVIVRIIGH 564

Query: 405 LDVASSALSQV 415
              + +A  ++
Sbjct: 565 FFASQTAQRKI 575

Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. May regulate translation of target mRNAs.

Homo sapiens (taxid: 9606)

>sp|O00425|IF2B3_HUMAN Insulin-like growth factor 2 mRNA-binding protein 3 OS=Homo sapiens GN=IGF2BP3 PE=1 SV=2

 Score = 80.9 bits (198), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 105/433 (24%), Positives = 196/433 (45%), Gaps = 60/433 (13%)

Query: 25  SKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETV 83
           S++ +PG  ++Q+     D   R L P + +G+IIGK G  ++ +  +T+S I +  +  
Sbjct: 180 SRQGSPGSVSKQKPC---DLPLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKEN 236

Query: 84  PGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITV 143
            G  E+ +TI S+ EGT          S A  ++  +  +        D +F E   I +
Sbjct: 237 AGAAEKSITILSTPEGT----------SAACKSILEIMHK-----EAQDIKFTEE--IPL 279

Query: 144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVR 203
           ++L   + +G +IGK G+ ++ I  +T  +I I   + L L   + +  + V G      
Sbjct: 280 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELTL--YNPERTITVKGNVETCA 337

Query: 204 KALVQIASRL---HENPSRSQHL--------------LLSSSSNIYQSSGVYLSAPLVGS 246
           KA  +I  ++   +EN   S +L              L   +S +   +    SA +   
Sbjct: 338 KAEEEIMKKIRESYENDIASMNLQAHLIPGLNLNALGLFPPTSGMPPPTSGPPSA-MTPP 396

Query: 247 YGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDD 306
           Y  +     E      ++ L  PA ++G +IGK G  IKQ+ + +GASIK+  + A    
Sbjct: 397 YPQFEQSETE------TVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAK 450

Query: 307 CIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPV-ITTRILVPSAQIGCLIGRG 365
             + I T      P     A  R+  +  E+      + V +   I VPS   G +IG+G
Sbjct: 451 VRMVIITG----PPEAQFKAQGRIYGKIKEENFVSPKEEVKLEAHIRVPSFAAGRVIGKG 506

Query: 366 GAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL---DVASSALSQVTLRLRAN 422
           G  ++E+++ + A + ++  +  P     D+ +V+ITG      VA   + ++  +++ +
Sbjct: 507 GKTVNELQNLSSAEV-VVPRDQTPD--ENDQVVVKITGHFYACQVAQRKIQEILTQVKQH 563

Query: 423 TFEREGALAAHPP 435
             +++ AL + PP
Sbjct: 564 --QQQKALQSGPP 574

RNA-binding protein that act as a regulator of mRNA translation and stability. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binds to sequences in the 3'-UTR of CD44 mRNA.

Homo sapiens (taxid: 9606)

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	512
296086352	583	unnamed protein product [Vitis vinifera]	0.886	0.778	0.784	0.0
359473301	517	PREDICTED: KH domain-containing protein	0.886	0.878	0.784	0.0
147853553	543	hypothetical protein VITISV_009249 [Viti	0.900	0.848	0.742	0.0
224112243	553	predicted protein [Populus trichocarpa]	0.988	0.915	0.660	0.0
53749469	533	KH domain containing protein [Solanum de	0.996	0.956	0.622	1e-178
356572762	548	PREDICTED: KH domain-containing protein	0.996	0.930	0.605	1e-176
356550877	561	PREDICTED: KH domain-containing protein	0.974	0.889	0.618	1e-176
113205451	600	KH domain containing protein, putative [	0.976	0.833	0.634	1e-175
449527609	546	PREDICTED: KH domain-containing protein	0.914	0.857	0.633	1e-174
449447377	545	PREDICTED: KH domain-containing protein	0.914	0.858	0.633	1e-174

>gi|296086352|emb|CBI31941.3| unnamed protein product [Vitis vinifera]

 Score =  684 bits (1765), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/463 (78%), Positives = 405/463 (87%), Gaps = 9/463 (1%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N +YGKR+H QSD   NGGSKRRNPGD+ EQ GIG EDTVYRYLCP+RKIGSIIG
Sbjct: 67  MAGQRN-DYGKRSHSQSDYGGNGGSKRRNPGDDKEQHGIGVEDTVYRYLCPVRKIGSIIG 125

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GG+I KQLRSETKSNIRI ET+PGC+ER+VTIYSSSE TN F D+GE VSPAQDALFRV
Sbjct: 126 RGGDIAKQLRSETKSNIRIGETMPGCEERVVTIYSSSEETNPFGDTGELVSPAQDALFRV 185

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDRIVA +  AD+E  E   +TVRMLVP+DQIGCVIGKGGQVIQNIR+ETRAQIRILKDE
Sbjct: 186 HDRIVAGELPADEEPEEAQQVTVRMLVPSDQIGCVIGKGGQVIQNIRSETRAQIRILKDE 245

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP CALS DELLQ+ G+ +VVRKAL Q+ASRLHENPSRSQHLLLSSS N+YQS G +  
Sbjct: 246 HLPPCALSSDELLQIIGDASVVRKALHQLASRLHENPSRSQHLLLSSSPNMYQSGGDW-- 303

Query: 241 APLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS 300
                S+  YSARRDE+SA+EFSLRLVCP GNIGGVIGKGGGIIKQIRQESGASIKVDSS
Sbjct: 304 -----SHSYYSARRDESSAKEFSLRLVCPTGNIGGVIGKGGGIIKQIRQESGASIKVDSS 358

Query: 301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGC 360
            AEGDDCIIFIS KEFFEDPSPTI AALRLQPRCSEK ERES D V+TTR+LVPS++IGC
Sbjct: 359 SAEGDDCIIFISAKEFFEDPSPTIDAALRLQPRCSEKAERESSDSVVTTRLLVPSSRIGC 418

Query: 361 LIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420
           LIG+GGAIISEMRS TRA+IRIL+ EN+PKVA ED+EMVQITG L+VAS+AL QVTLRL+
Sbjct: 419 LIGKGGAIISEMRSVTRANIRILSKENLPKVASEDDEMVQITGELNVASNALLQVTLRLK 478

Query: 421 ANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRG 463
           AN FEREGA+AA PP LPY+PMS D++DGSKYG+RD+Q R RG
Sbjct: 479 ANLFEREGAIAAIPPTLPYLPMS-DMSDGSKYGSRDSQPRERG 520

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473301|ref|XP_002272287.2| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  684 bits (1764), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/463 (78%), Positives = 405/463 (87%), Gaps = 9/463 (1%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N +YGKR+H QSD   NGGSKRRNPGD+ EQ GIG EDTVYRYLCP+RKIGSIIG
Sbjct: 1   MAGQRN-DYGKRSHSQSDYGGNGGSKRRNPGDDKEQHGIGVEDTVYRYLCPVRKIGSIIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GG+I KQLRSETKSNIRI ET+PGC+ER+VTIYSSSE TN F D+GE VSPAQDALFRV
Sbjct: 60  RGGDIAKQLRSETKSNIRIGETMPGCEERVVTIYSSSEETNPFGDTGELVSPAQDALFRV 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDRIVA +  AD+E  E   +TVRMLVP+DQIGCVIGKGGQVIQNIR+ETRAQIRILKDE
Sbjct: 120 HDRIVAGELPADEEPEEAQQVTVRMLVPSDQIGCVIGKGGQVIQNIRSETRAQIRILKDE 179

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP CALS DELLQ+ G+ +VVRKAL Q+ASRLHENPSRSQHLLLSSS N+YQS G +  
Sbjct: 180 HLPPCALSSDELLQIIGDASVVRKALHQLASRLHENPSRSQHLLLSSSPNMYQSGGDW-- 237

Query: 241 APLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS 300
                S+  YSARRDE+SA+EFSLRLVCP GNIGGVIGKGGGIIKQIRQESGASIKVDSS
Sbjct: 238 -----SHSYYSARRDESSAKEFSLRLVCPTGNIGGVIGKGGGIIKQIRQESGASIKVDSS 292

Query: 301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGC 360
            AEGDDCIIFIS KEFFEDPSPTI AALRLQPRCSEK ERES D V+TTR+LVPS++IGC
Sbjct: 293 SAEGDDCIIFISAKEFFEDPSPTIDAALRLQPRCSEKAERESSDSVVTTRLLVPSSRIGC 352

Query: 361 LIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420
           LIG+GGAIISEMRS TRA+IRIL+ EN+PKVA ED+EMVQITG L+VAS+AL QVTLRL+
Sbjct: 353 LIGKGGAIISEMRSVTRANIRILSKENLPKVASEDDEMVQITGELNVASNALLQVTLRLK 412

Query: 421 ANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRG 463
           AN FEREGA+AA PP LPY+PMS D++DGSKYG+RD+Q R RG
Sbjct: 413 ANLFEREGAIAAIPPTLPYLPMS-DMSDGSKYGSRDSQPRERG 454

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147853553|emb|CAN81693.1| hypothetical protein VITISV_009249 [Vitis vinifera]

 Score =  681 bits (1756), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/497 (74%), Positives = 413/497 (83%), Gaps = 36/497 (7%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N +YGKR+H QSD   NGGSKRRNPGD+ EQ GIG EDTVYRYLCP+RKIGSIIG
Sbjct: 1   MAGQRN-DYGKRSHSQSDYGGNGGSKRRNPGDDKEQHGIGVEDTVYRYLCPVRKIGSIIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GG+I KQLRSETKSNIRI ET+PGC+ER+VTIYSSSE TN F D+GE VSPAQDALFRV
Sbjct: 60  RGGDIAKQLRSETKSNIRIGETMPGCEERVVTIYSSSEETNPFGDTGELVSPAQDALFRV 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDRIVA +  AD+E  E   +TVRMLVP+DQIGCVIGKGGQVIQNIR+ETRAQIRILKDE
Sbjct: 120 HDRIVAGELPADEEPEEAQQVTVRMLVPSDQIGCVIGKGGQVIQNIRSETRAQIRILKDE 179

Query: 181 HLPLCALSFDELLQ------------VAGEPAVVRKALVQIASRLHENPSRSQHLLLSSS 228
           HLP CALS DELLQ            + G+ +VVRKAL Q+ASRLHENPSRSQHLLLSSS
Sbjct: 180 HLPPCALSSDELLQAFGNVFWALTSQIIGDASVVRKALHQLASRLHENPSRSQHLLLSSS 239

Query: 229 SNIYQSSGVYLS----------APLVGSYGNY------------SARRDEASAREFSLRL 266
            N+YQS G +++          APL+GSYG Y            SARRDE+SA+EFSLRL
Sbjct: 240 PNMYQSGGTFMTPNIDAPLVGVAPLMGSYGGYKGDTGDWSHSYYSARRDESSAKEFSLRL 299

Query: 267 VCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITA 326
           VCP GNIGGVIGKGGGIIKQIRQESGASIKVDSS AEGDDCIIFIS KEFFEDPSPTI A
Sbjct: 300 VCPTGNIGGVIGKGGGIIKQIRQESGASIKVDSSSAEGDDCIIFISAKEFFEDPSPTIDA 359

Query: 327 ALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNE 386
           ALRLQPRCSEK ERES D V+TTR+LVPS++IGCLIG+GGAIISEMRS TRA+IRIL+ E
Sbjct: 360 ALRLQPRCSEKAERESSDSVVTTRLLVPSSRIGCLIGKGGAIISEMRSVTRANIRILSKE 419

Query: 387 NVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDI 446
           N+PKVA ED+EMVQITG L+VAS+AL QVTLRL+AN FEREGA+AA PP LPY+PMS D+
Sbjct: 420 NLPKVASEDDEMVQITGELNVASNALLQVTLRLKANLFEREGAIAAIPPTLPYLPMS-DM 478

Query: 447 TDGSKYGNRDNQSRGRG 463
           +DGSKYG+RD+Q R RG
Sbjct: 479 SDGSKYGSRDSQPRERG 495

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112243|ref|XP_002316129.1| predicted protein [Populus trichocarpa] gi|222865169|gb|EEF02300.1| predicted protein [Populus trichocarpa]

 Score =  649 bits (1673), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/559 (66%), Positives = 434/559 (77%), Gaps = 53/559 (9%)

Query: 1   MAGQSNINYGKRT-HFQSDAATNGGSKRRNPGDE-TEQRGIGSEDTVYRYLCPLRKIGSI 58
           MAGQ N +YGKR+ H QSD    GG KRRNPGD+ ++Q  I +EDTVYRYLCPLRKIGSI
Sbjct: 1   MAGQRN-DYGKRSQHSQSDY---GGGKRRNPGDDPSDQNTITNEDTVYRYLCPLRKIGSI 56

Query: 59  IGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118
           IGKGGEI KQLR+++KSNIRISE +PG DERIVTIYSSSE TNLF ++GE+V PAQDALF
Sbjct: 57  IGKGGEIAKQLRADSKSNIRISEAMPGYDERIVTIYSSSEETNLFGETGEYVCPAQDALF 116

Query: 119 RVHDRIVAED--------SLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET 170
            VHDR++AED           +D FGE+  +TVRMLVPADQIGCVIGKGGQVIQNIR+ET
Sbjct: 117 MVHDRVIAEDLNNAAAEEEEGEDNFGEVQQVTVRMLVPADQIGCVIGKGGQVIQNIRSET 176

Query: 171 RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSN 230
            AQIRI KD+HLP  ALS DELL + GEP+ VRKAL Q+A+RLHENPSRSQHL+LSSS+N
Sbjct: 177 CAQIRITKDDHLPPLALSIDELLLIHGEPSAVRKALYQVATRLHENPSRSQHLILSSSAN 236

Query: 231 IYQSSGVYLSA----PLVGSYGNYSA---------RRDEASAREFSLRLVCPAGNIGGVI 277
           ++   GV+++A    P++G YGNY           +RDE+S +EFSLRLVCP  NIGGVI
Sbjct: 237 VH--GGVFVTANAGAPVLGLYGNYKGGWSSSFYPDQRDESSTKEFSLRLVCPTANIGGVI 294

Query: 278 GKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEK 337
           GKGGGIIKQIRQES ASIKVDSSGAEGDDCIIFIS KEFFED SPT+ AALRLQPRCS+K
Sbjct: 295 GKGGGIIKQIRQESRASIKVDSSGAEGDDCIIFISAKEFFEDQSPTMNAALRLQPRCSDK 354

Query: 338 TERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE 397
           TE+ESGD VITTR+LV  +QIGCL+G+GGAIISEMR+ TRA+IRI++ +N+PKVA ED+E
Sbjct: 355 TEKESGDSVITTRLLVGRSQIGCLMGKGGAIISEMRNQTRANIRIISEDNLPKVAVEDDE 414

Query: 398 M----------VQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDIT 447
           M          VQITGSL+VAS+AL QV LRL+AN F R+GAL A PP LPY+PMSLD +
Sbjct: 415 MVQVNVYNFNSVQITGSLEVASNALLQVILRLKANLFGRDGALTAFPPALPYIPMSLDTS 474

Query: 448 DGSKYGNRDNQSRGRGNSYATGNLPGR-----DSYGSYGGSLSGGGNAYGAY-------- 494
           DGSKYG+RD+QSRGRG + ++     R     DSYGS GGSL GG ++YGAY        
Sbjct: 475 DGSKYGSRDSQSRGRGYTSSSSGYGSRDVHPSDSYGSNGGSLIGGESSYGAYGGFSSGRS 534

Query: 495 -GDHSSGRGLSGHRKNHGY 512
            G   SG+     RK+HGY
Sbjct: 535 GGAGLSGQNPVSQRKHHGY 553

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|53749469|gb|AAU90323.1| KH domain containing protein [Solanum demissum]

 Score =  632 bits (1631), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 333/535 (62%), Positives = 407/535 (76%), Gaps = 25/535 (4%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N NYGKR   +SD + + GSKRR P DE E   IG EDTV+RYLCP  KIGSIIG
Sbjct: 1   MAGQRN-NYGKRMQSESDYSRSDGSKRRTPTDEKESNSIGPEDTVFRYLCPTGKIGSIIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
            GG+I KQLR+ET S IRISET+PGC+ER+VTIYS SE TN+ ED+G+ +SPAQDALFRV
Sbjct: 60  VGGDIAKQLRTETNSKIRISETIPGCEERVVTIYSGSEETNVSEDTGDLISPAQDALFRV 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR++AED   D++  +   ITVRMLVP+DQIGCVIGKGGQVIQN+R+ET AQIR+L  E
Sbjct: 120 HDRVLAEDLRMDEDLEDHQQITVRMLVPSDQIGCVIGKGGQVIQNLRSETGAQIRVLSSE 179

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP CAL+ DELLQ+ GE AVV+KAL Q+A+RLH+NPSRSQH LLSS S I++S   +++
Sbjct: 180 HLPPCALNSDELLQITGEGAVVKKALYQVAARLHDNPSRSQHQLLSSPS-IFRSGAGFVN 238

Query: 241 ----------APLVGSYGNYSA--RRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIR 288
                       L+G Y +Y +  R   +S +EF++RLVCP  N+G VIGKGGGIIKQ+R
Sbjct: 239 PHAGTQVMGVTSLMGPYASYKSDGRSKSSSVKEFAVRLVCPTENVGAVIGKGGGIIKQLR 298

Query: 289 QESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVIT 348
           QESGASIKVDS+ AEGDDCIIF+S KE FED SPTI A +RLQPR SEKTE+ESGD ++T
Sbjct: 299 QESGASIKVDSAAAEGDDCIIFVSAKEAFEDQSPTIDATMRLQPRSSEKTEKESGDAILT 358

Query: 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVA 408
           TR+LVPS+++GCLIG+GG+II+EMR++TRASIR+L+ EN+PKVA ED+EMVQITG  +VA
Sbjct: 359 TRLLVPSSRVGCLIGKGGSIINEMRNSTRASIRVLSKENLPKVASEDDEMVQITGDANVA 418

Query: 409 SSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYAT 468
           ++AL QV +RLRANTFE EG+  A  P L YVPMS  + DGS+YGNRDN+SR  G S  +
Sbjct: 419 TNALLQVLMRLRANTFEMEGSFPAFSPGLSYVPMSASMPDGSRYGNRDNRSRRHGYSSYS 478

Query: 469 GNLPGRD--SYGSYGGSLSGGGNAYGAYGDHSSGR----GLSGHR-----KNHGY 512
           G     D     SYGGS  GGG  Y  YG +SSGR    G+S H      K++GY
Sbjct: 479 GGHDYNDLSPSDSYGGSQVGGGGNYAPYGVYSSGRPSSAGVSSHNPSAYGKSYGY 533

Source: Solanum demissum

Species: Solanum demissum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572762|ref|XP_003554535.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  625 bits (1613), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 333/550 (60%), Positives = 403/550 (73%), Gaps = 40/550 (7%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           M GQ +  YGKR H QSD   NG +KRRN GD+ EQ  I  EDTVYRY+CP RKIGS+IG
Sbjct: 1   MGGQRS-GYGKRPHSQSDH-DNGPNKRRNHGDDREQFVIDLEDTVYRYVCPGRKIGSVIG 58

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GGEIVKQLR ETK+ IRI ETVPGC+ER+VTIYS S+ TN  E  G +VSPAQDALF+V
Sbjct: 59  RGGEIVKQLRVETKAKIRIGETVPGCEERVVTIYSPSDETNAVEGGGNYVSPAQDALFKV 118

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR+VAED   D +      +T ++LVP+DQIGCVIGKGG ++QNIR+ET AQIRILKD+
Sbjct: 119 HDRVVAEDFHGDQDDDGGQQVTAKLLVPSDQIGCVIGKGGSIVQNIRSETGAQIRILKDD 178

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLPLCALS DEL+Q+ G+ +VV+KAL QIASRLH+NPSRSQHLL S+   +Y + G  + 
Sbjct: 179 HLPLCALSSDELVQITGDASVVKKALCQIASRLHDNPSRSQHLLTSAVPGVYPAGGSLIG 238

Query: 241 ----------APLVGSYGN-------------YSARRDEASAREFSLRLVCPAGNIGGVI 277
                     APLVG+YG              YSA RDEAS +EFS+RLVCP GNIGGVI
Sbjct: 239 PGAGAPIVGIAPLVGAYGGYKGDTGDWPPRSMYSAPRDEASTKEFSVRLVCPTGNIGGVI 298

Query: 278 GKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDP-SPTITAALRLQPRCSE 336
           GKGG II QIRQESGA+IKVDSS  EGD+C+I ISTKEFFE+  SPTI AA+RLQPRCSE
Sbjct: 299 GKGGMIINQIRQESGATIKVDSSTTEGDECLIAISTKEFFEETFSPTIEAAVRLQPRCSE 358

Query: 337 KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDE 396
           K ER+SG    TTR+LVP+++IGCLIG+GG+II+EMR  T+A+IRI++ EN+PK+A ED+
Sbjct: 359 KVERDSGIISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRIISKENLPKIASEDD 418

Query: 397 EMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRD 456
           EMVQI+G LD+A  AL  V  RLRAN F+REGAL++  PVLPY+P+S D +DG  Y  RD
Sbjct: 419 EMVQISGDLDIAKDALVHVLTRLRANLFDREGALSSFLPVLPYLPVSADGSDGLNYDGRD 478

Query: 457 NQSRGRGN-----SYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGR----GLSGH- 506
            +  GRG+        + +L   D YGSYGGS  G  +AYGAYG +S GR    GLS   
Sbjct: 479 GKRHGRGHSYSSGYGGSSDLAAGDIYGSYGGSQLGSNSAYGAYGSYSLGRSSTAGLSSQS 538

Query: 507 ----RKNHGY 512
               R+NH Y
Sbjct: 539 GASRRRNHAY 548

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550877|ref|XP_003543809.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  623 bits (1607), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 328/530 (61%), Positives = 395/530 (74%), Gaps = 31/530 (5%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           M GQ +  YGKR H QSD   NG +KRRN GD+ EQ  I SEDTVYRY+CP RKIGS+IG
Sbjct: 1   MGGQRS-GYGKRPHSQSDH-DNGPNKRRNHGDDREQFVIDSEDTVYRYVCPGRKIGSVIG 58

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GGEIVKQLR ETK+ IRI ETVPGC+ER+VTIY  S+ TN  E  G +VSPAQDALF+V
Sbjct: 59  RGGEIVKQLRVETKAKIRIGETVPGCEERVVTIYGPSDETNAVEGGGNYVSPAQDALFKV 118

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR+VAED   D +      +T ++LVP+DQIGCVIGKGG ++QNIR ET AQIRILKD+
Sbjct: 119 HDRVVAEDFHGDQDDDGGQQVTAKLLVPSDQIGCVIGKGGSIVQNIRGETGAQIRILKDD 178

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP+CALS DEL+Q+ G+ AVV+KAL QIASRLH+NPSRSQHLL S+ S +Y + G  + 
Sbjct: 179 HLPMCALSSDELVQITGDAAVVKKALYQIASRLHDNPSRSQHLLTSAVSGVYPAGGSLIG 238

Query: 241 ----------APLVGSYGN-------------YSARRDEASAREFSLRLVCPAGNIGGVI 277
                     APLVGSYG              YSA RDEAS++EFS+RLVCP GNIGGVI
Sbjct: 239 PGAGAPIVGIAPLVGSYGGYKGDTGDWPPRSMYSAPRDEASSKEFSVRLVCPTGNIGGVI 298

Query: 278 GKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDP-SPTITAALRLQPRCSE 336
           GKGG II QIRQ+SGA+IKVDSS  EGD+C+I ISTKEFFE+  SPTI AA+RLQPRCSE
Sbjct: 299 GKGGMIINQIRQDSGATIKVDSSTIEGDECLIAISTKEFFEETFSPTIEAAVRLQPRCSE 358

Query: 337 KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDE 396
           K ER+SG    TTR+LVP+ +IGCLIG+GG+II++MR  T+A+IRI++ EN+PK+A ED+
Sbjct: 359 KVERDSGIISFTTRLLVPTTRIGCLIGKGGSIITDMRRLTKANIRIISKENLPKIANEDD 418

Query: 397 EMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRD 456
           EMVQI+G LDVA  AL  V  RLRAN F+REGAL+A  PVLPY+P+S D +DG  Y  RD
Sbjct: 419 EMVQISGDLDVAKDALVHVLTRLRANLFDREGALSAFLPVLPYLPVSADGSDGLNYDGRD 478

Query: 457 NQSRGRGN-----SYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGR 501
            +  GRG+        + +L   D YGSYGGS  G  +AYGAYG +S GR
Sbjct: 479 GKRHGRGHSYSSGYGGSSDLAAGDVYGSYGGSQLGSNSAYGAYGSYSLGR 528

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|113205451|gb|AAW28569.2| KH domain containing protein, putative [Solanum demissum]

 Score =  620 bits (1599), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 326/514 (63%), Positives = 395/514 (76%), Gaps = 14/514 (2%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N NYGKR   +SD + + GSKRR P DE E   IG EDTV+RYLCP  KIGSIIG
Sbjct: 1   MAGQRN-NYGKRMQSESDYSRSDGSKRRTPTDEKESNSIGPEDTVFRYLCPTGKIGSIIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
            GG+I KQLR+ET S IRISET+PGC+ER+VTIYS SE TN+ ED+G+ +SPAQDALFRV
Sbjct: 60  VGGDIAKQLRTETNSKIRISETIPGCEERVVTIYSGSEETNVSEDTGDLISPAQDALFRV 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR++AED   D++  +   ITVRMLVP+DQIGCVIGKGGQVIQN+R+ET AQIR+L  E
Sbjct: 120 HDRVLAEDLRMDEDLEDHQQITVRMLVPSDQIGCVIGKGGQVIQNLRSETGAQIRVLSSE 179

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSS---------NI 231
           HLP CAL+ DELLQ+ GE AVV+KAL Q+A+RLH+NPSRSQH LLSS S         N 
Sbjct: 180 HLPPCALNSDELLQITGEGAVVKKALYQVAARLHDNPSRSQHQLLSSPSIFRSGAGLVNP 239

Query: 232 YQSSGVYLSAPLVGSYGNYSA--RRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQ 289
           +  + V     L+G Y +Y +  R   +S +EF++RLVCP  N+G VIGKGGGIIKQ+RQ
Sbjct: 240 HAGTQVMGVTSLMGPYASYKSDGRSRSSSVKEFAVRLVCPTENVGAVIGKGGGIIKQLRQ 299

Query: 290 ESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349
           ESGASIKVDS+ AEGDDCIIF+S KE FED SPTI A +RLQPR SEKTE+ESGD ++TT
Sbjct: 300 ESGASIKVDSAAAEGDDCIIFVSAKEAFEDQSPTIDATMRLQPRSSEKTEKESGDAILTT 359

Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVAS 409
           R+LVPS+++GCLIG+GG+II+EMR++TRASIR+L+ EN+PKVA ED+EMVQITG  +VA+
Sbjct: 360 RLLVPSSRVGCLIGKGGSIINEMRNSTRASIRVLSKENLPKVASEDDEMVQITGDANVAA 419

Query: 410 SALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATG 469
           +AL QV +RLRANTFE EG+  A  P L YVPMS  + DGS+YGNRDN+SR   +S  +G
Sbjct: 420 NALLQVLMRLRANTFEMEGSFPAFSPGLSYVPMSASMPDGSRYGNRDNRSRRHSHSSYSG 479

Query: 470 NLPGRD--SYGSYGGSLSGGGNAYGAYGDHSSGR 501
                D     SYGGS  GGG  Y  YG +SSGR
Sbjct: 480 GHDYNDLSPSDSYGGSQVGGGGNYAPYGVYSSGR 513

Source: Solanum demissum

Species: Solanum demissum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449527609|ref|XP_004170802.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  618 bits (1593), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 304/480 (63%), Positives = 382/480 (79%), Gaps = 12/480 (2%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N +YGKR H QSD + NGG+KRR+ G++ +Q  I SEDTVYRYLCP++KIGS+IG
Sbjct: 1   MAGQRN-SYGKRNHSQSDYSENGGNKRRSHGEDRDQFVIDSEDTVYRYLCPVKKIGSVIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GGEIVKQLR +TKS IRI ETVPG DER++TIYS+S  TN  E+S ++VSPAQ+ALF++
Sbjct: 60  RGGEIVKQLRIDTKSKIRIGETVPGSDERVITIYSASNETNSLEESSDYVSPAQEALFKI 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR+VA+D + +D  G    +T R+LVP+DQIGC+IGKGGQ++QNIRTET AQ+RILKD+
Sbjct: 120 HDRVVADDYMDEDSEGGGHQVTARLLVPSDQIGCIIGKGGQIVQNIRTETGAQVRILKDD 179

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP CALS DEL+Q++GEP +V+KAL QIASRLH+NPSRSQHLL S+   +Y S G  ++
Sbjct: 180 HLPRCALSSDELVQISGEPLIVKKALYQIASRLHDNPSRSQHLLASAIPGVYSSGGSLMA 239

Query: 241 ----------APLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE 290
                     APLV  YG Y A R++ S++EFSLRL+CP  NIGGVIGKGG II QIRQE
Sbjct: 240 PTHGAPIMGLAPLVSPYGGYKAPREDLSSKEFSLRLICPTENIGGVIGKGGAIINQIRQE 299

Query: 291 SGASIKVDSSGAEGDDCIIFISTKEFFEDP-SPTITAALRLQPRCSEKTERESGDPVITT 349
           + A+IKVDSS  EGDDC+I IS+KEFFED  SPT+ AALRLQPRCSEK ER+SG    TT
Sbjct: 300 TKAAIKVDSSATEGDDCLINISSKEFFEDSYSPTLEAALRLQPRCSEKVERDSGIISFTT 359

Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVAS 409
           R+LVP+++IGCLIG+GGAII+E+R  T+A+IRIL+ EN+PKVA ED+EMVQI+G LDVA 
Sbjct: 360 RLLVPTSRIGCLIGKGGAIITELRRLTKANIRILSKENLPKVALEDDEMVQISGDLDVAK 419

Query: 410 SALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATG 469
            AL  +  RLRAN F+REGAL+A  PVLPY+P+S D +D   Y  R+ +  GRG+SY++G
Sbjct: 420 EALVHIVTRLRANLFDREGALSAVLPVLPYLPLSADGSDSLSYDGREGKRHGRGHSYSSG 479

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447377|ref|XP_004141445.1| PREDICTED: KH domain-containing protein At4g18375-like [Cucumis sativus]

 Score =  618 bits (1593), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 304/480 (63%), Positives = 382/480 (79%), Gaps = 12/480 (2%)

Query: 1   MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIG 60
           MAGQ N +YGKR H QSD + NGG+KRR+ G++ +Q  I SEDTVYRYLCP++KIGS+IG
Sbjct: 1   MAGQRN-SYGKRNHSQSDYSENGGNKRRSHGEDRDQFVIDSEDTVYRYLCPVKKIGSVIG 59

Query: 61  KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV 120
           +GGEIVKQLR +TKS IRI ETVPG DER++TIYS+S  TN  E+S ++VSPAQ+ALF++
Sbjct: 60  RGGEIVKQLRIDTKSKIRIGETVPGSDERVITIYSASNETNSLEESSDYVSPAQEALFKI 119

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           HDR+VA+D + +D  G    +T R+LVP+DQIGC+IGKGGQ++QNIRTET AQ+RILKD+
Sbjct: 120 HDRVVADDYMDEDSEGGGHQVTARLLVPSDQIGCIIGKGGQIVQNIRTETGAQVRILKDD 179

Query: 181 HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLS 240
           HLP CALS DEL+Q++GEP +V+KAL QIASRLH+NPSRSQHLL S+   +Y S G  ++
Sbjct: 180 HLPRCALSSDELVQISGEPLIVKKALYQIASRLHDNPSRSQHLLASAIPGVYSSGGSLMA 239

Query: 241 ----------APLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE 290
                     APLV  YG Y A R++ S++EFSLRL+CP  NIGGVIGKGG II QIRQE
Sbjct: 240 PTHGAPIMGLAPLVSPYGGYKAPREDLSSKEFSLRLICPTENIGGVIGKGGAIINQIRQE 299

Query: 291 SGASIKVDSSGAEGDDCIIFISTKEFFEDP-SPTITAALRLQPRCSEKTERESGDPVITT 349
           + A+IKVDSS  EGDDC+I IS+KEFFED  SPT+ AALRLQPRCSEK ER+SG    TT
Sbjct: 300 TKAAIKVDSSATEGDDCLINISSKEFFEDSYSPTLEAALRLQPRCSEKVERDSGIISFTT 359

Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVAS 409
           R+LVP+++IGCLIG+GGAII+E+R  T+A+IRIL+ EN+PKVA ED+EMVQI+G LDVA 
Sbjct: 360 RLLVPTSRIGCLIGKGGAIITELRRLTKANIRILSKENLPKVALEDDEMVQISGDLDVAK 419

Query: 410 SALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATG 469
            AL  +  RLRAN F+REGAL+A  PVLPY+P+S D +D   Y  R+ +  GRG+SY++G
Sbjct: 420 EALVHIVTRLRANLFDREGALSAVLPVLPYLPLSADGSDSLSYDGREGKRHGRGHSYSSG 479

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	512
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.894	0.956	0.542	2.9e-126
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.607	0.567	0.468	1.2e-72
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.398	0.316	0.341	6.4e-45
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.273	0.915	0.556	3e-37
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.412	0.323	0.297	5.4e-35
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.388	0.328	0.315	8.2e-33
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.345	0.285	0.345	2.5e-29
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.347	0.308	0.346	1.9e-18
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.330	0.267	0.301	1.5e-14
RGD|1307430	319	Pcbp3 "poly(rC) binding protei	0.259	0.416	0.306	2.3e-12

TAIR|locus:2035807 AT1G14170 "AT1G14170" [Arabidopsis thaliana (taxid:3702)]

 Score = 1240 (441.6 bits), Expect = 2.9e-126, P = 2.9e-126
 Identities = 254/468 (54%), Positives = 323/468 (69%)

Query:     6 NINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRXXXXXXXXXXXX 65
             NI +GKR++ QS+   NGGSKRRN  DET+Q  I SEDTVYRYLCP++            
Sbjct:     7 NI-HGKRSNLQSEFTGNGGSKRRNLHDETDQNVIASEDTVYRYLCPVKKTGSIIGKGGEI 65

Query:    66 XXQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV 125
               Q+RSETKSN+RI+E +PGC+ER+VT+YS++E  N F D GE V PA DALF+VHD +V
Sbjct:    66 AKQIRSETKSNMRINEALPGCEERVVTMYSTNEELNHFGDDGELVCPALDALFKVHDMVV 125

Query:   126 AE----DSLADD-EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
             A+    D   DD + GE   +TVRMLVP+DQIGCVIGKGGQVIQN+R +T AQIR++KD 
Sbjct:   126 ADADQDDGTDDDNDLGEKQTVTVRMLVPSDQIGCVIGKGGQVIQNLRNDTNAQIRVIKD- 184

Query:   181 HLPLCAL--SFDELLQVAGEPAVVRKALVQIASRLHENPXXXXXXX-XXXXXNIYQSSGV 237
             HLP CAL  S DELL + GEP VVR+AL Q+AS LH+NP             +++Q   +
Sbjct:   185 HLPACALTLSHDELLLIIGEPLVVREALYQVASLLHDNPSRFQHLLLSSSSSSMHQPGAM 244

Query:   238 YLSAPLVGSYGNYSARRDEASAREFSLRLVCPAXXXXXXXXXXXXXXXXXRQESGASIKV 297
              +SA L  S+ NY+ RRD A AREF +  +CPA                 RQE+GA+I+V
Sbjct:   245 LMSAALTSSHRNYAVRRDIADAREFCVCFICPAENVGGVIGKGGGFINQIRQETGATIRV 304

Query:   298 DSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQ 357
             ++S  + DDCIIFIS+KEF+ED SP + AA+RLQ RCSEK  +++ D  I+TR+LV S+Q
Sbjct:   305 NTSETDDDDCIIFISSKEFYEDQSPAVNAAIRLQQRCSEKVGKDANDLAISTRLLVSSSQ 364

Query:   358 IGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417
             IGCLIG+GGA+ISEMRS TRA+IRIL  E+VPK+A EDEEMVQITGS D A  AL+QV L
Sbjct:   365 IGCLIGKGGAVISEMRSVTRANIRILQKEDVPKIAREDEEMVQITGSPDAAMKALTQVIL 424

Query:   418 RLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNS 465
             RLRAN+F+ +  L   P   PY+P   + +  SKY  RD+ S+   NS
Sbjct:   425 RLRANSFDMDHGLVLLPTSFPYIPQVTESSSKSKYAKRDDHSKLNSNS 472

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

TAIR|locus:2150956 AT5G15270 "AT5G15270" [Arabidopsis thaliana (taxid:3702)]

 Score = 734 (263.4 bits), Expect = 1.2e-72, P = 1.2e-72
 Identities = 154/329 (46%), Positives = 211/329 (64%)

Query:     8 NYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRXXXXXXXXXXXXXX 67
             ++ KR+  QSD   NGGSKRR  GD+ +   I  +DTV+RYLCP++              
Sbjct:    14 SHRKRSRPQSDYDDNGGSKRRYRGDDRDSLVIDRDDTVFRYLCPVKKIGSVIGRGGDIVK 73

Query:    68 QLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAE 127
             QLR++T+S IRI E +PGCDER++TIYS S+ TN F D  + +SPAQDALFR+HDR+VA+
Sbjct:    74 QLRNDTRSKIRIGEAIPGCDERVITIYSPSDETNAFGDGEKVLSPAQDALFRIHDRVVAD 133

Query:   128 DSLADDE-FGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186
             D+ ++D   GE   +T ++LVP+DQIGC++G+GGQ++QNIR+ET AQIRI+KD ++PLCA
Sbjct:   134 DARSEDSPEGEKQ-VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLCA 192

Query:   187 LSFDELLQVAGEPAVVRKALVQIASRLHENPXXXXXXXXXX----XXNIYQSSG---VYL 239
             L+ DEL+Q++GE  +V+KAL+QIASRLHENP                ++   +G   +  
Sbjct:   193 LNSDELIQISGEVLIVKKALLQIASRLHENPSRSQNLLSSSGGYPAGSLMSHAGGPRLVG 252

Query:   240 SAPLVGSYGN---------YSARRDEASAREFSLRLVCPAXXXXXXXXXXXXXXXXXRQE 290
              APL+GSYG          Y   R++  A EF +RLV P                  RQE
Sbjct:   253 LAPLMGSYGRDAGDWSRPLYQPPRNDPPATEFFIRLVSPVENIASVIGKGGALINQLRQE 312

Query:   291 SGASIKVDSSGAEGDDCIIFISTKEFFED 319
             + A+IKVDSS  EG+DC+I IS +E FED
Sbjct:   313 TRATIKVDSSRTEGNDCLITISAREVFED 341

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2161413 AT5G46190 "AT5G46190" [Arabidopsis thaliana (taxid:3702)]

 Score = 296 (109.3 bits), Expect = 6.4e-45, Sum P(2) = 6.4e-45
 Identities = 79/231 (34%), Positives = 127/231 (54%)

Query:     7 INYGKRTH--FQSDAATNGGSKRRNPGDETEQRGIGSED---TVYRYLCPLRXXXXXXXX 61
             +  GKRTH  F+ +   N  ++RR    E+E++ I ++D    VYR LCP          
Sbjct:     2 VERGKRTHNRFRDNNNDNNRNQRRRLSYESEEKKIDNKDDLVVVYRILCPSGVMGSVIGK 61

Query:    62 XXXXXXQLRSETKSNIRISETVPGCDERIVTIYSS-SEGTNLFE-DSGEF-----VSPAQ 114
                    +R ET++ I++ +  PGC ER++TI+ S SE  ++ + +  E      +  AQ
Sbjct:    62 SGKVINLIRQETRARIKVVDPFPGCSERVITIFCSVSEKKDIVDIEYSELDYSVPLCSAQ 121

Query:   115 DALFRVHDRIVA------EDSLAD-DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIR 167
              AL +VHD IVA      E++  D D+F E      R+LVP+ Q   VIGK G +I+NIR
Sbjct:   122 AALLKVHDAIVASLATAAENTKIDRDDFREC-----RLLVPSSQCSIVIGKSGSIIKNIR 176

Query:   168 TETRAQIRIL-KDEHLP--LCALSFDELLQVAGEPAVVRKALVQIASRLHE 215
               TRA ++++ KD   P   CA+ FD ++ ++GE   V+KAL  +++ +++
Sbjct:   177 GRTRANVKVVSKDVSDPSHTCAMDFDNIVMISGETESVKKALFAVSAIMYK 227

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2056951 AT2G03110 "AT2G03110" [Arabidopsis thaliana (taxid:3702)]

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 84/151 (55%), Positives = 112/151 (74%)

Query:    77 IRISETVPGCDERIVTIYSSSEGTNLFEDSGE-FVSPAQDALFRVHDRIVAE-----DSL 130
             +R++E +PGCDER+VTIYS+SE  N  ED  E FV PA DALF+VHD +V E     D  
Sbjct:     1 MRVNEALPGCDERVVTIYSNSEERNRIEDDNEDFVCPAFDALFKVHDMVVVEEFDDDDDY 60

Query:   131 AD-DEFGE-LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL- 187
              D DE+ E  T++TVRMLVP+DQIG +IGKGG +IQ +R +T AQIR+ ++++LP+CAL 
Sbjct:    61 NDNDEYSEGQTVVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV-RNDNLPMCALA 119

Query:   188 -SFDELLQVAGEPAVVRKALVQIASRLHENP 217
              S DELLQ+ G+P+ VR+AL Q+A  L+ NP
Sbjct:   120 LSHDELLQIIGDPSAVREALYQVAFLLYNNP 150

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2168367 RCF3 "AT5G53060" [Arabidopsis thaliana (taxid:3702)]

 Score = 239 (89.2 bits), Expect = 5.4e-35, Sum P(2) = 5.4e-35
 Identities = 69/232 (29%), Positives = 109/232 (46%)

Query:     4 QSNINYGKRTHFQSDAATN-----GGSKRRNPGDETEQRGIGSEDTVYRYLCPLRXXXXX 58
             +S   Y    HF      N     GG      G  ++        T YR LC        
Sbjct:    23 RSKPRYNNNYHFGGGGGGNNRYRGGGGGGGGNGRPSKSHPETMATTTYRILCHDAKAGGV 82

Query:    59 XXXXXXXXXQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118
                       +R  T + I + E VPG  ERI+ I S +   +       F SPAQ+ALF
Sbjct:    83 IGKSGTIIKSIRQHTGAWINVHELVPGDAERIIEI-SDNRRRDPDGRMPSF-SPAQEALF 140

Query:   119 RVHDRIVAEDSL---------ADDEFGELT----LITVRMLVPADQIGCVIGKGGQVIQN 165
              VHDRI+  ++           ++++G +      +  R++V    +GC++GKGG++I+ 
Sbjct:   141 SVHDRILESEAQFGYGGPPPEEEEDYGGVRPGGGRVVTRLVVSRMHVGCLLGKGGKIIEQ 200

Query:   166 IRTETRAQIRIL-KDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216
             +R ET+  IRIL ++ +LP C    +E++Q+ GE   V+ AL  ++SRL E+
Sbjct:   201 MRIETKTHIRILPRESNLPRCVSLSEEIVQIVGELNAVKNALAIVSSRLRES 252

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2831364 AT4G18375 "AT4G18375" [Arabidopsis thaliana (taxid:3702)]

 Score = 253 (94.1 bits), Expect = 8.2e-33, Sum P(2) = 8.2e-33
 Identities = 70/222 (31%), Positives = 116/222 (52%)

Query:    11 KRTHFQ-SDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRXXXXXXXXXXXXXXQL 69
             KR   Q +++ +N   KRR   D+  +     E  VYR LCP+                +
Sbjct:     6 KRKQIQRNNSESNRNQKRRISHDKINR----DELVVYRILCPIDVVGGVIGKSGKVINAI 61

Query:    70 RSETKSNIRISETVPGCDERIVTIYSS----SEGTNLFEDSGEFVSPAQDALFRVHDRIV 125
             R  TK+ I++ + + GC +R++TIY S     E     +   E +  AQDAL +V+D IV
Sbjct:    62 RHNTKAKIKVFDQLHGCSQRVITIYCSVKEKQEEIGFTKSENEPLCCAQDALLKVYDAIV 121

Query:   126 AEDSLADDEFGELTLIT------VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL-K 178
             A    +D+E    T +        R+LVP  Q   +IGK G+ I+ IR  TRA ++++ K
Sbjct:   122 A----SDEENNTKTNVDRDDNKECRLLVPFSQSSSLIGKAGENIKRIRRRTRASVKVVSK 177

Query:   179 DEHLP--LCALSFDELLQVAGEPAVVRKALVQIASRLHE-NP 217
             D   P  +CA+ +D ++ ++GEP  V++AL  +++ +++ NP
Sbjct:   178 DVSDPSHVCAMEYDNVVVISGEPESVKQALFAVSAIMYKINP 219

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2017612 AT1G51580 "AT1G51580" [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 2.5e-29, Sum P(2) = 2.5e-29
 Identities = 64/185 (34%), Positives = 88/185 (47%)

Query:   261 EFSLRLVCPAXXXXXXXXXXXXXXXXXRQESGASIKVDSSGAEGDDCIIFISTKEFFEDP 320
             E + RL+CPA                 + ESGASIKV     + ++ II IS +E  E  
Sbjct:   275 EVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLERR 334

Query:   321 -SPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS 379
              S      +R+  R  E     S    +  R+LV S  IG L+G+GG +ISEMR AT AS
Sbjct:   335 HSLAQDGVMRVHNRIVEIGFEPSA--AVVARLLVHSPYIGRLLGKGGHLISEMRRATGAS 392

Query:   380 IRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFER----EGALAAHPP 435
             IR+   +   K   + +E+VQ+ G+L     AL Q+  RLR   F      +G     PP
Sbjct:   393 IRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLREAMFPGRLPFQGMGGPPPP 452

Query:   436 VL-PY 439
              + PY
Sbjct:   453 FMGPY 457

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

TAIR|locus:2084908 FLK "AT3G04610" [Arabidopsis thaliana (taxid:3702)]

 Score = 228 (85.3 bits), Expect = 1.9e-18, Sum P(2) = 1.9e-18
 Identities = 69/199 (34%), Positives = 100/199 (50%)

Query:    20 ATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRXXXXXXXXXXXXXXQLRSETKSNIRI 79
             AT GG ++R PG   E        TV+R L P +              ++  ET++ I+I
Sbjct:   171 ATVGGEEKRWPGWPGE--------TVFRMLVPAQKVGSIIGRKGDVIKKIVEETRARIKI 222

Query:    80 SETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGEL- 138
              +  PG  ER V +    E     E S   + P+ D L RVH RIV  D L D E  +  
Sbjct:   223 LDGPPGTTERAVMVSGKEEP----ESS---LPPSMDGLLRVHMRIV--DGL-DGEASQAP 272

Query:   139 --TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA 196
               + ++ R+LVPA Q G +IGK G  ++ I+  +   +R+L  E LP+ AL  D +++V 
Sbjct:   273 PPSKVSTRLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFALQDDRVVEVV 332

Query:   197 GEPAVVRKALVQIASRLHE 215
             GEP  V +AL  IAS L +
Sbjct:   333 GEPTSVHRALELIASHLRK 351

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0009911 "positive regulation of flower development" evidence=IMP

TAIR|locus:2066020 AT2G22600 "AT2G22600" [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 1.5e-14, Sum P(2) = 1.5e-14
 Identities = 59/196 (30%), Positives = 89/196 (45%)

Query:    42 EDTVYRYLCPLRXXXXXXXXXXXXXXQLRSETKSNIRISETVPGCDERIVTIYSSS---E 98
             ++T  R +C                 +LR ET + I     V G D  +V I  S+   +
Sbjct:    23 DETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWVVFIVGSTAVNQ 82

Query:    99 GTNLFEDSGEF------------VSPAQDALFRVHDR----IVAEDS--LADDEFGELTL 140
                L +  GEF            VS AQ AL RV +R    + A+D   + D E  E   
Sbjct:    83 SILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGGVVDGEDEEAYC 142

Query:   141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
                 +L   +QIG V+G GG+ ++ +R  + A IR+L     P+C    DEL+Q+ G+  
Sbjct:   143 ---GILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPP---PICGTKNDELIQITGDVL 196

Query:   201 VVRKALVQIASRLHEN 216
              V+KALV ++S +  N
Sbjct:   197 AVKKALVMVSSYIQNN 212

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

RGD|1307430 Pcbp3 "poly(rC) binding protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 144 (55.7 bits), Expect = 2.3e-12, Sum P(2) = 2.3e-12
 Identities = 46/150 (30%), Positives = 80/150 (53%)

Query:    68 QLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAE 127
             ++R E+ + I ISE    C ERIVTI   ++   +F+    F   A    ++  + I+  
Sbjct:    38 KMREESGARINISEG--NCPERIVTITGPTDA--IFK---AFAMIA----YKFEEDII-- 84

Query:   128 DSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187
             +S+++        +T+R++VPA Q G +IGKGG  I+ IR  T AQ+++  D  LP    
Sbjct:    85 NSMSNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDM-LPN--- 140

Query:   188 SFDELLQVAGEPAVVRKALVQIASRLHENP 217
             S +  + ++G P  + + + QI   + E+P
Sbjct:   141 STERAVTISGTPDAIIQCVKQICVVMLESP 170

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005829 "cytosol" evidence=IEA;ISO

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

GO:0005730 "nucleolus" evidence=ISO

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00036937001 SubName- Full=Chromosome chr1 scaffold_84, whole genome shotgun sequence; (551 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	512
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-18
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-17
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-16
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-13
pfam00013	59	pfam00013, KH_1, KH domain	2e-12
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	7e-11
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-11
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-09
pfam00013	59	pfam00013, KH_1, KH domain	3e-09
pfam13014	42	pfam13014, KH_3, KH domain	4e-09
pfam00013	59	pfam00013, KH_1, KH domain	5e-09
pfam00013	59	pfam00013, KH_1, KH domain	8e-09
smart00322	68	smart00322, KH, K homology RNA-binding domain	5e-08
pfam13014	42	pfam13014, KH_3, KH domain	5e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-07
pfam13014	42	pfam13014, KH_3, KH domain	7e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-06
pfam13014	42	pfam13014, KH_3, KH domain	7e-05
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	2e-04
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-04
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	5e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	6e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.001
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.001
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.002
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.002
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.003
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.004

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 78.3 bits (194), Expect = 4e-18
 Identities = 32/78 (41%), Positives = 43/78 (55%), Gaps = 14/78 (17%)

Query: 45  VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETV-PGCDERIVTIYSSSEGTNLF 103
             R L P  + GSIIGKGG  +K++R ET + IR+S++V PG  ER+VTI          
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTI---------- 50

Query: 104 EDSGEFVSPAQDALFRVH 121
             SG+  S  Q AL  + 
Sbjct: 51  --SGK-PSAVQKALLLIL 65

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 76.0 bits (188), Expect = 2e-17
 Identities = 29/69 (42%), Positives = 45/69 (65%), Gaps = 4/69 (5%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
           T+R+LVP+ Q G +IGKGG  I+ IR ET A+IR+ K         S + ++ ++G+P+ 
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV----LPGSTERVVTISGKPSA 56

Query: 202 VRKALVQIA 210
           V+KAL+ I 
Sbjct: 57  VQKALLLIL 65

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 72.9 bits (180), Expect = 2e-16
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
           T R+LVPS+Q G +IG+GG+ I E+R  T A IR+  +          E +V I+G    
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPG----STERVVTISGKPSA 56

Query: 408 ASSALSQVT 416
              AL  + 
Sbjct: 57  VQKALLLIL 65

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 23/51 (45%), Positives = 34/51 (66%), Gaps = 1/51 (1%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG-DDCIIFIS 312
           +LRL+ P+   G +IGKGG  IK+IR+E+GA I+V  S   G  + ++ IS
Sbjct: 1   TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTIS 51

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 65

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 9/68 (13%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
           T R+L+P D++G +IGKGG  I+ IR ET  +IRI  D          D+ + ++G P  
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR---------DDTVTISGTPEQ 51

Query: 202 VRKALVQI 209
           V KA   I
Sbjct: 52  VEKAKELI 59

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 24/55 (43%), Positives = 34/55 (61%)

Query: 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
            R L P   +G IIGKGG  +K++R ET + I+I ++  G +ERIVTI  + E 
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEA 55

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 58.7 bits (143), Expect = 2e-11
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
           T R+LVP+  +G +IGKGG  I+ IR ET A+I+I         + S + ++ + G P  
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-----SGSEERIVTITGTPEA 55

Query: 202 VRKALVQI 209
           V KA   I
Sbjct: 56  VEKAKELI 63

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 57.6 bits (140), Expect = 7e-11
 Identities = 21/50 (42%), Positives = 36/50 (72%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           + R++ P+  +G +IGKGG  IK+IR+E+GA IK+  SG+  ++ I+ I+
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTIT 50

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 57.3 bits (139), Expect = 8e-11
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 7/75 (9%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE 198
             +T+ +L+PAD++G +IGKGG  I+ I  ET  +I I           S + ++++ G 
Sbjct: 1   DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGP 53

Query: 199 PAVVRKALVQIASRL 213
           P  V KA   I   L
Sbjct: 54  PENVEKAAELILEIL 68

Length = 68

>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 5/68 (7%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
           T R+LVPS+ +G +IG+GG+ I E+R  T A I+I  + +       +E +V ITG+ + 
Sbjct: 1   TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSG-----SEERIVTITGTPEA 55

Query: 408 ASSALSQV 415
              A   +
Sbjct: 56  VEKAKELI 63

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension. Length = 64

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 9/59 (15%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           T RIL+P  ++G +IG+GG+ I E+R  T   IRI           + ++ V I+G+ +
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---------DRDDTVTISGTPE 50

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 51.8 bits (125), Expect = 4e-09
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query: 54 KIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTI 93
           +G+IIGKGGE +K++R ET + I+I +  PG  ERIVTI
Sbjct: 1  LVGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTI 40

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 52.2 bits (126), Expect = 5e-09
 Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98
            R L P  K+G IIGKGG  +K++R ET   IRI +      +  VTI  + E
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD----RDDTVTISGTPE 50

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|215657 pfam00013, KH_1, KH domain

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
           + R++ P   +G +IGKGG  IK+IR+E+G  I++     + DD +    T E
Sbjct: 1   TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD---DRDDTVTISGTPE 50

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Length = 59

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 49.6 bits (119), Expect = 5e-08
 Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          +      L P  K+G IIGKGG  +K++  ET   I I    PG +ER+V I    E 
Sbjct: 1  DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPEN 56

Length = 68

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 48.7 bits (117), Expect = 5e-08
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           +G +IGKGG  IK+IR+E+GA I++        + I+ I+
Sbjct: 2   VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 41

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 7/69 (10%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           +T  +L+P+ ++G +IG+GG+ I ++   T   I I            +E +V+ITG  +
Sbjct: 3   VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPE 55

Query: 407 VASSALSQV 415
               A   +
Sbjct: 56  NVEKAAELI 64

Length = 68

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 42.5 bits (101), Expect = 7e-06
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 5/47 (10%)

Query: 357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403
            +G +IG+GG  I E+R  T A I+I             E +V ITG
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIP-----KPEPGSGERIVTITG 42

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
           ++ ++ PA  +G +IGKGG  IK+I +E+G  I +   G+E     I
Sbjct: 4   TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEI 50

Length = 68

>gnl|CDD|221895 pfam13014, KH_3, KH domain

 Score = 39.8 bits (94), Expect = 7e-05
 Identities = 16/30 (53%), Positives = 22/30 (73%)

Query: 151 QIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
            +G +IGKGG+ I+ IR ET A+I+I K E
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQIPKPE 30

KH motifs bind RNA in vitro. This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus. RNA localisation is a widespread mechanism for achieving localised protein synthesis. Length = 42

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 39.0 bits (92), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 276 VIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
           +IGK G  I++I +E+G  I+    G++ D   I
Sbjct: 14  IIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI 47

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 42.7 bits (102), Expect = 4e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 6/40 (15%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           I  VIG GG  I++I +E+GA I ++      DD  + I+
Sbjct: 565 IRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIA 598

Length = 693

>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 31/123 (25%), Positives = 51/123 (41%), Gaps = 31/123 (25%)

Query: 54  KIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPA 113
            +G+ IGK G  VK +  E    I + E            +S        ED  EF+   
Sbjct: 86  PVGACIGKRGSRVKAVSEELGEKIDVVE------------WS--------EDPAEFI--- 122

Query: 114 QDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ 173
           ++AL      ++       ++ G + ++    +VP DQ+   IGKGGQ ++     T  +
Sbjct: 123 KNALAPA--EVL--SVNIKEDDGHVAIV----VVPPDQLSLAIGKGGQNVRLASQLTGWE 174

Query: 174 IRI 176
           I I
Sbjct: 175 IDI 177

Length = 190

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 16/37 (43%), Positives = 21/37 (56%)

Query: 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
             M +P D+I  VIG GG+ I+ I  ET  +I I  D
Sbjct: 4   ETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD 40

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 57 SIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
           IIGK G  ++++  ET   IR  +  PG     +TI    E 
Sbjct: 13 FIIGKKGSNIRKIMEETGVKIRFPD--PGSKSDTITITGPKEN 53

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 39.5 bits (93), Expect = 0.001
 Identities = 20/112 (17%), Positives = 42/112 (37%), Gaps = 26/112 (23%)

Query: 66  VKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV 125
           + +++ E K  I +S T+P   E++  I                       +  + D ++
Sbjct: 27  LYEVQKEAKGQIELSRTIPELLEKLFEI----------------------EVPEIGDGVI 64

Query: 126 AEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL 177
               +A D    +    V+     D +G  IGK G  ++ +  E   +I ++
Sbjct: 65  EIKCVARDPRAAVVSNVVK----IDPVGACIGKRGSRVKAVSEELGEKIDVV 112

Length = 190

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 13/29 (44%), Positives = 18/29 (62%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSG 301
           I  VIG GG  IK+I +E+G  I ++  G
Sbjct: 13  IRDVIGPGGKTIKKIIEETGVKIDIEDDG 41

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like

 Score = 36.3 bits (85), Expect = 0.002
 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
           T  + +P      +IGK G  I+ I  ET  +IR            S  + + + G    
Sbjct: 1   TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKEN 53

Query: 202 VRKALVQI 209
           V KA  +I
Sbjct: 54  VEKAKEEI 61

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 62

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 40.6 bits (96), Expect = 0.002
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
           + +  D+I  VIG GG+VI+ I  ET A+I I
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDI 586

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 6/45 (13%)

Query: 54 KIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98
          KI  +IG GG+ +K++  ET   I I       D+  V I +S +
Sbjct: 12 KIRDVIGPGGKTIKKIIEETGVKIDIE------DDGTVYIAASDK 50

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. Length = 61

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 39.6 bits (94), Expect = 0.004
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 6/45 (13%)

Query: 54  KIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98
           KI  +IG GG+ ++++  ET + I I       D+  V I ++  
Sbjct: 564 KIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDG 602

Length = 693

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	512
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.97
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.92
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.89
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.85
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.61
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.61
PRK13763	180	putative RNA-processing protein; Provisional	99.57
PRK13763	180	putative RNA-processing protein; Provisional	99.57
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.39
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.39
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.37
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.24
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.24
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.21
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.21
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.21
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.15
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.15
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.14
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.09
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.06
PF13014	43	KH_3: KH domain	98.96
PF13014	43	KH_3: KH domain	98.88
smart00322	69	KH K homology RNA-binding domain.	98.85
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.79
smart00322	69	KH K homology RNA-binding domain.	98.77
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.56
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	98.45
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.36
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.35
KOG2113	394	consensus Predicted RNA binding protein, contains	98.32
KOG2113	394	consensus Predicted RNA binding protein, contains	98.26
PRK08406	140	transcription elongation factor NusA-like protein;	98.15
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.94
PRK08406	140	transcription elongation factor NusA-like protein;	97.77
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.62
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.58
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.56
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.56
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.54
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.49
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.31
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.22
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.04
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.03
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.97
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.78
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.77
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.75
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.72
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.71
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.67
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.63
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.55
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.38
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.29
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.21
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.14
TIGR01953	341	NusA transcription termination factor NusA. This m	96.14
TIGR01953	341	NusA transcription termination factor NusA. This m	96.1
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.1
COG5176	269	MSL5 Splicing factor (branch point binding protein	96.0
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.96
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.92
PRK00468	75	hypothetical protein; Provisional	95.82
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.68
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.62
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.54
PRK00106	535	hypothetical protein; Provisional	95.53
PRK02821	77	hypothetical protein; Provisional	95.49
PRK12704	520	phosphodiesterase; Provisional	95.42
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.41
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.36
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.35
PRK02821	77	hypothetical protein; Provisional	95.18
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	95.09
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.05
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.05
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.04
PRK00468	75	hypothetical protein; Provisional	94.89
PRK01064	78	hypothetical protein; Provisional	94.82
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.77
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.72
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.63
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.61
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.59
PRK00106	535	hypothetical protein; Provisional	94.56
PRK01064	78	hypothetical protein; Provisional	94.08
PRK12704	520	phosphodiesterase; Provisional	93.98
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	92.77
PRK12705	508	hypothetical protein; Provisional	92.06
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	92.02
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	91.32
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	90.85
COG5166	657	Uncharacterized conserved protein [Function unknow	90.59
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	90.25
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.18
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.63
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	88.56
COG1855	604	ATPase (PilT family) [General function prediction	88.49
PRK12705	508	hypothetical protein; Provisional	88.24
COG5166	657	Uncharacterized conserved protein [Function unknow	88.1
COG1782	637	Predicted metal-dependent RNase, consists of a met	87.87
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	87.76
KOG2874	356	consensus rRNA processing protein [Translation, ri	86.48
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	86.37
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	86.22
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	85.95
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	85.66
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.4
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	85.27
KOG3875	362	consensus Peroxisomal biogenesis protein peroxin [	84.24
PRK13764	602	ATPase; Provisional	84.16
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	83.71
PRK13764	602	ATPase; Provisional	83.69
COG1855	604	ATPase (PilT family) [General function prediction	83.27
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	82.94
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	82.43
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	80.26

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=2.4e-48  Score=403.71  Aligned_cols=399  Identities=42%  Similarity=0.606  Sum_probs=319.0

Q ss_pred             cCCCccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCC
Q 010374            8 NYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCD   87 (512)
Q Consensus         8 ~~~kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~   87 (512)
                      ...++........+++...++...+.... ...+...+|||||+.+.+|.||||+|.+|++||++|.++|+|.+..++|.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~   86 (485)
T KOG2190|consen    8 LPRPKNSTTSNVGDNGSIKRPSLGDPVIS-TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCP   86 (485)
T ss_pred             CccccCCCcccccCCCcccccCCCCCccc-CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCC
Confidence            35566667777767777777777666443 34445555999999999999999999999999999999999999999999


Q ss_pred             ccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCC---cc---cCCCcceEEEEEeeCCceeEEecCCCh
Q 010374           88 ERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLAD---DE---FGELTLITVRMLVPADQIGCVIGKGGQ  161 (512)
Q Consensus        88 ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~---~~---~~~~~~~~~~llVP~~~vg~IIGk~G~  161 (512)
                      ||+|+|+|...+        ..++++++|++++++++......++   ++   +.....+++|||||.+++|+||||+|+
T Consensus        87 eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~  158 (485)
T KOG2190|consen   87 ERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGS  158 (485)
T ss_pred             cceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcH
Confidence            999999996222        2688899999999999987422111   11   122226899999999999999999999


Q ss_pred             hHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCC---CCcc
Q 010374          162 VIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQS---SGVY  238 (512)
Q Consensus       162 ~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~---gg~~  238 (512)
                      .||+|+++|||+|+|.++ ++|.   +++|.|+|.|++++|.+|+..|+.+|++++.+......+.  ..|.+   -+..
T Consensus       159 ~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st--~~y~P~~~~~~~  232 (485)
T KOG2190|consen  159 LIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVST--IPYRPSASQGGP  232 (485)
T ss_pred             HHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCc--ccCCCcccccCc
Confidence            999999999999999999 8998   5789999999999999999999999999765522211111  11211   0001


Q ss_pred             cCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccC
Q 010374          239 LSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFE  318 (512)
Q Consensus       239 ~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~  318 (512)
                      ..+.+......+........+.++.+++.+|...++.|+|+++..|+.|+.++++.|.+....++   |+++++..+.++
T Consensus       233 ~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~  309 (485)
T KOG2190|consen  233 VLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPE  309 (485)
T ss_pred             cccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCcc
Confidence            11111110101122233345677888999999999999999999999999999999999988754   999999999999


Q ss_pred             CC-chhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCce
Q 010374          319 DP-SPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE  397 (512)
Q Consensus       319 ~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r  397 (512)
                      +. +++++|++..++.+.+....+. ...++.+|+||.+++||||||+|.+|.+||+.|||.|+|...++.   ...+++
T Consensus       310 ~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~~~~e~  385 (485)
T KOG2190|consen  310 DRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---SGVREA  385 (485)
T ss_pred             cccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---CCccee
Confidence            88 8999999999999988777655 778999999999999999999999999999999999999877653   146899


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHHhhchhcccC
Q 010374          398 MVQITGSLDVASSALSQVTLRLRANTFEREG  428 (512)
Q Consensus       398 ~V~I~G~~~~v~~A~~~I~~~l~~~~~~~~~  428 (512)
                      +|+|+|+..+...|+.++..++........+
T Consensus       386 ~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (485)
T KOG2190|consen  386 LVQITGMLREDLLAQYLIRARLSAPKSSMGG  416 (485)
T ss_pred             EEEecchhHHHHhhhhhcccccccCccCCCC
Confidence            9999999999999999998888776554444

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=100.00  E-value=3.3e-44  Score=365.93  Aligned_cols=328  Identities=23%  Similarity=0.373  Sum_probs=256.5

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      ..++.+..||.+++++||||+|+.|..|..+++|+|.|.....+..+|.+.++|.++++             ++|..++-
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v-------------~~aK~li~  118 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV-------------EVAKQLIG  118 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH-------------HHHHHhhh
Confidence            55668999999999999999999999999999999999888778899999999999994             34443333


Q ss_pred             HHHhhhcccCC--cccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010374          122 DRIVAEDSLAD--DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP  199 (512)
Q Consensus       122 ~~i~~~~~~~~--~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~  199 (512)
                      +.+ .......  .+......++.+|+||.+.+|.||||+|++||.|++++||++.+..+.....   ..++.+.|+|++
T Consensus       119 evv-~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp  194 (600)
T KOG1676|consen  119 EVV-SRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP  194 (600)
T ss_pred             hhh-hccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence            322 2221000  1112256689999999999999999999999999999999999999865443   478899999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccC
Q 010374          200 AVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGK  279 (512)
Q Consensus       200 ~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk  279 (512)
                      +.|+.|..+|.++|.+....           .+..++.         ++    .   ......+++|.||...||.||||
T Consensus       195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~---------~g----~---~~g~~~~~~V~VPr~~VG~IIGk  247 (600)
T KOG1676|consen  195 DKVEQAKQLVADILREEDDE-----------VPGSGGH---------AG----V---RGGGSATREVKVPRSKVGIIIGK  247 (600)
T ss_pred             HHHHHHHHHHHHHHHhcccC-----------CCccccc---------cC----c---CccccceeEEeccccceeeEEec
Confidence            99999999999999963211           0100000         00    0   01122378999999999999999


Q ss_pred             CCccccchhhhcCCeEEecCCCC-CCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCC------CCcee--EEE
Q 010374          280 GGGIIKQIRQESGASIKVDSSGA-EGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES------GDPVI--TTR  350 (512)
Q Consensus       280 ~G~~Ik~I~~~tga~I~v~~~~~-~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~--t~~  350 (512)
                      +|++||+|+.+||++|+|.+++. ...+|++.|.|..      ..++.+.+++..+........      +....  ...
T Consensus       248 gGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy  321 (600)
T KOG1676|consen  248 GGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFY  321 (600)
T ss_pred             CchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEE
Confidence            99999999999999999998776 6788988888864      355555555544432221110      12223  788


Q ss_pred             EEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      |.||.+.||.||||+|++||.|..+|||++.+.+.   |+..+..+++|+|+|++.+|..|..||.+++...
T Consensus       322 ~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~  390 (600)
T KOG1676|consen  322 MKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI  390 (600)
T ss_pred             EeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence            99999999999999999999999999999999764   4455778999999999999999999999999774

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=8.7e-43  Score=339.07  Aligned_cols=353  Identities=25%  Similarity=0.348  Sum_probs=276.8

Q ss_pred             CCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHH
Q 010374           39 IGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL  117 (512)
Q Consensus        39 ~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~  117 (512)
                      ....+..+|+|||..++|.||||.|+|||.|.+.|.|+|+|.. +..|..|+.|+|.+++|.             +.+|+
T Consensus       194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac  260 (584)
T KOG2193|consen  194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKAC  260 (584)
T ss_pred             ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHH
Confidence            3467889999999999999999999999999999999999985 456899999999999998             67899


Q ss_pred             HHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec
Q 010374          118 FRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG  197 (512)
Q Consensus       118 ~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G  197 (512)
                      .+|++.+..+...    ++-...+.++++..+.+||+||||.|.+||+|+.+||++|.|++-.++..+  ..||.|++.|
T Consensus       261 ~~ILeimqkEA~~----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVkG  334 (584)
T KOG2193|consen  261 KMILEIMQKEAVD----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVKG  334 (584)
T ss_pred             HHHHHHHHHhhhc----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEecc
Confidence            9999988765532    233466789999999999999999999999999999999999987665543  6799999999


Q ss_pred             CHHHHHHHHHHHHHHHhcCCCccccccccCC---------CCccCCCCc--ccCCCCcCCCC-CCCccc--Cccccccce
Q 010374          198 EPAVVRKALVQIASRLHENPSRSQHLLLSSS---------SNIYQSSGV--YLSAPLVGSYG-NYSARR--DEASAREFS  263 (512)
Q Consensus       198 ~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~---------~~~~~~gg~--~~~~p~~~~~~-~~~~~~--~~~~~~~~~  263 (512)
                      ..|+|.+|..+|..+|++..+.+-  ..-+.         ...++.+..  .+++|+.-+.. -|..|.  .....+.-.
T Consensus       335 siEac~~AE~eImkKlre~yEnDl--~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~  412 (584)
T KOG2193|consen  335 SIEACVQAEAEIMKKLRECYENDL--AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQ  412 (584)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhhhH--HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhh
Confidence            999999999999999999765431  11110         011111111  11122111100 111111  112234457


Q ss_pred             EEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCC-CCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCC-
Q 010374          264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAE-GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE-  341 (512)
Q Consensus       264 ~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~-~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~-  341 (512)
                      +++.||...+|.|||++|.+||+|...+||.|++.++..+ ..+|+++|+|.         -++.++.+.++..++..+ 
T Consensus       413 V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp---------peaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  413 VRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP---------PEAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             eeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCC---------hHHHHhhhhhhhhhhhhhc
Confidence            8999999999999999999999999999999999986644 68999999995         356667776666554332 


Q ss_pred             ----CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010374          342 ----SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL  417 (512)
Q Consensus       342 ----~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~  417 (512)
                          ......++.+.||...+|+||||||.+++||++.|+|.|.|+++ +.|-  ..+..+|.|+|..-+.+.|...|.+
T Consensus       484 f~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--End~vivriiGhfyatq~aQrki~~  560 (584)
T KOG2193|consen  484 FFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--ENDQVIVRIIGHFYATQNAQRKIAH  560 (584)
T ss_pred             cCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--ccceeeeeeechhhcchHHHHHHHH
Confidence                23456788999999999999999999999999999999999765 4553  3566789999999999999999999


Q ss_pred             HHhhchh
Q 010374          418 RLRANTF  424 (512)
Q Consensus       418 ~l~~~~~  424 (512)
                      +|.+...
T Consensus       561 iv~qvkq  567 (584)
T KOG2193|consen  561 IVNQVKQ  567 (584)
T ss_pred             HHHHHHH
Confidence            9987544

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=100.00  E-value=5e-34  Score=263.22  Aligned_cols=354  Identities=20%  Similarity=0.335  Sum_probs=227.8

Q ss_pred             CccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccE
Q 010374           11 KRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERI   90 (512)
Q Consensus        11 kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~erv   90 (512)
                      |+-|+..+.+   .-.+|...|- +...+....+.+|||+.++.+|.||||+|++||+|+.+.+|.|.|++.  ..+||+
T Consensus        19 ~~~~~~e~g~---~~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri   92 (390)
T KOG2192|consen   19 ETFPNTETGG---EFGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI   92 (390)
T ss_pred             hcCCCCcccc---cccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence            3444444443   3334433333 344456778999999999999999999999999999999999999987  678999


Q ss_pred             EEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhc
Q 010374           91 VTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET  170 (512)
Q Consensus        91 v~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~t  170 (512)
                      ++|+...+.             +-+-|.+|+..+. +.      ......+++||||+.+++|.|||++|+.||+||+++
T Consensus        93 ~tisad~~t-------------i~~ilk~iip~le-e~------f~~~~pce~rllihqs~ag~iigrngskikelrekc  152 (390)
T KOG2192|consen   93 LTISADIET-------------IGEILKKIIPTLE-EG------FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC  152 (390)
T ss_pred             EEEeccHHH-------------HHHHHHHHhhhhh-hC------CCCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence            999987443             3444444444442 22      234567899999999999999999999999999999


Q ss_pred             CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccccc--CCCCccCCCCcccCCCCcCCCC
Q 010374          171 RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLS--SSSNIYQSSGVYLSAPLVGSYG  248 (512)
Q Consensus       171 ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~--~~~~~~~~gg~~~~~p~~~~~~  248 (512)
                      .|+++|...    .|..++||+|.|.|.+.+|..+++.|.+.|.+.|-+.....+.  .....|..||..|++......-
T Consensus       153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~p  228 (390)
T KOG2192|consen  153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRP  228 (390)
T ss_pred             hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCC
Confidence            999999765    5668999999999999999999999999999987665432111  1122344455444321110000


Q ss_pred             CCCcccC-ccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHH
Q 010374          249 NYSARRD-EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAA  327 (512)
Q Consensus       249 ~~~~~~~-~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~  327 (512)
                      +...++. +..        .-|.......+-++|.-=    +.+--.+.|....+.          ...++..++. +.+
T Consensus       229 gpapqrggqgp--------p~~~~sdlmay~r~GrpG----~rydg~vdFs~detw----------~saidtw~~S-ewq  285 (390)
T KOG2192|consen  229 GPAPQRGGQGP--------PPPRGSDLMAYDRRGRPG----DRYDGMVDFSADETW----------PSAIDTWSPS-EWQ  285 (390)
T ss_pred             CCCCCCCCCCC--------CCCCccccceeccCCCCC----ccccccccccccccC----------CCcCCCcCcc-ccc
Confidence            0000000 000        000011111122222100    011111222221111          0000000111 001


Q ss_pred             HhhCCcc--------cc--cccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCce
Q 010374          328 LRLQPRC--------SE--KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEE  397 (512)
Q Consensus       328 ~~~~~~~--------~~--~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r  397 (512)
                      +..-+.-        ..  ..-.+.+....|..+.||.++-|.||||+|++|++|+.++||.|+|..    | .+++.+|
T Consensus       286 maYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide----p-leGsedr  360 (390)
T KOG2192|consen  286 MAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE----P-LEGSEDR  360 (390)
T ss_pred             cccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC----c-CCCCCce
Confidence            1110000        00  001123456788999999999999999999999999999999999953    3 2478899


Q ss_pred             EEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          398 MVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       398 ~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      +++|+||.++++.|++++...+++.
T Consensus       361 IitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  361 IITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             EEEEeccHHHHhhHHHHHHHHHHhh
Confidence            9999999999999999999999864

>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]

Probab=99.97  E-value=1.9e-29  Score=258.08  Aligned_cols=229  Identities=28%  Similarity=0.378  Sum_probs=181.7

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCC--CCCCccEEEEEcCCCCcccccCCcccCcHHHHHHH
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETV--PGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF  118 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~--~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~  118 (512)
                      ...++.+|+||..++|+||||+|++||+|++.+||++.+-.+.  .....+-+.|+|+++.             ++.|..
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~-------------ve~a~~  202 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDK-------------VEQAKQ  202 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHH-------------HHHHHH
Confidence            5678999999999999999999999999999999999886542  2236788999999887             466777


Q ss_pred             HHHHHHhhhcccCCc-----ccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010374          119 RVHDRIVAEDSLADD-----EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (512)
Q Consensus       119 ~i~~~i~~~~~~~~~-----~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v  193 (512)
                      ++++.+.++.-....     ........+++|.||.+.||.||||+|++||+|+.+|||||+|.++ +.|   .+.||.+
T Consensus       203 lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p---~speR~~  278 (600)
T KOG1676|consen  203 LVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDP---SSPERPA  278 (600)
T ss_pred             HHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC-CCC---CCcccee
Confidence            777777643211110     1123344589999999999999999999999999999999999998 445   3889999


Q ss_pred             EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCC
Q 010374          194 QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNI  273 (512)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~v  273 (512)
                      .|.|+.++|..|.++|.++|.+.....             ++++....|                .....+.+.||.++|
T Consensus       279 ~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------~~~~~~G~P----------------~~~~~fy~~VPa~Kc  329 (600)
T KOG1676|consen  279 QIIGTVDQIEHAAELINEIIAEAEAGA-------------GGGMGGGAP----------------GLVAQFYMKVPADKC  329 (600)
T ss_pred             eeecCHHHHHHHHHHHHHHHHHHhccC-------------CCCcCCCCc----------------cceeeEEEecccccc
Confidence            999999999999999999998853211             011000000                011167899999999


Q ss_pred             cccccCCCccccchhhhcCCeEEecCCC--CCCCCeEEEecCCc
Q 010374          274 GGVIGKGGGIIKQIRQESGASIKVDSSG--AEGDDCIIFISTKE  315 (512)
Q Consensus       274 g~IIGk~G~~Ik~I~~~tga~I~v~~~~--~~~~~~ii~i~g~~  315 (512)
                      |+||||+|++||.|..++||++.+.+..  ....+++|+|.|.+
T Consensus       330 GLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~  373 (600)
T KOG1676|consen  330 GLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDK  373 (600)
T ss_pred             ccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCc
Confidence            9999999999999999999999999872  22578999999976

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=8.5e-27  Score=221.71  Aligned_cols=237  Identities=28%  Similarity=0.396  Sum_probs=174.5

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEec---CCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHH
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF  118 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~---~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~  118 (512)
                      ..+.++||||+..+|.||||+|++|.+|+++|||+|+++   +..|++.||||.|.|+.|+             ....+.
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~ea-------------i~av~e  103 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEA-------------LNAVHE  103 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHH-------------HHHHHH
Confidence            459999999999999999999999999999999999997   4689999999999998665             233445


Q ss_pred             HHHHHHhhhcccCCc-cc-----CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCce
Q 010374          119 RVHDRIVAEDSLADD-EF-----GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL  192 (512)
Q Consensus       119 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~  192 (512)
                      .|.++|.+.....+. .+     ..+..-.++|+||++..|.||||+|.+||.|+|+++|.|+|++.  .|.-....||+
T Consensus       104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqerv  181 (402)
T KOG2191|consen  104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERV  181 (402)
T ss_pred             HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEE
Confidence            556666543322211 11     11112358999999999999999999999999999999999953  23333467999


Q ss_pred             EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCC
Q 010374          193 LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGN  272 (512)
Q Consensus       193 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~  272 (512)
                      |+++|++++.++|+.+|.++|.++|+....+..+..   +-.|.+-...|.-.+|+. ...   ...........++...
T Consensus       182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaNsnPtGspya~-~~~---~~~astas~~sva~~~  254 (402)
T KOG2191|consen  182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVANSNPTGSPYAY-QAH---VLPASTASTISVAAGL  254 (402)
T ss_pred             EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccccCCCCCCCCC-CCc---cccccchhhccccccc
Confidence            999999999999999999999999887665542221   111222112222222221 111   1222334456788889


Q ss_pred             CcccccCCCccccchhhhcCCeEEecCC
Q 010374          273 IGGVIGKGGGIIKQIRQESGASIKVDSS  300 (512)
Q Consensus       273 vg~IIGk~G~~Ik~I~~~tga~I~v~~~  300 (512)
                      .|..-|.++.++-.|-.-+|+.+.++..
T Consensus       255 iG~a~gaG~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  255 IGGANGAGGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             cccccccccccceeeecccccceeeccc
Confidence            9999999999999999999998887763

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=3.5e-28  Score=237.29  Aligned_cols=242  Identities=25%  Similarity=0.401  Sum_probs=189.5

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS  218 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~  218 (512)
                      ....+|+|||..+||.||||.|.+||+|.+.|.|+|.|...++    ++..|++|+|-+++|...+|+++|.+++..+..
T Consensus       197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~  272 (584)
T KOG2193|consen  197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN----AGAAEKIITVHSTPEGTSKACKMILEIMQKEAV  272 (584)
T ss_pred             cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc----CCcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence            3568999999999999999999999999999999999998743    357899999999999999999999999988533


Q ss_pred             ccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEec
Q 010374          219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD  298 (512)
Q Consensus       219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~  298 (512)
                      ..                                    ....++.++++..+.+||++|||.|.+||+|+++||++|.|.
T Consensus       273 ~~------------------------------------k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis  316 (584)
T KOG2193|consen  273 DD------------------------------------KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS  316 (584)
T ss_pred             cc------------------------------------chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence            22                                    234677889999999999999999999999999999999999


Q ss_pred             CCCCC---CCCeEEEecCC-cccCCCchhHHH-----------HHhhCCccccc--------------c-cC---C----
Q 010374          299 SSGAE---GDDCIIFISTK-EFFEDPSPTITA-----------ALRLQPRCSEK--------------T-ER---E----  341 (512)
Q Consensus       299 ~~~~~---~~~~ii~i~g~-~~~~~~~~~~~a-----------~~~~~~~~~~~--------------~-~~---~----  341 (512)
                      +...-   ..||+|++.|. |.+..+...+.+           +..++..+...              + .+   .    
T Consensus       317 ~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~  396 (584)
T KOG2193|consen  317 KLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVT  396 (584)
T ss_pred             ehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccc
Confidence            75432   47999999883 111111111111           11111111000              0 00   0    


Q ss_pred             ---------CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHH
Q 010374          342 ---------SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSAL  412 (512)
Q Consensus       342 ---------~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~  412 (512)
                               .....-..+|.||...||.||||+|..||.|.+.+||.|+|...+    ..+..+|+|+|+|++++.-+|.
T Consensus       397 ~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE----~pdvseRMViItGppeaqfKAQ  472 (584)
T KOG2193|consen  397 FASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE----IPDVSERMVIITGPPEAQFKAQ  472 (584)
T ss_pred             cCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC----CCCcceeEEEecCChHHHHhhh
Confidence                     011334678999999999999999999999999999999997543    3367899999999999999999


Q ss_pred             HHHHHHHhhchh
Q 010374          413 SQVTLRLRANTF  424 (512)
Q Consensus       413 ~~I~~~l~~~~~  424 (512)
                      -.|..+|++..+
T Consensus       473 grifgKikEenf  484 (584)
T KOG2193|consen  473 GRIFGKIKEENF  484 (584)
T ss_pred             hhhhhhhhhhcc
Confidence            999999998655

>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.92  E-value=3.5e-23  Score=197.14  Aligned_cols=170  Identities=25%  Similarity=0.450  Sum_probs=138.4

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                      ..+.+++|||+..+|.||||+|++|.+|+.+|||+|++++..+ +|   ..+||+|.|+|+.+++...+..|.++|++.+
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP---GTTeRvcli~Gt~eai~av~efI~dKire~p  113 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP---GTTERVCLIQGTVEALNAVHEFIADKIREKP  113 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC---CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence            3489999999999999999999999999999999999998744 45   4899999999999999999999999999853


Q ss_pred             CccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEe
Q 010374          218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV  297 (512)
Q Consensus       218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v  297 (512)
                      .....                                        ...++-|+                           
T Consensus       114 ~~~~k----------------------------------------~v~~~~pq---------------------------  126 (402)
T KOG2191|consen  114 QAVAK----------------------------------------PVDILQPQ---------------------------  126 (402)
T ss_pred             HhhcC----------------------------------------CccccCCC---------------------------
Confidence            31100                                        00000000                           


Q ss_pred             cCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhC
Q 010374          298 DSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATR  377 (512)
Q Consensus       298 ~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TG  377 (512)
                                                                  ..+.....++.||..-+|.||||+|.+||.|++++|
T Consensus       127 --------------------------------------------t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsg  162 (402)
T KOG2191|consen  127 --------------------------------------------TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSG  162 (402)
T ss_pred             --------------------------------------------CccccceeEEeccCCcccceecCCcchHHHHHHhhC
Confidence                                                        000113468899999999999999999999999999


Q ss_pred             CeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchh
Q 010374          378 ASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (512)
Q Consensus       378 a~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~  424 (512)
                      |.|+|.+.  .|..-.-.+|+|++.|++|+..+|..+|+++|.+++.
T Consensus       163 a~iqisPq--kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq  207 (402)
T KOG2191|consen  163 AWIQISPQ--KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ  207 (402)
T ss_pred             cceEeccc--CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence            99999853  3433356789999999999999999999999999865

>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]

Probab=99.89  E-value=1.3e-22  Score=187.91  Aligned_cols=174  Identities=26%  Similarity=0.383  Sum_probs=142.7

Q ss_pred             cccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccc
Q 010374          259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT  338 (512)
Q Consensus       259 ~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~  338 (512)
                      ...+.+++++..+..|+||||+|.+||.|+.+++|+|.|+++..  .+++.+|++..     ....+-..++.+++.+.+
T Consensus        45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~-----~ti~~ilk~iip~lee~f  117 (390)
T KOG2192|consen   45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADI-----ETIGEILKKIIPTLEEGF  117 (390)
T ss_pred             hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccH-----HHHHHHHHHHhhhhhhCC
Confidence            34578999999999999999999999999999999999998774  68899998743     122333334455554443


Q ss_pred             cCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 010374          339 ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLR  418 (512)
Q Consensus       339 ~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~  418 (512)
                      ..   ....+.+|+|+++++|.|||++|++|||||+++.|+++|... ++|   .++||+|.|.|.+..|..++..|++.
T Consensus       118 ~~---~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~  190 (390)
T KOG2192|consen  118 QL---PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDL  190 (390)
T ss_pred             CC---CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHH
Confidence            22   245889999999999999999999999999999999999865 666   58999999999999999999999999


Q ss_pred             HhhchhcccCcCCCCCCCCcCCCCCCCCCCCCCCCCCC
Q 010374          419 LRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRD  456 (512)
Q Consensus       419 l~~~~~~~~~~~~~~~p~~~y~p~~~~~~~~~~yg~~~  456 (512)
                      |.+.++        ++...||+|+.+++.+  .||++.
T Consensus       191 i~e~pi--------kgsa~py~p~fyd~t~--dyggf~  218 (390)
T KOG2192|consen  191 ISESPI--------KGSAQPYDPNFYDETY--DYGGFT  218 (390)
T ss_pred             hhcCCc--------CCcCCcCCccccCccc--ccCCce
Confidence            999766        6778899998888753  566543

>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]

Probab=99.85  E-value=2e-20  Score=195.27  Aligned_cols=175  Identities=33%  Similarity=0.599  Sum_probs=139.3

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec---------CHHHHHHHHHHHH
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG---------EPAVVRKALVQIA  210 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G---------~~~~V~~A~~~I~  210 (512)
                      ..++|||++.+.+|.||||+|.+|++|+.+|.++|+|...  ++.   ..+|+|+|+|         ..+++.+|..+|.
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv  116 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LPG---CPERIITITGNRVELNLSPATDALFKAFDMIV  116 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CCC---CCcceEEEecccccccCCchHHHHHHHHHHHh
Confidence            3458999999999999999999999999999999999765  455   4799999999         9999999999998


Q ss_pred             HHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhh
Q 010374          211 SRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE  290 (512)
Q Consensus       211 ~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~  290 (512)
                      ..++++.....                                                 +                   
T Consensus       117 ~~~~~d~~~~~-------------------------------------------------d-------------------  128 (485)
T KOG2190|consen  117 FKLEEDDEAAE-------------------------------------------------D-------------------  128 (485)
T ss_pred             hcccccccccc-------------------------------------------------c-------------------
Confidence            87664211000                                                 0                   


Q ss_pred             cCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHH
Q 010374          291 SGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIIS  370 (512)
Q Consensus       291 tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik  370 (512)
                                                                     .+.+.....++.+|+||.+++|+||||+|++||
T Consensus       129 -----------------------------------------------~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik  161 (485)
T KOG2190|consen  129 -----------------------------------------------NGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIK  161 (485)
T ss_pred             -----------------------------------------------CCccccCCceEEEEEechhheeeeeccCcHHHH
Confidence                                                           000001124789999999999999999999999


Q ss_pred             HHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchhcccCcCCCCCCCCcCCC
Q 010374          371 EMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVP  441 (512)
Q Consensus       371 eI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~~~~~~~~~~~p~~~y~p  441 (512)
                      +|++.|||+|+|..+ .+|.   .++|.|+|.|.+++|.+|+.+|..+|.++...   ..+...-..+|.|
T Consensus       162 ~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~---~~~~~~st~~y~P  225 (485)
T KOG2190|consen  162 EIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPR---SPPPLVSTIPYRP  225 (485)
T ss_pred             HHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence            999999999999776 7785   68889999999999999999999999996532   1122223356666

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.61  E-value=2.1e-15  Score=138.31  Aligned_cols=137  Identities=21%  Similarity=0.220  Sum_probs=97.8

Q ss_pred             EEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEE---cCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010374           48 YLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY---SSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (512)
Q Consensus        48 ilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~---G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i  124 (512)
                      +.||.+.+|.|||++|++|++|+++|+|+|++.+.     +..|.|+   ++++.             ++.|...|....
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~i~   63 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKAIG   63 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHHHH
Confidence            56899999999999999999999999999999864     4568883   33322             344444443322


Q ss_pred             hhhcccCCcc-cCCCcceEEE-EEeeC---------CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010374          125 VAEDSLADDE-FGELTLITVR-MLVPA---------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (512)
Q Consensus       125 ~~~~~~~~~~-~~~~~~~~~~-llVP~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v  193 (512)
                      ....+  ++. ......++.+ +-|+.         ..+|+|||++|++++.|++.|||+|.|..            +.|
T Consensus        64 ~gf~~--e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v  129 (172)
T TIGR03665        64 RGFSP--EKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTV  129 (172)
T ss_pred             cCCCH--HHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEE
Confidence            21010  000 0001111222 33333         36899999999999999999999999853            469


Q ss_pred             EEecCHHHHHHHHHHHHHHHhcC
Q 010374          194 QVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      .|.|++++++.|..+|.+++...
T Consensus       130 ~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       130 GIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             EEECCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999653

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.61  E-value=7e-15  Score=134.79  Aligned_cols=147  Identities=22%  Similarity=0.342  Sum_probs=105.6

Q ss_pred             EEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEE---ecCHHHHHHHHHHHHHHHhcCCCccc
Q 010374          145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQV---AGEPAVVRKALVQIASRLHENPSRSQ  221 (512)
Q Consensus       145 llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~  221 (512)
                      |.||.+.+|.|||++|++|+.|+++|||+|.+..+          +..|.|   +++++++.+|..+|..+.........
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A   71 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKA   71 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            57899999999999999999999999999999755          246888   89999999999999987654110000


Q ss_pred             cccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCC
Q 010374          222 HLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG  301 (512)
Q Consensus       222 ~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~  301 (512)
                      ..                                 ...+.+..++                            +.+.+- 
T Consensus        72 ~~---------------------------------l~gd~y~~~V----------------------------i~I~~~-   89 (172)
T TIGR03665        72 LK---------------------------------LLDDDYMLEV----------------------------IDLKEY-   89 (172)
T ss_pred             HH---------------------------------hcCCcceEEE----------------------------EEhhhc-
Confidence            00                                 0000000000                            011000 


Q ss_pred             CCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEE
Q 010374          302 AEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIR  381 (512)
Q Consensus       302 ~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~  381 (512)
                                +.       ++                      ..+       ...+|.|||++|++++.|++.|||+|.
T Consensus        90 ----------~~-------~~----------------------~~~-------~~~~griIG~~G~t~~~ie~~t~~~i~  123 (172)
T TIGR03665        90 ----------GK-------SP----------------------NAL-------RRIKGRIIGEGGKTRRIIEELTGVSIS  123 (172)
T ss_pred             ----------cC-------CH----------------------HHH-------HHHHhhhcCCCcHHHHHHHHHHCCeEE
Confidence                      00       00                      000       236899999999999999999999999


Q ss_pred             EecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          382 ILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       382 i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      |..            ..|.|.|++++++.|..+|.+++..
T Consensus       124 i~~------------~~v~i~G~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665       124 VYG------------KTVGIIGDPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             EcC------------CEEEEECCHHHHHHHHHHHHHHHcC
Confidence            952            4799999999999999999998854

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.57  E-value=1.2e-14  Score=134.04  Aligned_cols=141  Identities=20%  Similarity=0.155  Sum_probs=100.6

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEE----cCCCCcccccCCcccCcHHHHHHHH
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY----SSSEGTNLFEDSGEFVSPAQDALFR  119 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~----G~~e~~~~~~~~~~~~~~a~~a~~~  119 (512)
                      +...+.||.+.++.|||++|++|+.|+++|+|+|++.+.     +..|.|+    ++++.             +..|...
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~~   64 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARDI   64 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHHH
Confidence            567899999999999999999999999999999999865     4678886    33322             3444444


Q ss_pred             HHHHHhhhcccCCcc-cCCCcceEEEE-E----ee-----CCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCC
Q 010374          120 VHDRIVAEDSLADDE-FGELTLITVRM-L----VP-----ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALS  188 (512)
Q Consensus       120 i~~~i~~~~~~~~~~-~~~~~~~~~~l-l----VP-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  188 (512)
                      |.+.......+  +. ......+..++ -    .+     ...+|+|||++|++++.|++.|||+|.|..+         
T Consensus        65 I~ai~~gf~~e--~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~---------  133 (180)
T PRK13763         65 VKAIGRGFSPE--KALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK---------  133 (180)
T ss_pred             HHHHhcCCCHH--HHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC---------
Confidence            44332210100  00 00011112221 1    11     1368999999999999999999999999633         


Q ss_pred             CCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          189 FDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       189 ~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                         .|.|.|++++++.|...|..++...
T Consensus       134 ---~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        134 ---TVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             ---EEEEEeCHHHHHHHHHHHHHHHcCC
Confidence               4999999999999999999999654

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.57  E-value=5e-14  Score=130.04  Aligned_cols=65  Identities=23%  Similarity=0.340  Sum_probs=57.6

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe----cCHHHHHHHHHHHHHHHhc
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----GEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~----G~~~~V~~A~~~I~~~l~~  215 (512)
                      +...+.||.+.++.|||++|++|+.|+++|||+|++..+          +..|.|.    ++++++.+|..+|..++..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~----------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g   71 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG   71 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence            367899999999999999999999999999999999755          2468884    8999999999999997764

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=99.39  E-value=2.1e-12  Score=131.86  Aligned_cols=175  Identities=24%  Similarity=0.354  Sum_probs=129.4

Q ss_pred             ccCCCCCcCCCCCCCCCCCCCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEE
Q 010374           12 RTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIV   91 (512)
Q Consensus        12 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv   91 (512)
                      |.||....+++++..+.-.-.--..-....+++..++.+|...+..+|||.|++|+.|++.|++||.+.... -.++++.
T Consensus        36 k~RNdEee~~~~~~~~~~g~~~~~~e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~  114 (608)
T KOG2279|consen   36 KYRNDEEERDSGGQLTFVGIRGQTEEQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVL  114 (608)
T ss_pred             hhccccccccccccceeeeecccceecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccch
Confidence            345555565666655544322111222356889999999999999999999999999999999999998652 2235666


Q ss_pred             EEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010374           92 TIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR  171 (512)
Q Consensus        92 ~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg  171 (512)
                      ++.|-+..          ++++..++   +..+.           .+..+...+-+|...++.|+|++|+++++|+.-++
T Consensus       115 ~~~~~p~~----------v~~a~a~~---~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~  170 (608)
T KOG2279|consen  115 LISGFPVQ----------VCKAKAAI---HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSG  170 (608)
T ss_pred             hhccCCCC----------CChHHHHH---HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccc
Confidence            66554333          55555444   33332           23456778999999999999999999999999999


Q ss_pred             ceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          172 AQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       172 a~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      |+|.+....   .|  ..+++..|.+...-++.|..++.+.+.++
T Consensus       171 aki~~d~ng---r~--g~~~~~~i~~qqk~~~~a~~~~~~~~~ed  210 (608)
T KOG2279|consen  171 AKITCDKNG---RL--GLSRLIKISGQQKEVAAAKHLILEKVSED  210 (608)
T ss_pred             ccccccccc---cc--ccccceecccccchHHHHHhhhhccccch
Confidence            999997662   22  56788899999988999999998888775

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.39  E-value=1.1e-12  Score=100.45  Aligned_cols=63  Identities=40%  Similarity=0.621  Sum_probs=56.9

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV  415 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I  415 (512)
                      .+|+||.+.+|+|||++|++|++|+++|||+|.+.+... +   ..++|.|+|+|+++++..|+.+|
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence            689999999999999999999999999999999976432 2   46789999999999999999987

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.37  E-value=1.4e-12  Score=99.83  Aligned_cols=64  Identities=47%  Similarity=0.783  Sum_probs=58.0

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I  209 (512)
                      +++|+||.+.+|+||||+|.+|++|+++|||+|.+.+... +   ...+|+|+|+|++++|.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence            3689999999999999999999999999999999987632 2   36799999999999999999887

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.24  E-value=1.6e-11  Score=135.77  Aligned_cols=312  Identities=21%  Similarity=0.267  Sum_probs=197.3

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCccc-----------ccC-----
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNL-----------FED-----  105 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~-----------~~~-----  105 (512)
                      .-+..++.+-...+.+|||++|.+++.++.++.+.|+|+....  ......|.+..+.+..           ++.     
T Consensus       199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~  276 (753)
T KOG2208|consen  199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYD  276 (753)
T ss_pred             eeEEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhhh
Confidence            3467889999999999999999999999999999999986522  2223344443332111           000     


Q ss_pred             --------------CcccCcHHHHHHHHHHHHHhhhcccCC--------cc--------------cCCCcceEEEEEeeC
Q 010374          106 --------------SGEFVSPAQDALFRVHDRIVAEDSLAD--------DE--------------FGELTLITVRMLVPA  149 (512)
Q Consensus       106 --------------~~~~~~~a~~a~~~i~~~i~~~~~~~~--------~~--------------~~~~~~~~~~llVP~  149 (512)
                                    ..+.+....+....+.-.. ......+        +.              .-....+.+.+-+-.
T Consensus       277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~-~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~  355 (753)
T KOG2208|consen  277 EIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIF-QNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFP  355 (753)
T ss_pred             hhhhccccccccccccchhhHHHhhcchhhhhh-ccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecH
Confidence                          0001111111100000000 0000000        00              011223677788889


Q ss_pred             CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCC
Q 010374          150 DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSS  229 (512)
Q Consensus       150 ~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~  229 (512)
                      ..+..|+||+|.+|.+|++++.|.|.+...       .+.+..+.++|...++.+|...|...+.+...           
T Consensus       356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-----------  417 (753)
T KOG2208|consen  356 EELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-----------  417 (753)
T ss_pred             HhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc-----------
Confidence            999999999999999999999999999774       25677899999999999999999998887421           


Q ss_pred             CccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcC-CeEEecCCCCCCCCeE
Q 010374          230 NIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSSGAEGDDCI  308 (512)
Q Consensus       230 ~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~v~~~~~~~~~~i  308 (512)
                                                    ......+.+|...+..+||.+|..|+.|..+++ ..|++.......+.- 
T Consensus       418 ------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~-  466 (753)
T KOG2208|consen  418 ------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMV-  466 (753)
T ss_pred             ------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccc-
Confidence                                          023456899999999999999999999999999 777777655432222 


Q ss_pred             EEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCC
Q 010374          309 IFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENV  388 (512)
Q Consensus       309 i~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~  388 (512)
                       ++.+..  .+......-.+.+....    .........+...+.|..+.+..+|+.|..+..    .+...-++..   
T Consensus       467 -~~~~~~--~dv~~~~~~~~~~~~~a----~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~----~~~~~i~~~~---  532 (753)
T KOG2208|consen  467 -TIRGIS--KDVEKSVSLLKALKADA----KNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDS----LGDKSIFPPN---  532 (753)
T ss_pred             -eEeccc--cccchhHHHHHhhhhhh----hcchhhhhhhccccchHHhhcccccCceeeecc----CCceeecccc---
Confidence             222211  00000111111111000    000111235566778888888888887776654    4444444322   


Q ss_pred             CCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          389 PKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       389 p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                         ...++..++|.|..+.|..|.+.+..++...
T Consensus       533 ---~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  533 ---EDEDHEKITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             ---cccccceeeecccccchhhhHHHHHhcchhh
Confidence               1345668999999999999988888776653

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.24  E-value=1.1e-11  Score=94.03  Aligned_cols=61  Identities=20%  Similarity=0.335  Sum_probs=54.6

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT  416 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~  416 (512)
                      .+|.||.+++++|||++|++|++|+++|||+|.+++..       +.++.|+|+|++++|..|+.+|+
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i~   62 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEIL   62 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHhC
Confidence            57899999999999999999999999999999996532       45679999999999999988763

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.21  E-value=8.8e-11  Score=130.01  Aligned_cols=296  Identities=17%  Similarity=0.250  Sum_probs=187.1

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      ....+.+-+-...+..|+||+|.+|.+|++++.|+|.++..  +..+..+++++...++          .+|.+.+..+.
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~  412 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKII  412 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHH
Confidence            33566777788999999999999999999999999999984  5678889999998873          23444444444


Q ss_pred             HHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC-ceEEEeecCCCCcccCCCCceEEEecCHH
Q 010374          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR-AQIRILKDEHLPLCALSFDELLQVAGEPA  200 (512)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~dr~v~I~G~~~  200 (512)
                      ..+..            ..+...+.+|...+.+|||.+|..|..|.++++ ..|++....       +....+++.|...
T Consensus       413 ~ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~  473 (753)
T KOG2208|consen  413 AEILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISK  473 (753)
T ss_pred             Hhhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEecccc
Confidence            43321            134567999999999999999999999999999 666665442       2222355555544


Q ss_pred             HHHHHHHHHHHHHh------------------------------------------------------------------
Q 010374          201 VVRKALVQIASRLH------------------------------------------------------------------  214 (512)
Q Consensus       201 ~V~~A~~~I~~~l~------------------------------------------------------------------  214 (512)
                      .|.++..+...+..                                                                  
T Consensus       474 dv~~~~~~~~~~~~~a~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~~~~~i~i~gk~~~v~~a~  553 (753)
T KOG2208|consen  474 DVEKSVSLLKALKADAKNLKFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDEDHEKITIEGKLELVLEAP  553 (753)
T ss_pred             ccchhHHHHHhhhhhhhcchhhhhhhccccchHHhhcccccCceeeeccCCceeecccccccccceeeecccccchhhhH
Confidence            44444333322222                                                                  


Q ss_pred             --------cCCCccc---------c--ccccCC----CCccCCCCcccCCCCcCCCCC----------CCc---c---cC
Q 010374          215 --------ENPSRSQ---------H--LLLSSS----SNIYQSSGVYLSAPLVGSYGN----------YSA---R---RD  255 (512)
Q Consensus       215 --------~~~~~~~---------~--~~~~~~----~~~~~~gg~~~~~p~~~~~~~----------~~~---~---~~  255 (512)
                              ...+...         +  ++....    ....-.+|+.+.+|-......          +.+   .   -.
T Consensus       554 ~~L~~~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~~~~~e~~i~g~~~~v~aa~~~~~~i~  633 (753)
T KOG2208|consen  554 AELKALIEALIKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSPTSSDEVSIKGAKDEVKAAKGRLEEIV  633 (753)
T ss_pred             HHHHhcchhhhhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCCCCchhhhccchhHHHHHHhhccchhhh
Confidence                    1100000         0  000000    000011222222222111110          000   0   01


Q ss_pred             ccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccc
Q 010374          256 EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCS  335 (512)
Q Consensus       256 ~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~  335 (512)
                      +......+.++.+|...+..+.|.+|..+++++..+++.+.+++.........+.+.+..      +..+++.-+     
T Consensus       634 ~~~~~~~~~~~~i~~~~~~~~~~~~g~~~~~~t~~~~~~~~~~~~~~~~s~~~~~~~~~~------~~~e~~~~~-----  702 (753)
T KOG2208|consen  634 EYLSAYATTNTKIPDKFHRSIVGYRGHIIEEITSKFGVGGYFGDAPTEGSVNTIHVSGEK------MQSEIAKIA-----  702 (753)
T ss_pred             hhcccccceeeecccccceeeecCCCcccccceeecCccceeCCCCCccccCcchhhhhh------hhhhhcccc-----
Confidence            123344456699999999999999999999999999999999987644222112222211      111111000     


Q ss_pred             ccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010374          336 EKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (512)
Q Consensus       336 ~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~  384 (512)
                           ......++..+.+|.+++..+||.+|++++.+..++++.+.++.
T Consensus       703 -----~~~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~  746 (753)
T KOG2208|consen  703 -----LEAKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN  746 (753)
T ss_pred             -----cccccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence                 11224578999999999999999999999999999999998864

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.21  E-value=5.3e-11  Score=89.68  Aligned_cols=58  Identities=26%  Similarity=0.354  Sum_probs=52.5

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQV  415 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I  415 (512)
                      ....|.||.+++|+|||++|++|++|+++|||+|.|..           ++.|.|+|+ +++++.|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            45789999999999999999999999999999999952           357999998 99999998887

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.21  E-value=1.3e-11  Score=92.91  Aligned_cols=60  Identities=33%  Similarity=0.530  Sum_probs=54.0

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV  415 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I  415 (512)
                      |.+|.||.+++|+|||++|++|++|+++|||+|++++.       + +...|+|+|++++|+.|+.+|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-------~-~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-------D-ERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-------T-EEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-------C-CcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999999999999999999643       2 345999999999999999876

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.15  E-value=5.8e-11  Score=90.05  Aligned_cols=60  Identities=28%  Similarity=0.369  Sum_probs=54.9

Q ss_pred             EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010374          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (512)
Q Consensus       143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I  209 (512)
                      .+|.||..++++|||++|++|++|+++|||+|.|++..       +.++.|+|+|+.++|.+|+.+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence            57999999999999999999999999999999998762       4578899999999999999876

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.15  E-value=3e-11  Score=91.03  Aligned_cols=60  Identities=37%  Similarity=0.573  Sum_probs=54.2

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I  209 (512)
                      |.+|.||.+++++|||++|.+|++|+++|||+|.|+++        ..+..|+|+|++++|.+|+++|
T Consensus         1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--------~~~~~v~I~G~~~~v~~A~~~I   60 (60)
T PF00013_consen    1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--------DERDIVTISGSPEQVEKAKKMI   60 (60)
T ss_dssp             EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--------TEEEEEEEEESHHHHHHHHHHH
T ss_pred             CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--------CCcEEEEEEeCHHHHHHHHhhC
Confidence            67899999999999999999999999999999999765        1234899999999999999876

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.14  E-value=1.7e-10  Score=87.91  Aligned_cols=62  Identities=37%  Similarity=0.627  Sum_probs=55.3

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV  415 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I  415 (512)
                      .+|.||.+++++|||++|++|++|+++|||+|.|.....     +..++.|+|.|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999975321     35688999999999999998876

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=99.09  E-value=4.4e-10  Score=84.70  Aligned_cols=58  Identities=34%  Similarity=0.437  Sum_probs=52.3

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHH
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQI  209 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I  209 (512)
                      ....|.||.+++++||||+|++|++|+++|||+|.|.+           ++.|.|+|+ +++|++|+.+|
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I   60 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI   60 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence            35679999999999999999999999999999999864           346999998 99999999876

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=99.06  E-value=5.7e-10  Score=85.03  Aligned_cols=62  Identities=40%  Similarity=0.629  Sum_probs=55.9

Q ss_pred             EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010374          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (512)
Q Consensus       143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I  209 (512)
                      .+|.||.+++++|||++|++|++|+++|+|+|.|.....     ...++.|.|.|+.+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999987632     25688999999999999998876

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PF13014 KH_3: KH domain

Probab=98.96  E-value=1.1e-09  Score=76.42  Aligned_cols=42  Identities=48%  Similarity=0.823  Sum_probs=38.9

Q ss_pred             ceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEc
Q 010374           54 KIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYS   95 (512)
Q Consensus        54 ~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G   95 (512)
                      ++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence            4899999999999999999999999998 56788899999987

>PF13014 KH_3: KH domain

Probab=98.88  E-value=3.5e-09  Score=73.90  Aligned_cols=43  Identities=47%  Similarity=0.734  Sum_probs=37.3

Q ss_pred             ceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc
Q 010374          357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG  403 (512)
Q Consensus       357 ~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G  403 (512)
                      +||+|||++|++|++|+++|||+|+|++ +..|   .++++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~---~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP---GSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC---CCCceEEEEEC
Confidence            5899999999999999999999999976 2233   47889999998

>smart00322 KH K homology RNA-binding domain

Probab=98.85  E-value=1.7e-08  Score=77.34  Aligned_cols=66  Identities=29%  Similarity=0.538  Sum_probs=58.6

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      .+.++.||.++++++||++|++|++|++.||++|.+....       .....|+|.|+++++..|+.+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5788999999999999999999999999999999995321       24678999999999999999998876

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=98.79  E-value=1.5e-07  Score=85.80  Aligned_cols=149  Identities=21%  Similarity=0.236  Sum_probs=102.3

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      ......+.||.+..+.+||+.|++.+.|.+.++++|.++..     +..|.|..+.....       ++ ....|...|.
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~D-------p~-~~~ka~d~Vk   72 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTED-------PL-ALLKARDVVK   72 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCC-------hH-HHHHHHHHHH
Confidence            44567799999999999999999999999999999999755     77899988732110       01 1122221111


Q ss_pred             HHHhhhcccCCccc-CCCcceEEEE-----Eee--C----CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCC
Q 010374          122 DRIVAEDSLADDEF-GELTLITVRM-----LVP--A----DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSF  189 (512)
Q Consensus       122 ~~i~~~~~~~~~~~-~~~~~~~~~l-----lVP--~----~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~  189 (512)
                       .| ...+..+..- -....+.+.+     ++-  .    ...|+|||++|.+-+.|++-|+|.|.|...          
T Consensus        73 -AI-grGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~----------  140 (194)
T COG1094          73 -AI-GRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK----------  140 (194)
T ss_pred             -HH-hcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----------
Confidence             11 1222221110 0000112211     111  2    246999999999999999999999999755          


Q ss_pred             CceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          190 DELLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       190 dr~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                        .|.|.|.+++|+.|...|..++...+
T Consensus       141 --tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         141 --TVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             --EEEEecChhhhHHHHHHHHHHHcCCC
Confidence              69999999999999999999987643

>smart00322 KH K homology RNA-binding domain

Probab=98.77  E-value=4.2e-08  Score=75.12  Aligned_cols=66  Identities=39%  Similarity=0.664  Sum_probs=59.2

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      .+.++.||...++.|||++|.+|++|++.|+++|.+....       .....|.|.|+.+++..|..+|.+.+
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5788999999999999999999999999999999997551       24678999999999999999998865

>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]

Probab=98.56  E-value=5.1e-07  Score=82.30  Aligned_cols=140  Identities=25%  Similarity=0.318  Sum_probs=97.5

Q ss_pred             ceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHH--HHhhCCccccccc
Q 010374          262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITA--ALRLQPRCSEKTE  339 (512)
Q Consensus       262 ~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a--~~~~~~~~~~~~~  339 (512)
                      .+..+.+|.+-.+.+||+.|...+.|.+.++++|.++.     .+..+.|...+...++.....|  .+++..+.   +.
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---F~   79 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG---FP   79 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC---CC
Confidence            35679999999999999999999999999999999998     4556677665444444211111  11111111   11


Q ss_pred             CCC-----CCceeEEEEEe------c----CCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC
Q 010374          340 RES-----GDPVITTRILV------P----SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS  404 (512)
Q Consensus       340 ~~~-----~~~~~t~~l~V------P----~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~  404 (512)
                      ++.     .+...-..+.+      +    ....|+|||++|.+-+-|++.|+|+|.|...            +|.|.|.
T Consensus        80 pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVaiiG~  147 (194)
T COG1094          80 PEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVAIIGG  147 (194)
T ss_pred             HHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEEEecC
Confidence            000     00111111221      1    2356999999999999999999999999632            8999999


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 010374          405 LDVASSALSQVTLRLRA  421 (512)
Q Consensus       405 ~~~v~~A~~~I~~~l~~  421 (512)
                      +++|+.|...|..++..
T Consensus       148 ~~~v~iAr~AVemli~G  164 (194)
T COG1094         148 FEQVEIAREAVEMLING  164 (194)
T ss_pred             hhhhHHHHHHHHHHHcC
Confidence            99999999998888755

>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]

Probab=98.45  E-value=2e-07  Score=95.88  Aligned_cols=231  Identities=27%  Similarity=0.385  Sum_probs=168.0

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      +...++.+++.||...|-+++|+.|.+|+.|+..++++|.+..++ .     ..++...+.|.+.+|.+|...+..++.+
T Consensus        63 e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~  136 (608)
T KOG2279|consen   63 KPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTE  136 (608)
T ss_pred             CchhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhc
Confidence            344677899999999999999999999999999999999998773 2     3456667777999999999999999987


Q ss_pred             CCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeE
Q 010374          216 NPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASI  295 (512)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I  295 (512)
                      ++                                           .+...+.+|...++.|+|++|.+++.++..++++|
T Consensus       137 ~~-------------------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki  173 (608)
T KOG2279|consen  137 NT-------------------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKI  173 (608)
T ss_pred             CC-------------------------------------------cccccccchhhhcccccccchhhhcchhccccccc
Confidence            42                                           34567789999999999999999999999999999


Q ss_pred             EecCCCCCCCCeEEEecCCcccCCCc--------hhHHHHHhh-----CCcc---------cccc---------------
Q 010374          296 KVDSSGAEGDDCIIFISTKEFFEDPS--------PTITAALRL-----QPRC---------SEKT---------------  338 (512)
Q Consensus       296 ~v~~~~~~~~~~ii~i~g~~~~~~~~--------~~~~a~~~~-----~~~~---------~~~~---------------  338 (512)
                      .++........+++.|.+........        ..-+...+.     +.+.         .+.+               
T Consensus       174 ~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t  253 (608)
T KOG2279|consen  174 TCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNT  253 (608)
T ss_pred             ccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccc
Confidence            99998776677777777653211000        000000000     0000         0000               


Q ss_pred             ----cC-------CC-----------------------CCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010374          339 ----ER-------ES-----------------------GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (512)
Q Consensus       339 ----~~-------~~-----------------------~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~  384 (512)
                          .+       +.                       .....--.|.||..++|.+||+.|+.|+.+...|++.+.|..
T Consensus       254 ~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t  333 (608)
T KOG2279|consen  254 SSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT  333 (608)
T ss_pred             hhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEe
Confidence                00       00                       011123478899999999999999999999999999988853


Q ss_pred             CCCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHH
Q 010374          385 NENVPKVAYE-DEEMVQITGSLDVASSALSQVTLR  418 (512)
Q Consensus       385 ~~~~p~~~~~-~~r~V~I~G~~~~v~~A~~~I~~~  418 (512)
                         .|-.... .--++.+.|+..-+..|+.|+..+
T Consensus       334 ---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~  365 (608)
T KOG2279|consen  334 ---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVH  365 (608)
T ss_pred             ---ccccchhhhhhhheecchhHHHHHHHhhhhcc
Confidence               2321000 113678999999999999998833

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.36  E-value=1.5e-06  Score=74.47  Aligned_cols=67  Identities=21%  Similarity=0.328  Sum_probs=51.9

Q ss_pred             CCceeeeecCCchhHHHHHHHhCCeEEEecCCCC-----------CC-CCCCCceEEEEEcC---HHHHHHHHHHHHHHH
Q 010374          355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PK-VAYEDEEMVQITGS---LDVASSALSQVTLRL  419 (512)
Q Consensus       355 ~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~-----------p~-~~~~~~r~V~I~G~---~~~v~~A~~~I~~~l  419 (512)
                      .+++|.|||++|++||+|+++|||+|.|..+...           |. ...++.-.|.|++.   .++++.|+.+|..+|
T Consensus        14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll   93 (120)
T cd02395          14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL   93 (120)
T ss_pred             CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999765211           00 01123357899995   599999999999888


Q ss_pred             hh
Q 010374          420 RA  421 (512)
Q Consensus       420 ~~  421 (512)
                      ..
T Consensus        94 ~~   95 (120)
T cd02395          94 KP   95 (120)
T ss_pred             cc
Confidence            74

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=98.35  E-value=1.6e-06  Score=74.39  Aligned_cols=73  Identities=23%  Similarity=0.396  Sum_probs=55.1

Q ss_pred             EEEee------CCceeEEecCCChhHHHHHhhcCceEEEeecCCC-----------Cccc-CCCCceEEEecCH---HHH
Q 010374          144 RMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL-----------PLCA-LSFDELLQVAGEP---AVV  202 (512)
Q Consensus       144 ~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------p~~~-~~~dr~v~I~G~~---~~V  202 (512)
                      +++||      .+.+|.|||++|.+||+|+++|||+|.|..+...           |... ...+--|.|++..   +++
T Consensus         3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~   82 (120)
T cd02395           3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL   82 (120)
T ss_pred             EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence            45566      4678999999999999999999999999876211           0100 1122458898865   999


Q ss_pred             HHHHHHHHHHHhcC
Q 010374          203 RKALVQIASRLHEN  216 (512)
Q Consensus       203 ~~A~~~I~~~l~~~  216 (512)
                      .+|+.+|..++...
T Consensus        83 ~~A~~~I~~ll~~~   96 (120)
T cd02395          83 AKAVEAIEELLKPA   96 (120)
T ss_pred             HHHHHHHHHHhccC
Confidence            99999999998864

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=98.32  E-value=1.4e-06  Score=83.66  Aligned_cols=136  Identities=22%  Similarity=0.334  Sum_probs=103.3

Q ss_pred             ccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccc-
Q 010374          260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT-  338 (512)
Q Consensus       260 ~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~-  338 (512)
                      ..++..+.+|..+++.|+|++|..||.|+.+|.++|+-+...   .+.++.++|..      +.++.+.+..+...+.+ 
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~------edv~~aRrei~saaeH~~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRH------EDVRRARREIPSAAEHFG   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCc------hhHHHHhhcCccccceee
Confidence            567888999999999999999999999999999999998866   56888888864      23444444333222211 


Q ss_pred             ------------cCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010374          339 ------------ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD  406 (512)
Q Consensus       339 ------------~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~  406 (512)
                                  .........+..+.||...+|.|.|..|.+|+.|++.+...|.-+-++        .+-++.++|.+.
T Consensus        95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~  166 (394)
T KOG2113|consen   95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPK  166 (394)
T ss_pred             eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCc
Confidence                        111123456788999999999999999999999999999998876543        344899999888


Q ss_pred             H-HHHHH
Q 010374          407 V-ASSAL  412 (512)
Q Consensus       407 ~-v~~A~  412 (512)
                      . +++|.
T Consensus       167 nC~kra~  173 (394)
T KOG2113|consen  167 NCVKRAR  173 (394)
T ss_pred             chhhhcc
Confidence            7 55554

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]

Probab=98.26  E-value=1.8e-06  Score=83.00  Aligned_cols=142  Identities=22%  Similarity=0.333  Sum_probs=104.5

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                      ...++..+.||..+++.|.|++|.+||.|+.+|.+.|+-+....+|        ++.++|..+.|+.|.+.|...-+.  
T Consensus        23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eeP--------iF~vTg~~edv~~aRrei~saaeH--   92 (394)
T KOG2113|consen   23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEP--------IFPVTGRHEDVRRARREIPSAAEH--   92 (394)
T ss_pred             CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCC--------cceeccCchhHHHHhhcCccccce--
Confidence            3678899999999999999999999999999999999988775444        688999999999999877552211  


Q ss_pred             CccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEe
Q 010374          218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV  297 (512)
Q Consensus       218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v  297 (512)
                           +-+.-....+. |+.          -+|+      ...+....+.+|...++.+.|..|.+|+.+++.++..|.-
T Consensus        93 -----~~l~~~s~s~S-gg~----------~~~s------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T  150 (394)
T KOG2113|consen   93 -----FGLIRASRSFS-GGT----------NGAS------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIAT  150 (394)
T ss_pred             -----eeeeeeccccc-CCC----------cccc------ccCCCceeeeccceeeeeccccccCccchheecccceEee
Confidence                 11100000000 000          0111      2334456778899999999999999999999999999988


Q ss_pred             cCCCCCCCCeEEEecCC
Q 010374          298 DSSGAEGDDCIIFISTK  314 (512)
Q Consensus       298 ~~~~~~~~~~ii~i~g~  314 (512)
                      +...   .+.++.++|.
T Consensus       151 ~v~~---~~~Vf~Vtg~  164 (394)
T KOG2113|consen  151 PVRC---GEPVFCVTGA  164 (394)
T ss_pred             eccC---CCceEEEecC
Confidence            8766   5567777763

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.15  E-value=3.9e-06  Score=74.11  Aligned_cols=104  Identities=19%  Similarity=0.262  Sum_probs=70.7

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHH
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDR  123 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~  123 (512)
                      -.+.++|+...+|..||++|++|+.|++..|-+|.|-+-.              ++             +.+-+..++..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s--------------~d-------------~~~fI~n~l~P   84 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS--------------DD-------------PEEFIKNIFAP   84 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC--------------CC-------------HHHHHHHHcCC
Confidence            4577888999999999999999999999998888874321              11             12222211111


Q ss_pred             HhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEe
Q 010374          124 IVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL  177 (512)
Q Consensus       124 i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  177 (512)
                      ..-....-   ........+.+.|+....|.+|||+|++|+.++.-++-.+.|.
T Consensus        85 a~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         85 AAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             CEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            11010000   0112234667889999999999999999999999999887663

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.94  E-value=3e-05  Score=84.89  Aligned_cols=97  Identities=25%  Similarity=0.347  Sum_probs=77.2

Q ss_pred             cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCccc
Q 010374          107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA  186 (512)
Q Consensus       107 ~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~  186 (512)
                      .+.+..|.++...|++.+....... .+-.........+.||.+.++.|||++|.+||.|+++|||+|.|..+       
T Consensus       545 ~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~-------  616 (719)
T TIGR02696       545 ASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD-------  616 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC-------
Confidence            4567778888899988776544333 22233445678899999999999999999999999999999999654       


Q ss_pred             CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010374          187 LSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (512)
Q Consensus       187 ~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~  215 (512)
                          ..|.|.+ +.+.+++|+.+|..++..
T Consensus       617 ----G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 ----GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             ----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                4688877 588899999999998874

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.77  E-value=6.2e-05  Score=66.51  Aligned_cols=104  Identities=19%  Similarity=0.305  Sum_probs=71.0

Q ss_pred             ceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCC
Q 010374          262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE  341 (512)
Q Consensus       262 ~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~  341 (512)
                      -.+-+.++...+|..||++|++|+.|++..|-+|.+-.-+.+                +..-+..++.... + ....-.
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d----------------~~~fI~n~l~Pa~-V-~~v~I~   93 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD----------------PEEFIKNIFAPAA-V-RSVTIK   93 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC----------------HHHHHHHHcCCCE-E-EEEEEE
Confidence            356788889999999999999999999999988887653311                1111222211110 0 000000


Q ss_pred             CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEe
Q 010374          342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (512)
Q Consensus       342 ~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~  383 (512)
                      .........+.|+.+..|..|||+|++|+.++..++-++.|.
T Consensus        94 ~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         94 KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            011224566789999999999999999999999999888773

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.62  E-value=9.4e-05  Score=65.14  Aligned_cols=103  Identities=22%  Similarity=0.243  Sum_probs=68.9

Q ss_pred             EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010374           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (512)
Q Consensus        45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i  124 (512)
                      .+-++|....+|..||++|++|+.|++..|-+|.|-+-           +.++++                   .+.+.+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~~-------------------fI~N~l   83 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLEE-------------------FVANKL   83 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHHH-------------------HHHHcC
Confidence            67788899999999999999999999888888887432           111110                   000101


Q ss_pred             hhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEe
Q 010374          125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL  177 (512)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  177 (512)
                      .......-.-........+.+.||.+..+..|||+|++++...+-++-++.|.
T Consensus        84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            10000000000111234677899999999999999999999999998877664

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=97.58  E-value=0.00051  Score=70.50  Aligned_cols=76  Identities=17%  Similarity=0.314  Sum_probs=58.9

Q ss_pred             eeEEEEEec------CCceeeeecCCchhHHHHHHHhCCeEEEecCCC-------------CCCCCCCCceEEEEEc-CH
Q 010374          346 VITTRILVP------SAQIGCLIGRGGAIISEMRSATRASIRILTNEN-------------VPKVAYEDEEMVQITG-SL  405 (512)
Q Consensus       346 ~~t~~l~VP------~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~-------------~p~~~~~~~r~V~I~G-~~  405 (512)
                      .++.+|.||      .++||.|||..|.+.|.|+++|||+|.|-.+..             .++  ..++--+.|+. |.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~--~~epLH~~Isadt~  214 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPK--ENEPLHCLISADTQ  214 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccc--cccceeEEEecchH
Confidence            466778887      468999999999999999999999999976211             111  22334577888 78


Q ss_pred             HHHHHHHHHHHHHHhhch
Q 010374          406 DVASSALSQVTLRLRANT  423 (512)
Q Consensus       406 ~~v~~A~~~I~~~l~~~~  423 (512)
                      |.|++|+++|..+|.+..
T Consensus       215 eki~~Ai~vienli~~av  232 (554)
T KOG0119|consen  215 EKIKKAIAVIENLIQSAV  232 (554)
T ss_pred             HHHHHHHHHHHHHHHhhc
Confidence            899999999999888643

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.56  E-value=0.00015  Score=80.70  Aligned_cols=97  Identities=24%  Similarity=0.299  Sum_probs=71.7

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++...|++.+.........+...-......+.||.+.++.|||++|.+||.|+++|||+|.|..+        
T Consensus       518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd--------  589 (684)
T TIGR03591       518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD--------  589 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------
Confidence            455667777778877665433222222223345577899999999999999999999999999999999654        


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010374          188 SFDELLQVAG-EPAVVRKALVQIASRLHE  215 (512)
Q Consensus       188 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~  215 (512)
                         -.|.|.+ ..+.+.+|..+|..+..+
T Consensus       590 ---G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       590 ---GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             ---eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence               3567665 577889999998887653

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=97.56  E-value=0.00051  Score=70.53  Aligned_cols=79  Identities=16%  Similarity=0.230  Sum_probs=58.6

Q ss_pred             CCcceEEEEEee------CCceeEEecCCChhHHHHHhhcCceEEEeecC---------CCCccc--CCCCceEEEecC-
Q 010374          137 ELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDE---------HLPLCA--LSFDELLQVAGE-  198 (512)
Q Consensus       137 ~~~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~---------~~p~~~--~~~dr~v~I~G~-  198 (512)
                      ....++.+|.||      .++||+|||..|.|.|+|+++|||+|.|-...         +.+...  ...+--|.|+.+ 
T Consensus       134 ~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt  213 (554)
T KOG0119|consen  134 PPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADT  213 (554)
T ss_pred             cccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecch
Confidence            333778889998      46799999999999999999999999997621         001111  122233678776 


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010374          199 PAVVRKALVQIASRLHE  215 (512)
Q Consensus       199 ~~~V~~A~~~I~~~l~~  215 (512)
                      -|.|++|++.|..+|.+
T Consensus       214 ~eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  214 QEKIKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            56689999999999986

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.54  E-value=0.0002  Score=78.61  Aligned_cols=66  Identities=23%  Similarity=0.293  Sum_probs=58.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~  421 (512)
                      ......+.||.+.+|.|||+||.+||+|+++|||+|.|..           +..|.|.+ +.+++++|+.+|...+..
T Consensus       576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            4567889999999999999999999999999999999942           45888888 788999999999988874

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.49  E-value=0.00019  Score=63.21  Aligned_cols=103  Identities=21%  Similarity=0.317  Sum_probs=70.7

Q ss_pred             eEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCC
Q 010374          263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES  342 (512)
Q Consensus       263 ~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  342 (512)
                      .+-+.+....+|..||++|++|+.|++..|-+|.+-.-+.+                +..-+..  .+.|.-...+....
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D----------------~~~fI~N--~l~PA~V~~V~i~~   95 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN----------------LEEFVAN--KLAPAEVKNVTVSE   95 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------HHHHHHH--cCCCceEEEEEEEc
Confidence            56678888999999999999999999888888877653311                1111111  11111111110000


Q ss_pred             CCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEe
Q 010374          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (512)
Q Consensus       343 ~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~  383 (512)
                      .+......+.||.+..+..|||+|++|+...+-++-++.|.
T Consensus        96 ~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        96 FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            11235577889999999999999999999999999888773

This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.31  E-value=0.00027  Score=71.22  Aligned_cols=65  Identities=23%  Similarity=0.414  Sum_probs=55.4

Q ss_pred             CCCCcccCCCCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010374           31 GDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (512)
Q Consensus        31 ~~~~~~~~~~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (512)
                      .++++......++.++.+.|-+.+||.|||++|+.|+.|+..|+++|+|.+.   ..+-.|+|.|..+
T Consensus        34 ~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   34 RDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH   98 (629)
T ss_pred             CCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence            3455566678899999999999999999999999999999999999999764   3467799999644

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.22  E-value=0.00039  Score=77.96  Aligned_cols=98  Identities=16%  Similarity=0.236  Sum_probs=75.7

Q ss_pred             cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCce-EEEeecCCCCcc
Q 010374          107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLC  185 (512)
Q Consensus       107 ~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~  185 (512)
                      .+.+..|.++...|++.+.+.......+..........|.||.+.++.|||.+|.+||.|.++||++ |.+..+      
T Consensus       651 ~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------  724 (891)
T PLN00207        651 ERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------  724 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC------
Confidence            3556778888888888776544333222233445678899999999999999999999999999999 887543      


Q ss_pred             cCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010374          186 ALSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (512)
Q Consensus       186 ~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~  215 (512)
                           -.|.|.+ +.+.+++|+.+|..++.+
T Consensus       725 -----g~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        725 -----GTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             -----eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence                 3577777 688899999999988764

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.04  E-value=0.001  Score=61.62  Aligned_cols=104  Identities=26%  Similarity=0.296  Sum_probs=68.1

Q ss_pred             EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHH
Q 010374           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (512)
Q Consensus        45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i  124 (512)
                      .+-+.+-.+.+|..||++|++|+.|.++.|=+|+|-+-.+           ++++            -+.+|+.      
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~-----------d~~~------------fI~nal~------  127 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE-----------DPAE------------FIKNALA------  127 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC-----------CHHH------------HHHHhcC------
Confidence            3444445577899999999999999999987776643210           0000            0112211      


Q ss_pred             hhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                       ......-.....+.. .+.+.||.++.+.+|||+|.+++.+.+-||-++.|...
T Consensus       128 -Pa~v~~V~~~~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         128 -PAEVLSVNIKEDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             -cceEeEEEEEeCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence             100000000011111 77889999999999999999999999999999999754

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.03  E-value=0.0009  Score=74.49  Aligned_cols=66  Identities=24%  Similarity=0.302  Sum_probs=55.8

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~  421 (512)
                      .....++.||.+.++.|||++|++||+|+++|||+|.|..           +..|.|.+ ..+.+++|..+|......
T Consensus       549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            4567889999999999999999999999999999999952           34677776 678899998888877654

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.97  E-value=0.0014  Score=70.67  Aligned_cols=97  Identities=24%  Similarity=0.270  Sum_probs=73.0

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|..|...|+..+.+.......+...-..-...+.|+.+.+.-+||++|.+|++|.++|||+|.+..+        
T Consensus       519 ~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd--------  590 (692)
T COG1185         519 KALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD--------  590 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC--------
Confidence            456667788888877765433222222222234467789999999999999999999999999999999733        


Q ss_pred             CCCceEEEecCH-HHHHHHHHHHHHHHhc
Q 010374          188 SFDELLQVAGEP-AVVRKALVQIASRLHE  215 (512)
Q Consensus       188 ~~dr~v~I~G~~-~~V~~A~~~I~~~l~~  215 (512)
                         -.|.|.+.. +.+.+|+..|..+..+
T Consensus       591 ---Gtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         591 ---GTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             ---CcEEEEecchHHHHHHHHHHHHHHhh
Confidence               358888875 7789999999998866

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=96.78  E-value=0.0016  Score=65.81  Aligned_cols=72  Identities=22%  Similarity=0.365  Sum_probs=59.5

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .....+.+.+.|-+++||.|||++|++|+.|+..|+++|++.+.        ..+-.|+|-|...--.+|...|...+..
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            34456788899999999999999999999999999999999876        3455799999888777887766655544

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.77  E-value=0.003  Score=58.57  Aligned_cols=102  Identities=25%  Similarity=0.327  Sum_probs=68.0

Q ss_pred             EEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCC
Q 010374          264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESG  343 (512)
Q Consensus       264 ~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  343 (512)
                      +...+-.+.+|..||++|.+|+.|.++-|-+|.+-.-+.+                  +.....-.+.+.-...+.-...
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d------------------~~~fI~nal~Pa~v~~V~~~~~  139 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED------------------PAEFIKNALAPAEVLSVNIKED  139 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC------------------HHHHHHHhcCcceEeEEEEEeC
Confidence            3445556778999999999999999999977766543211                  1111111111111111100000


Q ss_pred             CceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010374          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (512)
Q Consensus       344 ~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~  384 (512)
                      +.. ...+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus       140 d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         140 DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            111 6788899999999999999999999999999999964

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=96.75  E-value=0.0015  Score=62.59  Aligned_cols=41  Identities=29%  Similarity=0.476  Sum_probs=35.8

Q ss_pred             CCCCeEEEEEecCC------ceeeeccCCchHHHHHHHhhCCeEEec
Q 010374           40 GSEDTVYRYLCPLR------KIGSIIGKGGEIVKQLRSETKSNIRIS   80 (512)
Q Consensus        40 ~~~~~~~rilvp~~------~~g~IIGk~G~~I~~I~~~tga~I~i~   80 (512)
                      +.-.++.+|+||.+      +||.|+|.+|.++|+|+++|+|+|-|-
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            34556679999986      799999999999999999999998774

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.72  E-value=0.0013  Score=64.61  Aligned_cols=69  Identities=29%  Similarity=0.328  Sum_probs=55.1

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~  122 (512)
                      +....+++++...+.|||++|.|.++|++||+++|.++.+  +.....|+|.|-..++            +..|+.+|..
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~------------V~~a~~Ri~~  121 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNC------------VIQALERIAK  121 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHH------------HHHHHHHHHH
Confidence            4567799999999999999999999999999999999976  4445567777765543            6677777766


Q ss_pred             HHh
Q 010374          123 RIV  125 (512)
Q Consensus       123 ~i~  125 (512)
                      .|.
T Consensus       122 ~id  124 (345)
T KOG2814|consen  122 LID  124 (345)
T ss_pred             HHH
Confidence            553

>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]

Probab=96.71  E-value=0.0015  Score=62.56  Aligned_cols=44  Identities=27%  Similarity=0.516  Sum_probs=38.8

Q ss_pred             CCCcceEEEEEeeC------CceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          136 GELTLITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       136 ~~~~~~~~~llVP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      .....++.+|+||-      +.||+|+|.+|.++|+|+++|+|+|.|-..
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            45567788999994      489999999999999999999999999765

>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]

Probab=96.67  E-value=0.0018  Score=63.69  Aligned_cols=71  Identities=24%  Similarity=0.342  Sum_probs=59.0

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ....-++|++...+.|||++|.+-++|+++|+++|.++....      ..+.++.+.+..++|.+|...|..+|.+.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            456679999999999999999999999999999999987621      33444555567888999999999988775

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.63  E-value=0.0019  Score=72.19  Aligned_cols=97  Identities=25%  Similarity=0.330  Sum_probs=71.2

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++..+|++.+.........+-.........+.||.+.++.+||++|.+|+.|.++||++|.+..+        
T Consensus       521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~--------  592 (693)
T PRK11824        521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD--------  592 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC--------
Confidence            456678888888888776543222222122233455677799999999999999999999999998887433        


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010374          188 SFDELLQVAG-EPAVVRKALVQIASRLHE  215 (512)
Q Consensus       188 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~  215 (512)
                         -.|.|.+ ..+.+.+|..+|..+..+
T Consensus       593 ---G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        593 ---GTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             ---ceEEEEcccHHHHHHHHHHHHHhccc
Confidence               3578877 578889999999887753

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=96.55  E-value=0.0037  Score=46.93  Aligned_cols=37  Identities=30%  Similarity=0.433  Sum_probs=34.5

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI   79 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i   79 (512)
                      ...+.+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            4688999999999999999999999999999988876

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.38  E-value=0.0039  Score=70.23  Aligned_cols=67  Identities=18%  Similarity=0.252  Sum_probs=57.5

Q ss_pred             CceeEEEEEecCCceeeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010374          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (512)
Q Consensus       344 ~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~-I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~  421 (512)
                      .......+.||.+.++.|||.||.+||+|.++||+. |.+.           ++-.|.|.+ +.+.+++|+.+|...+.+
T Consensus       682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            345678899999999999999999999999999999 8873           245788888 788999999998888764

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.29  E-value=0.0053  Score=66.29  Aligned_cols=69  Identities=25%  Similarity=0.286  Sum_probs=58.4

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhhch
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL-DVASSALSQVTLRLRANT  423 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~~~~  423 (512)
                      ..-..++.|+.+.++.|||++|.+|++|.++|||+|.|.           ++-.|.|.++. +.+..|+..|...+++..
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            345678899999999999999999999999999999995           23378888855 789999999999987743


Q ss_pred             h
Q 010374          424 F  424 (512)
Q Consensus       424 ~  424 (512)
                      .
T Consensus       619 v  619 (692)
T COG1185         619 V  619 (692)
T ss_pred             c
Confidence            3

>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH)

Probab=96.21  E-value=0.0076  Score=45.21  Aligned_cols=36  Identities=39%  Similarity=0.596  Sum_probs=33.6

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEE
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI  176 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i  176 (512)
                      ..+.+.||.+.+|.+|||+|.+|+.+++.++-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            578899999999999999999999999999988876

NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.14  E-value=0.02  Score=58.38  Aligned_cols=96  Identities=20%  Similarity=0.116  Sum_probs=64.0

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|++|+.|.++. |=+|+|-.-.++..   .+                    +.+|       +.......
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~---~f--------------------I~Na-------l~Pa~V~~  300 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPE---IF--------------------IARA-------LAPAIISS  300 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHh-------CCCceeeE
Confidence            458999999999999999998 77777743211000   00                    0111       10000000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (512)
                      -.  -....-.+.+.||..+.+..|||+|++++-..+-||.+|.|..-+
T Consensus       301 V~--i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~  347 (374)
T PRK12328        301 VK--IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG  347 (374)
T ss_pred             EE--EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence            00  001123678999999999999999999999999999999998754

>TIGR01953 NusA transcription termination factor NusA

Probab=96.14  E-value=0.012  Score=59.99  Aligned_cols=95  Identities=24%  Similarity=0.359  Sum_probs=64.4

Q ss_pred             CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccccccc-CCCCCceeE
Q 010374          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT  348 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t  348 (512)
                      +-+|..||.+|++|+.|.++- |-+|.+-.-+.+                  +...-.-.+.|.-...+. .+.  ....
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~Pa~v~~v~i~~~--~~~~  302 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD------------------PAEFIANALSPAKVISVEVLDE--DKHS  302 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhcCCceEEEEEEEcC--CCcE
Confidence            357999999999999999888 677766543321                  111111111111111110 011  1246


Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      ..+.||.+..+..|||+|.+++-..+.||.+|.|.+.
T Consensus       303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            7899999999999999999999999999999999653

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>TIGR01953 NusA transcription termination factor NusA

Probab=96.10  E-value=0.016  Score=58.92  Aligned_cols=96  Identities=22%  Similarity=0.304  Sum_probs=63.6

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|++|+.|.++. |=+|+|-.-..+..   .+                    +.+||       .......
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~---~f--------------------i~nal-------~Pa~v~~  292 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA---EF--------------------IANAL-------SPAKVIS  292 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHhc-------CCceEEE
Confidence            458999999999999999998 77777743210000   00                    01111       0000000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      -. -.....-.+.+.||.++.+..|||+|++++-...-||.+|.|...
T Consensus       293 v~-i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       293 VE-VLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EE-EEcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            00 000011378899999999999999999999999999999999764

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.10  E-value=0.014  Score=59.49  Aligned_cols=97  Identities=23%  Similarity=0.221  Sum_probs=65.5

Q ss_pred             CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEE
Q 010374          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~  349 (512)
                      +-+|..||.+|.+|+.|.++- |-+|.+-.-+.+                  +....+-.+.|.-...+...  ......
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D------------------~~~fI~Nal~Pa~V~~V~i~--~~~~~~  310 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV------------------PEIFIARALAPAIISSVKIE--EEEKKA  310 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCceeeEEEEc--CCCcEE
Confidence            457999999999999999888 677766543311                  11111111111111111111  122467


Q ss_pred             EEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCC
Q 010374          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN  387 (512)
Q Consensus       350 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~  387 (512)
                      .+.||.+..+..|||+|.+++-..+.||.+|.|.+-+.
T Consensus       311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            88999999999999999999999999999999987543

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=96.00  E-value=0.017  Score=53.09  Aligned_cols=44  Identities=20%  Similarity=0.399  Sum_probs=38.0

Q ss_pred             CCCcceEEEEEee------CCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          136 GELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       136 ~~~~~~~~~llVP------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      .....++-++.||      .+.||.|||..|.++++|+..|+|+|-|-..
T Consensus       143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            4455667788888      5689999999999999999999999999765

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.96  E-value=0.0092  Score=61.09  Aligned_cols=96  Identities=22%  Similarity=0.260  Sum_probs=63.9

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|+.|+.|.++. |=+|+|-.-..+.                           .+   .|...+.......
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~---------------------------~~---fi~nal~Pa~v~~  294 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP---------------------------AE---FVANALSPAKVVS  294 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH---------------------------HH---HHHHhCCCceEEE
Confidence            458999999999999999998 7788774321100                           00   0001010000000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      -. -.....-.+.+.||..+.+..|||+|++++--..-||.+|.|...
T Consensus       295 v~-i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        295 VE-VDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EE-EEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            00 000112368899999999999999999999999999999999876

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.92  E-value=0.016  Score=56.02  Aligned_cols=64  Identities=17%  Similarity=0.264  Sum_probs=52.2

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhhc
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRAN  422 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~~~  422 (512)
                      -..+.||.++++.+||++|.+|+.|.+.|++.|.|-           .+-.|.|.++ .+++..|+.+|...-++.
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            367889999999999999999999999999999993           2347888885 557888877777655543

>PRK00468 hypothetical protein; Provisional

Probab=95.82  E-value=0.0089  Score=46.71  Aligned_cols=34  Identities=26%  Similarity=0.546  Sum_probs=30.0

Q ss_pred             CCCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010374           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (512)
Q Consensus        40 ~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t   73 (512)
                      .++.+.+++.|..+.+|.||||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3456889999999999999999999999998754

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.68  E-value=0.021  Score=59.17  Aligned_cols=96  Identities=22%  Similarity=0.236  Sum_probs=62.8

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|+.|+.|.++. |=+|.|-.-.++..   .+                    +.+|       +.......
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~---~f--------------------I~Na-------LsPA~V~~  326 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA---TY--------------------IANA-------LSPARVDE  326 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HH--------------------HHHh-------cCCceeeE
Confidence            458999999999999999998 77777743211000   00                    0011       00000000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      -.- .....-.+.+.||.++.+..|||+|++++--..-||.+|.|...
T Consensus       327 V~i-~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~  373 (449)
T PRK12329        327 VRL-VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS  373 (449)
T ss_pred             EEE-EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence            000 00111357899999999999999999999999999999998654

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.62  E-value=0.022  Score=58.37  Aligned_cols=96  Identities=23%  Similarity=0.297  Sum_probs=64.6

Q ss_pred             CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEE
Q 010374          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~  349 (512)
                      +-+|..||.+|.+|+.|.++. |-+|.+-.-+.+                  +...-.-.+.|.-...+... .......
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d------------------~~~fi~nal~Pa~v~~v~i~-~~~~~~~  305 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED------------------PAEFVANALSPAKVVSVEVD-DEEEKAA  305 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCceEEEEEEE-cCCCcEE
Confidence            357999999999999998888 677776543321                  11111111111111111000 0122467


Q ss_pred             EEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       350 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      .+.||.+..+..|||+|.+++-..+.||.+|.|.+.
T Consensus       306 ~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        306 RVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             EEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            899999999999999999999999999999999754

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.54  E-value=0.032  Score=60.14  Aligned_cols=66  Identities=20%  Similarity=0.248  Sum_probs=50.2

Q ss_pred             ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010374          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR  420 (512)
Q Consensus       345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~  420 (512)
                      ...+..|.+|+ ++-|.||||.|.||+-+...||++|.|.   +       +...|+|++ +|---+.|..-|..++.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence            34667788997 6779999999999999999999999994   2       334888999 67555556555444443

>PRK00106 hypothetical protein; Provisional

Probab=95.53  E-value=0.033  Score=59.91  Aligned_cols=66  Identities=23%  Similarity=0.272  Sum_probs=50.7

Q ss_pred             ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010374          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR  420 (512)
Q Consensus       345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~  420 (512)
                      ...+..+.+|+ ++-|.||||-|.+|+-+...||++|.|.          ++...|+|++ +|---+.|..-+..++.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence            44667788997 6779999999999999999999999994          2334888999 77666666555544443

>PRK02821 hypothetical protein; Provisional

Probab=95.49  E-value=0.013  Score=45.92  Aligned_cols=35  Identities=20%  Similarity=0.400  Sum_probs=30.7

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCC
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS   75 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga   75 (512)
                      ++.+.++|.|..+.+|.||||+|.+|+.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            45578999999999999999999999999987543

>PRK12704 phosphodiesterase; Provisional

Probab=95.42  E-value=0.038  Score=59.71  Aligned_cols=65  Identities=20%  Similarity=0.231  Sum_probs=48.8

Q ss_pred             ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 010374          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRL  419 (512)
Q Consensus       345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l  419 (512)
                      ...+..+.+|+ ++-|.||||.|.||+-+...||++|.|.   +       +...|.|+| +|-.-+.|..-+...+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~  274 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLV  274 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHH
Confidence            34566788897 6779999999999999999999999994   2       334888999 6655445544444333

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.41  E-value=0.25  Score=46.90  Aligned_cols=132  Identities=14%  Similarity=0.132  Sum_probs=88.0

Q ss_pred             EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHh
Q 010374           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV  125 (512)
Q Consensus        46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~  125 (512)
                      +.+.++....-++...+|..++.|-...||+|.+...     +..|.|+|+...++.          +...+..++..+.
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~----------i~~~i~~~l~~i~   92 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEY----------IEASINEILSNIR   92 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHH----------HHHHHHHHHhhcE
Confidence            3445558888999999999999998888999999766     678999998665322          3344444444433


Q ss_pred             hhcccCCcccCCCcceEEEEEeeCCceeEEe----cCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----
Q 010374          126 AEDSLADDEFGELTLITVRMLVPADQIGCVI----GKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA-----  196 (512)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~llVP~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~-----  196 (512)
                                      +..|-++.-.--.-.    -.....++.|++.|++-|...+++          ..+.|+     
T Consensus        93 ----------------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~  146 (210)
T PF14611_consen   93 ----------------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASP  146 (210)
T ss_pred             ----------------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeec
Confidence                            333444422111111    124678999999999999987652          234444     


Q ss_pred             cCHHHHHHHHHHHHHHHhcCCC
Q 010374          197 GEPAVVRKALVQIASRLHENPS  218 (512)
Q Consensus       197 G~~~~V~~A~~~I~~~l~~~~~  218 (512)
                      -....+..|..++...+..++.
T Consensus       147 ~~~~~~~~a~RlL~~a~~~~~~  168 (210)
T PF14611_consen  147 ENEKRADRAKRLLLWALDYNPH  168 (210)
T ss_pred             cccchHHHHHHHHHHhccCCcc
Confidence            3567788898888887754433

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.36  E-value=0.039  Score=58.60  Aligned_cols=95  Identities=20%  Similarity=0.235  Sum_probs=63.4

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|++|+.|.++. |=+|.|-.-.++   ...+                    +.+|       +.......
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~~~f--------------------i~na-------l~pa~v~~  294 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDD---PAQF--------------------IINA-------LSPAEVSS  294 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---HHHH--------------------HHHh-------CCCCEEEE
Confidence            358999999999999999998 777777432110   0000                    0111       11000000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      ---+.  ..-.+.+.||..+.+..|||+|++++...+-||.+|.|...
T Consensus       295 v~~~~--~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        295 VVVDE--DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEeC--CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            00000  11278899999999999999999999999999999999875

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.35  E-value=0.024  Score=58.73  Aligned_cols=94  Identities=24%  Similarity=0.327  Sum_probs=63.3

Q ss_pred             CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccccccc-CCCCCceeE
Q 010374          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT  348 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t  348 (512)
                      +-+|..||.+|.+|+.|.++- |-+|.|-.-+.+                  +...-.-.+.+.-...+. .+  .....
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D------------------p~~fI~NaLsPA~V~~V~i~~--~~~k~  336 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD------------------PATYIANALSPARVDEVRLVD--PEGRH  336 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhcCCceeeEEEEEc--CCCcE
Confidence            457999999999999999888 666666543311                  111111111111111110 01  11235


Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEec
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~  384 (512)
                      ..+.||.++.+..|||+|.+|+-..+.||.+|.|..
T Consensus       337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            689999999999999999999999999999999954

>PRK02821 hypothetical protein; Provisional

Probab=95.18  E-value=0.041  Score=43.20  Aligned_cols=35  Identities=31%  Similarity=0.462  Sum_probs=29.6

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR  171 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg  171 (512)
                      ......++|.|..+-+|.||||+|.+|+.||.--.
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            34457889999999999999999999999996533

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=95.09  E-value=0.068  Score=56.29  Aligned_cols=114  Identities=17%  Similarity=0.211  Sum_probs=80.1

Q ss_pred             EEEEcCCCCcccccCC----cccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHH
Q 010374           91 VTIYSSSEGTNLFEDS----GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNI  166 (512)
Q Consensus        91 v~I~G~~e~~~~~~~~----~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I  166 (512)
                      ..|.|+.+.+-++.-+    .+.+.+|.+|...|++.+..........+.....+...|.|+.+....+||.+|...|+|
T Consensus       543 FKiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki  622 (760)
T KOG1067|consen  543 FKIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKI  622 (760)
T ss_pred             eeeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeE
Confidence            3455555555443221    255667778888888877654433333345556778889999999999999999999999


Q ss_pred             HhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010374          167 RTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       167 ~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~~  216 (512)
                      +.|||+.-.+.            +..+.|-- ++.+.++|...|..++..+
T Consensus       623 ~~EtGai~~vD------------e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  623 EVETGAISQVD------------EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             eeeccceeeec------------CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence            99999655443            22455544 5677899999999988764

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.05  E-value=0.037  Score=58.74  Aligned_cols=94  Identities=22%  Similarity=0.319  Sum_probs=63.9

Q ss_pred             CCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEE
Q 010374          272 NIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTR  350 (512)
Q Consensus       272 ~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~  350 (512)
                      -+|..||.+|++|+.|..+- |-+|.|-.-+.+                  +...-.-.+.+.-...+..+.  ..-...
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~pa~v~~v~~~~--~~~~~~  305 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD------------------PAQFIINALSPAEVSSVVVDE--DEHSAD  305 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCCEEEEEEEeC--CCCEEE
Confidence            47999999999999999888 677766543311                  111111111111111110011  123778


Q ss_pred             EEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      +.||.+..+..|||+|.+|+-..+.||.+|.|...
T Consensus       306 v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        306 VVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            99999999999999999999999999999999764

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=95.05  E-value=0.022  Score=44.35  Aligned_cols=33  Identities=18%  Similarity=0.391  Sum_probs=29.9

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t   73 (512)
                      +..+.+++.+..+.+|.||||+|.+|+.||.--
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            567789999999999999999999999998754

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.04  E-value=0.47  Score=44.97  Aligned_cols=87  Identities=11%  Similarity=0.210  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEE
Q 010374          115 DALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ  194 (512)
Q Consensus       115 ~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~  194 (512)
                      ..+.+|+..+..-...+..+    ..-.+.+.++....-.|...+|..++.|-...||+|.+..+          +..|.
T Consensus         4 ~l~~~Il~d~W~l~v~e~v~----~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~   69 (210)
T PF14611_consen    4 KLAERILRDCWNLEVSEEVD----ELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIR   69 (210)
T ss_pred             HHHHHHHHHhcCCcccceee----ccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEE
Confidence            34556666666544332211    11134455568888999999999999999999999999765          45799


Q ss_pred             EecCHHHHHHHHHHHHHHHhc
Q 010374          195 VAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       195 I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      |+|+...++.+...|.+++..
T Consensus        70 I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   70 ITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             EEccHHHHHHHHHHHHHHHhh
Confidence            999999999999999998876

>PRK00468 hypothetical protein; Provisional

Probab=94.89  E-value=0.028  Score=43.89  Aligned_cols=34  Identities=29%  Similarity=0.490  Sum_probs=29.6

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  169 (512)
                      .....+.++|.+..+-+|.||||+|.+|+.||.-
T Consensus        25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             eCCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            3445578999999999999999999999999964

>PRK01064 hypothetical protein; Provisional

Probab=94.82  E-value=0.032  Score=43.93  Aligned_cols=33  Identities=30%  Similarity=0.548  Sum_probs=29.8

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhh
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~t   73 (512)
                      ...+.+++.|.....|.+|||+|.+|+.||.-.
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~   59 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL   59 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence            466889999999999999999999999998754

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.77  E-value=0.047  Score=52.80  Aligned_cols=62  Identities=21%  Similarity=0.241  Sum_probs=51.0

Q ss_pred             EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHH-HHHHHHHHHHHHHhc
Q 010374          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA-VVRKALVQIASRLHE  215 (512)
Q Consensus       143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~-~V~~A~~~I~~~l~~  215 (512)
                      +.+.||.+.++.|||++|.+|+.|.++|+++|.+-.+           -.|.|.+... ++.+|..+|..+-++
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N-----------G~VwI~~~~~~~~~~a~~~I~~~e~~  209 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN-----------GRIWIKGPDEEDEEIAIEAIKKIERE  209 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC-----------cEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence            4588999999999999999999999999999998543           3688888755 788888888765544

>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]

Probab=94.72  E-value=0.063  Score=49.36  Aligned_cols=40  Identities=30%  Similarity=0.528  Sum_probs=34.3

Q ss_pred             eeEEEEEec------CCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          346 VITTRILVP------SAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       346 ~~t~~l~VP------~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      .++..+.||      .++||.|||..|.++++|++.|+|+|-|-.+
T Consensus       147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            455667776      5789999999999999999999999999654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.63  E-value=0.026  Score=63.12  Aligned_cols=65  Identities=28%  Similarity=0.341  Sum_probs=54.6

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhh
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~  421 (512)
                      .....+.||.+.++.+||.||.+||+|.++||+.|.+.           ++-.|.|.+ ..+.+++|+.+|......
T Consensus       553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            44567888999999999999999999999999988772           234788888 788999999998887754

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.61  E-value=0.075  Score=57.33  Aligned_cols=52  Identities=27%  Similarity=0.314  Sum_probs=43.9

Q ss_pred             CCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010374           39 IGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS   95 (512)
Q Consensus        39 ~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G   95 (512)
                      ...+.++-.+-+|+ ++-|.||||.|.||+.++.-||+.|-|+++     ..+|+|+|
T Consensus       199 ~~~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~  251 (514)
T TIGR03319       199 HVAETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSG  251 (514)
T ss_pred             hhhhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC-----CCeEEecC
Confidence            34567777888998 678999999999999999999999999876     34577877

>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]

Probab=94.59  E-value=0.041  Score=42.90  Aligned_cols=34  Identities=38%  Similarity=0.561  Sum_probs=30.2

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  169 (512)
                      ..+..++++|.+...-+|.||||+|.+|+.||.-
T Consensus        25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            3466788999999999999999999999999954

>PRK00106 hypothetical protein; Provisional

Probab=94.56  E-value=0.082  Score=56.89  Aligned_cols=52  Identities=27%  Similarity=0.373  Sum_probs=44.1

Q ss_pred             CCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010374           39 IGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS   95 (512)
Q Consensus        39 ~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G   95 (512)
                      ...+.++-.+.+|+ ++-|.||||-|.||+.++.-||+.|-|+++     ...|+|+|
T Consensus       220 ~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~v~lS~  272 (535)
T PRK00106        220 YVTEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT-----PEVVVLSG  272 (535)
T ss_pred             hhhhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC-----CCeEEEeC
Confidence            34567778888998 688999999999999999999999999876     34577877

>PRK01064 hypothetical protein; Provisional

Probab=94.08  E-value=0.07  Score=41.99  Aligned_cols=34  Identities=35%  Similarity=0.477  Sum_probs=29.8

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhh
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~  169 (512)
                      .....+.+++.|...-.|.+|||+|.+|+.||.-
T Consensus        25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             eCCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            3456688999999999999999999999999964

>PRK12704 phosphodiesterase; Provisional

Probab=93.98  E-value=0.2  Score=54.23  Aligned_cols=64  Identities=22%  Similarity=0.348  Sum_probs=47.3

Q ss_pred             EEEEEeeC-CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010374          142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (512)
Q Consensus       142 ~~~llVP~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I~~~l~~  215 (512)
                      .-.+.+|+ ++.|+|||+.|.+|+.++.-||+.|.|.+.   |       ..|.|+|. +-.-+.|...+..++.+
T Consensus       211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC---C-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            33466776 689999999999999999999999999543   3       36889983 44434566566555544

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=92.77  E-value=0.061  Score=41.85  Aligned_cols=35  Identities=17%  Similarity=0.230  Sum_probs=30.3

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCC
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS   75 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga   75 (512)
                      .+...+.+.|..+..|.||||.|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            46678889999999999999999999999876543

>PRK12705 hypothetical protein; Provisional

Probab=92.06  E-value=0.17  Score=54.15  Aligned_cols=39  Identities=28%  Similarity=0.379  Sum_probs=33.8

Q ss_pred             ceeEEEEEecC-CceeeeecCCchhHHHHHHHhCCeEEEe
Q 010374          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRIL  383 (512)
Q Consensus       345 ~~~t~~l~VP~-~~vG~IIGkgG~~IkeI~~~TGa~I~i~  383 (512)
                      ......+.+|. ++-|.||||-|.+|+-+...||+.|.|.
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid  235 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID  235 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence            34566788886 5669999999999999999999999995

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=92.02  E-value=0.34  Score=44.44  Aligned_cols=56  Identities=25%  Similarity=0.354  Sum_probs=50.2

Q ss_pred             CCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      +..+|+|+||+|.+=-.|++-|.++|.+...            .|.|-|..+++.-|...|+.++.-.
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~------------kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS------------KIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecCc------------eEEEeecchhhHHHHHhhHhhhccC
Confidence            4568999999999999999999999998643            5999999999999999999999764

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=91.32  E-value=0.78  Score=51.40  Aligned_cols=28  Identities=11%  Similarity=0.222  Sum_probs=14.9

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHH
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSA  375 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~  375 (512)
                      ...|.|..+.+.||+|-.-+.=.-+.+.
T Consensus      1085 WIklqIshEaAAcItgLr~AmEaLvvev 1112 (1282)
T KOG0921|consen 1085 WIKLQISHEAAACITGLRPAMEALVVEV 1112 (1282)
T ss_pred             eeeEeccHHHHHHHhhhHHHHHHHHHHH
Confidence            3455566666666666555443333333

>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH)

Probab=90.85  E-value=1.5  Score=38.63  Aligned_cols=93  Identities=24%  Similarity=0.373  Sum_probs=60.5

Q ss_pred             CCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccCCCcc
Q 010374           61 KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTL  140 (512)
Q Consensus        61 k~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~  140 (512)
                      ..+..|++|-++..-+|.|-.+              +..          +.+-.+|...|.+.+-++. .-.+-..  +.
T Consensus        23 ~~~dli~~lAk~lrKRIvvR~d--------------ps~----------l~~~e~A~~~I~~ivP~ea-~i~di~F--d~   75 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIRPD--------------PSV----------LKPPEEAIKIILEIVPEEA-GITDIYF--DD   75 (145)
T ss_pred             cccHHHHHHHHHHhceEEEcCC--------------hhh----------cCCHHHHHHHHHHhCCCcc-CceeeEe--cC
Confidence            4678899999998777777432              111          1123456666665443221 1000000  11


Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (512)
                      .+-++.|-...-|.+|||+|.++++|..+||-+-.|....
T Consensus        76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp  115 (145)
T cd02410          76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP  115 (145)
T ss_pred             CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence            1456778888889999999999999999999999998763

The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=90.59  E-value=0.64  Score=48.70  Aligned_cols=204  Identities=14%  Similarity=0.142  Sum_probs=125.4

Q ss_pred             eeccCCchHHHHHHHhhCCeEEe--cCCCCCCCccEEEE-EcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCc
Q 010374           57 SIIGKGGEIVKQLRSETKSNIRI--SETVPGCDERIVTI-YSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADD  133 (512)
Q Consensus        57 ~IIGk~G~~I~~I~~~tga~I~i--~~~~~~~~ervv~I-~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~  133 (512)
                      +|=||+--.+.+|++...|.+.+  .+.. |  .++.++ .|..-.          +   ++++    ..+         
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~-g--s~~~~~~~g~~~~----------F---~k~~----~~~---------  443 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSST-G--SIVETNGIGEKMS----------F---SKKL----SIP---------  443 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecC-C--cEEEEeccCcchh----------h---HHHh----cCC---------
Confidence            67787766699999999888544  3321 1  233333 221100          1   1221    111         


Q ss_pred             ccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          134 EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       134 ~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                        ..+..-++.+.||...|..|||.||..|++++...++.|++...-.+|.                +          ..
T Consensus       444 --~~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q----------------s----------~~  495 (657)
T COG5166         444 --PTEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ----------------S----------QW  495 (657)
T ss_pred             --cccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch----------------h----------hh
Confidence              1112235679999999999999999999999999999888865433332                0          12


Q ss_pred             hcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhc--
Q 010374          214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQES--  291 (512)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~t--  291 (512)
                      ++                                               .+-+.+|.+..+.|+|++......+++..  
T Consensus       496 ~d-----------------------------------------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f  528 (657)
T COG5166         496 HD-----------------------------------------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRF  528 (657)
T ss_pred             hc-----------------------------------------------ceEEECCccCccchhcccccHHHHHhhhccc
Confidence            22                                               14567899999999999888777777554  


Q ss_pred             --CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeec---CCc
Q 010374          292 --GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIG---RGG  366 (512)
Q Consensus       292 --ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIG---kgG  366 (512)
                        ...|.|.+.    ..+++++-+-.      ..++.+.+- ..+       .........+.+|.+.++.-+|   -.|
T Consensus       529 ~~Kgdirf~~~----~~sI~~v~~~~------~~I~rv~kn-e~v-------~~~~p~~~~~y~~se~h~~g~gena~R~  590 (657)
T COG5166         529 NLKGDIRFCPQ----STSIFTVDIYS------DEIERVIKN-ETV-------LLEFPAEMHFYVPSEIHKKGIGENAFRG  590 (657)
T ss_pred             ccccceEEcCC----ceEEEEEcccc------cHHHHHhhc-cce-------EEecccccccccchhhhhccCCcccccc
Confidence              344555543    33466665532      234433331 111       0112355678899999999999   677


Q ss_pred             hhHHHHHHHhCCeEEE
Q 010374          367 AIISEMRSATRASIRI  382 (512)
Q Consensus       367 ~~IkeI~~~TGa~I~i  382 (512)
                      ++|..+.....-.|..
T Consensus       591 ~ni~~~t~~y~~~ie~  606 (657)
T COG5166         591 ENIQRVTKLYNSYIEF  606 (657)
T ss_pred             cchhhhhhhhhcccee
Confidence            8877777665555554

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=90.25  E-value=0.079  Score=59.96  Aligned_cols=69  Identities=22%  Similarity=0.183  Sum_probs=57.2

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      -.+.+|.....+|||++|++|+-+|..|||.|.|..-  -|.  ...+|.+.+.|+++.++.|...|...+.+
T Consensus      1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence            4577888889999999999999999999999999642  121  25689999999999999998877766654

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=90.18  E-value=0.41  Score=35.94  Aligned_cols=35  Identities=17%  Similarity=0.245  Sum_probs=28.5

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeE
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI   77 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I   77 (512)
                      .....+.+.....|.+|||+|.+|++|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            45566666666789999999999999999997554

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>cd02409 KH-II KH-II (K homology RNA-binding domain, type II)

Probab=88.63  E-value=0.72  Score=34.54  Aligned_cols=35  Identities=31%  Similarity=0.440  Sum_probs=28.5

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceE
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI  174 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I  174 (512)
                      ...+.+.+.....|.+|||+|++|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35666777766789999999999999999988544

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=88.56  E-value=0.19  Score=38.99  Aligned_cols=33  Identities=18%  Similarity=0.300  Sum_probs=27.9

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcC
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETR  171 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tg  171 (512)
                      ....+.+-+..+..|.||||+|.+++.||--.+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~   59 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN   59 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence            344778888999999999999999999996544

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=88.49  E-value=0.81  Score=47.67  Aligned_cols=39  Identities=33%  Similarity=0.436  Sum_probs=36.1

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (512)
                      .+.+.||...++.+|||+|.+|++|++..|-+|.|...+
T Consensus       487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e  525 (604)
T COG1855         487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE  525 (604)
T ss_pred             eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence            577899999999999999999999999999999998763

>PRK12705 hypothetical protein; Provisional

Probab=88.24  E-value=0.37  Score=51.68  Aligned_cols=53  Identities=26%  Similarity=0.317  Sum_probs=42.7

Q ss_pred             CCCCCCeEEEEEecC-CceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc
Q 010374           38 GIGSEDTVYRYLCPL-RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS   95 (512)
Q Consensus        38 ~~~~~~~~~rilvp~-~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G   95 (512)
                      ....+.++-.+.+|+ ++-|.||||.|.+|+.++..||+.|-|++.     .++|+|.+
T Consensus       192 ~~~~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~V~ls~  245 (508)
T PRK12705        192 ETASDLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-----PEAVVISS  245 (508)
T ss_pred             chhhhheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC-----ccchhhcc
Confidence            334566777788887 678999999999999999999999999876     33455655

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=88.10  E-value=1.2  Score=46.71  Aligned_cols=156  Identities=13%  Similarity=0.096  Sum_probs=103.2

Q ss_pred             EEecCCChhHHHHHhhcCceEEE--eecCCCCcccCCCCceE-EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCC
Q 010374          154 CVIGKGGQVIQNIRTETRAQIRI--LKDEHLPLCALSFDELL-QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSN  230 (512)
Q Consensus       154 ~IIGk~G~~Ik~I~~~tga~I~i--~~~~~~p~~~~~~dr~v-~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~  230 (512)
                      +|=||+--.+.+|++..-|-+.+  ..++        ..++. .+.|..-+-.+++..+..   +               
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~--------gs~~~~~~~g~~~~F~k~~~~~~~---E---------------  446 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSST--------GSIVETNGIGEKMSFSKKLSIPPT---E---------------  446 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecC--------CcEEEEeccCcchhhHHHhcCCcc---c---------------
Confidence            56677766688999888887443  3331        11222 256666666666543321   1               


Q ss_pred             ccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEE
Q 010374          231 IYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIF  310 (512)
Q Consensus       231 ~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~  310 (512)
                       |+                            -.+.+.||...|..|||.||..|++.+.+.++.|++...-.-       
T Consensus       447 -Fp----------------------------ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~-------  490 (657)
T COG5166         447 -FP----------------------------AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKF-------  490 (657)
T ss_pred             -Cc----------------------------hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhc-------
Confidence             11                            145788999999999999999999999999998887652200       


Q ss_pred             ecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHh----CCeEEEecCC
Q 010374          311 ISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT----RASIRILTNE  386 (512)
Q Consensus       311 i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~T----Ga~I~i~~~~  386 (512)
                               .  +  .+                 .....-+..|..-.+.|+|++......+++..    ...|++.+  
T Consensus       491 ---------~--q--s~-----------------~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~--  538 (657)
T COG5166         491 ---------G--Q--SQ-----------------WHDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP--  538 (657)
T ss_pred             ---------c--h--hh-----------------hhcceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC--
Confidence                     0  0  00                 01224577899999999999999988888665    56677742  


Q ss_pred             CCCCCCCCCceEEEEEcCHHHHHH
Q 010374          387 NVPKVAYEDEEMVQITGSLDVASS  410 (512)
Q Consensus       387 ~~p~~~~~~~r~V~I~G~~~~v~~  410 (512)
                             ...+.+++-|-.+-+..
T Consensus       539 -------~~~sI~~v~~~~~~I~r  555 (657)
T COG5166         539 -------QSTSIFTVDIYSDEIER  555 (657)
T ss_pred             -------CceEEEEEcccccHHHH
Confidence                   23447887776655544

>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]

Probab=87.87  E-value=1.8  Score=45.54  Aligned_cols=128  Identities=22%  Similarity=0.376  Sum_probs=79.2

Q ss_pred             eeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccCCcccC
Q 010374           57 SIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFG  136 (512)
Q Consensus        57 ~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~~~~~~  136 (512)
                      .++=+.|..|++|-++..-+|.|-.+.        .+                +.+..+|...|++.+-++.--.+ .  
T Consensus        42 ~~~~~~~dlik~lAk~lrKRI~iR~dP--------sv----------------l~~~e~A~~~I~eivP~ea~i~~-i--   94 (637)
T COG1782          42 ELFAKDGDLIKDLAKDLRKRIIIRPDP--------SV----------------LKPPEEARKIILEIVPEEAGITD-I--   94 (637)
T ss_pred             HHhccchhHHHHHHHHHhhceEeccCc--------hh----------------cCCHHHHHHHHHHhCccccCcee-E--
Confidence            345578899999999998888775431        11                22246677777765533321111 0  


Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEE----EecCHHHHHHHHHHHHHH
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ----VAGEPAVVRKALVQIASR  212 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~----I~G~~~~V~~A~~~I~~~  212 (512)
                      .=...+-+++|-.+.-|.+|||+|++.+.|..+||-.-+|.....++.     .-+-.    +.-..+.-++.++.|..+
T Consensus        95 ~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PPi~S-----~ti~~ir~~l~~~~~eR~~iL~~vg~r  169 (637)
T COG1782          95 YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPPIQS-----RTIKSIREILRSERKERREILRNVGRR  169 (637)
T ss_pred             EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCCCch-----hhHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            001125568888999999999999999999999998888887633321     11111    122233444556666666


Q ss_pred             HhcC
Q 010374          213 LHEN  216 (512)
Q Consensus       213 l~~~  216 (512)
                      |+..
T Consensus       170 Ihr~  173 (637)
T COG1782         170 IHRE  173 (637)
T ss_pred             hcCC
Confidence            6654

>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=87.76  E-value=0.26  Score=45.17  Aligned_cols=55  Identities=24%  Similarity=0.335  Sum_probs=48.7

Q ss_pred             CCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       355 ~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      +..+|.|+||+|.+---|.+.|.++|.+..            ..|.|-|..++++.|...|+.+|-.
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence            467899999999999999999999999852            2799999999999999999988843

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=86.48  E-value=1.2  Score=43.14  Aligned_cols=51  Identities=12%  Similarity=0.193  Sum_probs=45.9

Q ss_pred             eEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      -+|||.+|.+++.|+--|.|-|-|...            .|.+.|....+..+...|.+.+.+
T Consensus       161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N  211 (356)
T KOG2874|consen  161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN  211 (356)
T ss_pred             HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence            469999999999999999999998654            589999999999999999888876

>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]

Probab=86.37  E-value=0.3  Score=55.53  Aligned_cols=60  Identities=20%  Similarity=0.155  Sum_probs=51.3

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCc
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGT  100 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~  100 (512)
                      ......++-+|...+..|||++|++|+.++.-||+.|.|.+ ...+..||.+.+.|.++.+
T Consensus      1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred             CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence            34445678889999999999999999999999999999986 3445789999999998874

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=86.22  E-value=0.45  Score=36.55  Aligned_cols=38  Identities=26%  Similarity=0.476  Sum_probs=30.4

Q ss_pred             EEEEEeeCCc-----eeEEecCCChhHHHHHhhc-CceEEEeec
Q 010374          142 TVRMLVPADQ-----IGCVIGKGGQVIQNIRTET-RAQIRILKD  179 (512)
Q Consensus       142 ~~~llVP~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~  179 (512)
                      .+.+.|-+..     +|..||++|..|+.|+++. |-+|.|...
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            3566777777     8999999999999999999 999999865

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=85.95  E-value=0.87  Score=35.74  Aligned_cols=33  Identities=27%  Similarity=0.509  Sum_probs=26.6

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceE
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI  174 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I  174 (512)
                      .+.+-|..+..|.||||.|+++..||--++.-+
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~   57 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL   57 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence            456777788899999999999999996655433

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=85.66  E-value=0.72  Score=36.20  Aligned_cols=35  Identities=20%  Similarity=0.214  Sum_probs=27.7

Q ss_pred             EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010374           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI   79 (512)
Q Consensus        45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i   79 (512)
                      .+.+.+..+..|.+|||.|++++.||--++.-+.-
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            45566677889999999999999999887654443

The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=85.40  E-value=0.7  Score=35.51  Aligned_cols=36  Identities=25%  Similarity=0.488  Sum_probs=28.1

Q ss_pred             EEEEecCCc-----eeeeecCCchhHHHHHHHh-CCeEEEec
Q 010374          349 TRILVPSAQ-----IGCLIGRGGAIISEMRSAT-RASIRILT  384 (512)
Q Consensus       349 ~~l~VP~~~-----vG~IIGkgG~~IkeI~~~T-Ga~I~i~~  384 (512)
                      ..+.|-...     +|..||++|++|+.|.++. |-+|.|-.
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            345555555     8999999999999999999 89999865

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=85.27  E-value=1.2  Score=47.40  Aligned_cols=68  Identities=18%  Similarity=0.226  Sum_probs=56.9

Q ss_pred             CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010374          342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR  420 (512)
Q Consensus       342 ~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~  420 (512)
                      .....+...+.|+.+....+||.+|...|.|..+||+.-.+            ++.+|.|.- ++.+.+.|+.+|...+.
T Consensus       592 ~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~  659 (760)
T KOG1067|consen  592 KEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIK  659 (760)
T ss_pred             cccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence            34466788999999999999999999999999999965554            234777777 78899999999998887


Q ss_pred             h
Q 010374          421 A  421 (512)
Q Consensus       421 ~  421 (512)
                      .
T Consensus       660 ~  660 (760)
T KOG1067|consen  660 D  660 (760)
T ss_pred             C
Confidence            6

>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.24  E-value=1.7  Score=42.80  Aligned_cols=12  Identities=17%  Similarity=0.545  Sum_probs=6.0

Q ss_pred             CCCCCCCCCCCC
Q 010374          489 NAYGAYGDHSSG  500 (512)
Q Consensus       489 ~~yg~~~~~~~~  500 (512)
                      +||+.++.|+..
T Consensus        91 gGyN~~~~~g~n  102 (362)
T KOG3875|consen   91 GGYNRFGPYGTN  102 (362)
T ss_pred             cccccccccccC
Confidence            455555555533

>PRK13764 ATPase; Provisional

Probab=84.16  E-value=1.1  Score=49.11  Aligned_cols=43  Identities=23%  Similarity=0.405  Sum_probs=38.7

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCC
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVP  389 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p  389 (512)
                      .+..+.||...++.+|||+|.+|++|.+..|.+|.|...+..|
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            4678899999999999999999999999999999998776554

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=83.71  E-value=2.7  Score=40.16  Aligned_cols=55  Identities=24%  Similarity=0.374  Sum_probs=43.2

Q ss_pred             EEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHH-HHHHHHHH
Q 010374          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV-VRKALVQI  209 (512)
Q Consensus       144 ~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~-V~~A~~~I  209 (512)
                      -+.||...|.++||++|..++-|.++|+|+|-|-...           .|-|.++.+. ..-|...|
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG-----------~IWV~~~~~~~e~~~~~aI  204 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG-----------RIWVDGENESLEELAIEAI  204 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC-----------EEEecCCCcchHHHHHHHH
Confidence            4789999999999999999999999999999996552           4777777664 33343333

>PRK13764 ATPase; Provisional

Probab=83.69  E-value=2.6  Score=46.36  Aligned_cols=44  Identities=30%  Similarity=0.400  Sum_probs=38.8

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCC
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLP  183 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p  183 (512)
                      .-.+.+.||...++.+|||+|.+|++|.++.|..|.|...+..+
T Consensus       480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            33678999999999999999999999999999999998775443

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=83.27  E-value=0.95  Score=47.18  Aligned_cols=41  Identities=27%  Similarity=0.349  Sum_probs=36.7

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCC
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN  387 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~  387 (512)
                      ....+.||..+++.+|||+|.+|++|.+..|-+|.|...+.
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~  526 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE  526 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence            34678899999999999999999999999999999976544

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=82.94  E-value=0.67  Score=36.84  Aligned_cols=38  Identities=16%  Similarity=0.316  Sum_probs=32.0

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~   81 (512)
                      ..+++.|-...-|.|||++|+.|++|+++..-...+.+
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~   67 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE   67 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence            34788888899999999999999999998877666643

S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=82.43  E-value=0.67  Score=36.37  Aligned_cols=35  Identities=23%  Similarity=0.397  Sum_probs=29.3

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEE
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR   78 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~   78 (512)
                      ....+.+.....+.|||++|++|++|.++..-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            45678888999999999999999999887765553

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=80.26  E-value=0.78  Score=35.97  Aligned_cols=35  Identities=26%  Similarity=0.452  Sum_probs=29.2

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEE
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIR  381 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~  381 (512)
                      ....+.+....-|.|||++|++|++|++..+-.+.
T Consensus        25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            34677888999999999999999999988765553

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	512
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-07
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		5e-04
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		6e-04
1j5k_A	89	Complex Of The Kh3 Domain Of Hnrnp K With A Single_		8e-04

>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains Length = 160

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/157 (29%), Positives = 75/157 (47%), Gaps = 33/157 (21%)
Query: 68  QLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAE 127
           ++R E+ + I ISE    C ERI+T+   +                 +A+F+    I+  
Sbjct: 29  KMREESGARINISEG--NCPERIITLAGPT-----------------NAIFKAFAMII-- 67
Query: 128 DSLADDEFGELT--------LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
           D L +D    +T         +T+R++VPA Q G +IGKGG  I+ IR  T AQ+++  D
Sbjct: 68  DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD 127
Query: 180 EHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216
             LP    S +  + +AG P  + + + QI   + E 
Sbjct: 128 -MLP---NSTERAITIAGIPQSIIECVKQICVVMLET 160

>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT RNA Hairpin Length = 178

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 76/160 (47%), Gaps = 22/160 (13%)
Query: 68  QLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVS------PAQDALF 118
           QL+ ET + I++S++    PG  ER+  I  + E  N       F++      P   A  
Sbjct: 30  QLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHG---FIAEKIREXPQNVAKT 86
Query: 119 RVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI-L 177
                +  + ++  D   +     V+++VP    G +IGKGG  ++ I  ++ A +++  
Sbjct: 87  EPVSILQPQTTVNPDRANQ-----VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQ 141
Query: 178 KDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217
           K + + L     + ++ V+GEP   RKA+  I  ++ E+P
Sbjct: 142 KPDGINLQ----NRVVTVSGEPEQNRKAVELIIQKIQEDP 177

>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25 NT RNA Hairpin Length = 178

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 76/160 (47%), Gaps = 22/160 (13%)
Query: 68  QLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVS------PAQDALF 118
           QL+ ET + I++S++    PG  ER+  I  + E  N       F++      P   A  
Sbjct: 30  QLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHG---FIAEKIREMPQNVAKT 86
Query: 119 RVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI-L 177
                +  + ++  D   +     V+++VP    G +IGKGG  ++ I  ++ A +++  
Sbjct: 87  EPVSILQPQTTVNPDRANQ-----VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQ 141
Query: 178 KDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217
           K + + L     + ++ V+GEP   RKA+  I  ++ E+P
Sbjct: 142 KPDGINLQ----NRVVTVSGEPEQNRKAVELIIQKIQEDP 177

>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A Single_stranded 10mer Dna Oligonucleotide Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 7/84 (8%)
Query: 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT 402
           G P+ITT++ +P    G +IG+GG  I ++R  + ASI+I    + P    ED  ++ IT
Sbjct: 10  GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSED-RIITIT 64
Query: 403 GSLDVASSA--LSQVTLRLRANTF 424
           G+ D   +A  L Q +++  +  F
Sbjct: 65  GTQDQIQNAQYLLQNSVKQYSGKF 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	512
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-42
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-31
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-24
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-40
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-31
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-21
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-07
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-39
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-33
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-23
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-37
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	5e-32
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-26
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-35
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	9e-27
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-25
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-10
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-09
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-17
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	7e-14
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	2e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-15
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	7e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	4e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	7e-09
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-15
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	5e-12
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	7e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	9e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-14
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	2e-10
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	6e-09
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	6e-09
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-14
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-13
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	6e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	4e-14
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	9e-14
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	1e-13
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-10
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-13
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-09
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-08
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-13
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	8e-12
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-11
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	3e-10
1we8_A	104	Tudor and KH domain containing protein; structural	7e-12
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
1we8_A	104	Tudor and KH domain containing protein; structural	5e-08
1we8_A	104	Tudor and KH domain containing protein; structural	7e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	8e-12
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	2e-11
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-07
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	1e-07
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	3e-10
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	8e-09
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	7e-04
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-10
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	4e-09
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	7e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	3e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	6e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-09
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	7e-08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	9e-09
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	2e-06
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	3e-06
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	2e-07
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-04
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	4e-04
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	2e-07
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	7e-07
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	6e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	4e-07
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	5e-06
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	9e-05
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	2e-04
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	5e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	7e-05
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	3e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	6e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
2cxc_A	144	NUSA; transcription termination, RNA binding prote	1e-05
2cxc_A	144	NUSA; transcription termination, RNA binding prote	5e-04
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	7e-05
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	1e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	1e-05
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	6e-04
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	9e-04
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	2e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	2e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	3e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	3e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	4e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	4e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	6e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	5e-04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	6e-04

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score =  148 bits (374), Expect = 2e-42
 Identities = 45/185 (24%), Positives = 82/185 (44%), Gaps = 16/185 (8%)

Query: 40  GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSS 96
                  + L P    GSIIGKGG+ + QL+ ET + I++S   +  PG  ER+  I  +
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 97  SEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA----DDEFGELTLITVRMLVPADQI 152
            E  N             + +  +   +   + ++               V+++VP    
Sbjct: 62  IEALN------AVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTA 115

Query: 153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASR 212
           G +IGKGG  ++ I  ++ A +++ +    P      + ++ V+GEP   RKA+  I  +
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQLSQK---PDGINLQNRVVTVSGEPEQNRKAVELIIQK 172

Query: 213 LHENP 217
           + E+P
Sbjct: 173 IQEDP 177

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score =  119 bits (299), Expect = 1e-31
 Identities = 40/173 (23%), Positives = 78/173 (45%), Gaps = 16/173 (9%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG---AEGDDCIIFIS-TKEF 316
           ++ L+++ P+   G +IGKGG  I Q+++E+GA+IK+  S        + +  I  T E 
Sbjct: 5   QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA 64

Query: 317 FEDPSPTITAALRLQPRCSEKTERESGDP---------VITTRILVPSAQIGCLIGRGGA 367
                  I   +R  P+   KTE  S                +I+VP++  G +IG+GGA
Sbjct: 65  LNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGA 124

Query: 368 IISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420
            +  +   + A +++      P        +V ++G  +    A+  +  +++
Sbjct: 125 TVKAIMEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQ 174

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 98.4 bits (245), Expect = 3e-24
 Identities = 35/174 (20%), Positives = 69/174 (39%), Gaps = 25/174 (14%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
             +++L+P+   G +IGKGGQ I  ++ ET A I++ K +       + + +  + G   
Sbjct: 6   YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFY--PGTTERVCLIQGTIE 63

Query: 201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAR 260
            +      IA ++ E P                                   +      R
Sbjct: 64  ALNAVHGFIAEKIREMPQNV---------------------AKTEPVSILQPQTTVNPDR 102

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS--GAEGDDCIIFIS 312
              ++++ P    G +IGKGG  +K I ++SGA +++     G    + ++ +S
Sbjct: 103 ANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVS 156

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A* Length = 178

 Score = 55.2 bits (133), Expect = 3e-09
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 18  DAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI 77
           +   N          + +           + + P    G IIGKGG  VK +  ++ + +
Sbjct: 78  EMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWV 137

Query: 78  RISETV--PGCDERIVTIYSSSE 98
           ++S+         R+VT+    E
Sbjct: 138 QLSQKPDGINLQNRVVTVSGEPE 160

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score =  142 bits (359), Expect = 3e-40
 Identities = 40/181 (22%), Positives = 77/181 (42%), Gaps = 20/181 (11%)

Query: 42  EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET-VPGCDERIVTIYSSSEGT 100
           E  + +   P + +G+IIGK G+ +KQL     ++I+I+    P    R+V I    E  
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA- 59

Query: 101 NLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGG 160
                          A  R++ ++  E+     E  +   +   + VPA   G VIGKGG
Sbjct: 60  ------------QFKAQGRIYGKLKEENFFGPKEEVK---LETHIRVPASAAGRVIGKGG 104

Query: 161 QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRS 220
           + +  ++  T A++ + +D        +   ++++ G     + A  +I   L +   + 
Sbjct: 105 KTVNELQNLTAAEVVVPRD---QTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQQH 161

Query: 221 Q 221
           Q
Sbjct: 162 Q 162

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score =  116 bits (292), Expect = 8e-31
 Identities = 38/162 (23%), Positives = 76/162 (46%), Gaps = 10/162 (6%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG-DDCIIFISTKEFFED 319
           +  +++  PA  +G +IGK G  IKQ+ + + ASIK+           ++ I+       
Sbjct: 2   QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITG-----P 56

Query: 320 PSPTITAALRLQPRCSEKTERESGDPV-ITTRILVPSAQIGCLIGRGGAIISEMRSATRA 378
           P     A  R+  +  E+      + V + T I VP++  G +IG+GG  ++E+++ T A
Sbjct: 57  PEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAA 116

Query: 379 SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420
            + +  ++   +    D+ +V+I G    +  A  ++   L 
Sbjct: 117 EVVVPRDQTPDE---NDQVIVKIIGHFYASQMAQRKIRDILA 155

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 90.6 bits (225), Expect = 1e-21
 Identities = 38/174 (21%), Positives = 61/174 (35%), Gaps = 41/174 (23%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
             V++ +PA  +G +IGK GQ I+ +     A I+I   E       S   ++ + G P 
Sbjct: 3   EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE----TPDSKVRMVIITGPPE 58

Query: 201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAR 260
              KA  +I  +L E                                             
Sbjct: 59  AQFKAQGRIYGKLKEENFFGP-----------------------------------KEEV 83

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV--DSSGAEGDDCIIFIS 312
           +    +  PA   G VIGKGG  + +++  + A + V  D +  E D  I+ I 
Sbjct: 84  KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKII 137

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 50.5 bits (121), Expect = 1e-07
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 32  DETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGC--DER 89
           +E                 P    G +IGKGG+ V +L++ T + + +         D+ 
Sbjct: 73  EENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQV 132

Query: 90  IVTI 93
           IV I
Sbjct: 133 IVKI 136

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score =  140 bits (354), Expect = 1e-39
 Identities = 52/177 (29%), Positives = 84/177 (47%), Gaps = 21/177 (11%)

Query: 41  SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGT 100
           +     R L   +++GSIIGK GE VK++R E+ + I ISE    C ERI+T+   +   
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTN-- 57

Query: 101 NLFEDSGEFVSPAQDALFRVHDRIV--AEDSLADDEFGELTLITVRMLVPADQIGCVIGK 158
                          A   + D++      S+ +        +T+R++VPA Q G +IGK
Sbjct: 58  -----------AIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGK 106

Query: 159 GGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215
           GG  I+ IR  T AQ+++  D        S +  + +AG P  + + + QI   + E
Sbjct: 107 GGCKIKEIRESTGAQVQVAGDM----LPNSTERAITIAGIPQSIIECVKQICVVMLE 159

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score =  122 bits (309), Expect = 3e-33
 Identities = 40/162 (24%), Positives = 71/162 (43%), Gaps = 7/162 (4%)

Query: 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS-TKEFFE 318
              ++RL+     +G +IGK G  +K++R+ESGA I +        + II ++       
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLAGPTNAIF 60

Query: 319 DPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA 378
                I   L      S      +  P +T R++VP++Q G LIG+GG  I E+R +T A
Sbjct: 61  KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA 120

Query: 379 SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420
            +++  +          E  + I G        + Q+ + + 
Sbjct: 121 QVQVAGDML----PNSTERAITIAGIPQSIIECVKQICVVML 158

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 96.0 bits (239), Expect = 2e-23
 Identities = 43/166 (25%), Positives = 71/166 (42%), Gaps = 37/166 (22%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           +T+R+L+   ++G +IGK G+ ++ +R E+ A+I I +           + ++ +AG   
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTN 57

Query: 201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAR 260
            + KA   I  +L E+ S S                                    AS  
Sbjct: 58  AIFKAFAMIIDKLEEDISSSM------------------------------TNSTAASRP 87

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDD 306
             +LRLV PA   G +IGKGG  IK+IR+ +GA ++V         
Sbjct: 88  PVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNST 133

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 58.2 bits (141), Expect = 2e-10
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 7/92 (7%)

Query: 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403
           +  +T R+L+   ++G +IG+ G  + +MR  + A I I             E ++ + G
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-------PERIITLAG 54

Query: 404 SLDVASSALSQVTLRLRANTFEREGALAAHPP 435
             +    A + +  +L  +         A   
Sbjct: 55  PTNAIFKAFAMIIDKLEEDISSSMTNSTAASR 86

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens} Length = 160

 Score = 56.7 bits (137), Expect = 7e-10
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 26  KRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETVP 84
           +       T            R + P  + GS+IGKGG  +K++R  T + ++++ + +P
Sbjct: 71  EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP 130

Query: 85  GCDERIVTI 93
              ER +TI
Sbjct: 131 NSTERAITI 139

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score =  134 bits (339), Expect = 3e-37
 Identities = 34/175 (19%), Positives = 67/175 (38%), Gaps = 6/175 (3%)

Query: 43  DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG-TN 101
             +     P   +G +IG+ GE++K+++++    I+         ERI  I    +   +
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 102 LFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFG---ELTLITVRMLVPADQIGCVIGK 158
             E   + +   Q                    +       L     +VP  + G +IGK
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 159 GGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213
           GG+ I++I  ++ A+I +    + P  A    +L  + G P  +  A   I  ++
Sbjct: 122 GGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score =  119 bits (301), Expect = 5e-32
 Identities = 31/175 (17%), Positives = 61/175 (34%), Gaps = 18/175 (10%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS-------- 312
              + +  P   +G VIG+ G +IK+I+ ++G  I+         + I  I+        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61

Query: 313 --------TKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGR 364
                    +              R + R            +     +VP+ + G +IG+
Sbjct: 62  AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121

Query: 365 GGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL 419
           GG  I  +   + A I +    N P  A  + ++  I G+      A   +  ++
Sbjct: 122 GGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score =  104 bits (261), Expect = 2e-26
 Identities = 35/165 (21%), Positives = 63/165 (38%), Gaps = 20/165 (12%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            + + +P   +G VIG+ G++I+ I+ +   +I+   D+       + + + Q+ G P  
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD-----GTTPERIAQITGPPDR 58

Query: 202 VRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASARE 261
            + A   I   L    + +            +  G +   P                   
Sbjct: 59  AQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGP---------------PGGL 103

Query: 262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDD 306
                + P G  G +IGKGG  IK I Q+SGA I++  +     D
Sbjct: 104 QEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 148

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 58.7 bits (142), Expect = 2e-10
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 16  QSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75
            +      G + R  G      G       + ++ P  K G IIGKGGE +K +  ++ +
Sbjct: 76  GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGA 135

Query: 76  NIRISETVPGC---DERIVTIYSSSE 98
            I +    P     + ++ TI  + +
Sbjct: 136 RIELQRNPPPNADPNMKLFTIRGTPQ 161

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1 Length = 174

 Score = 58.0 bits (140), Expect = 4e-10
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              + +P   +G +IGR G +I ++++     I+       P      E + QITG  D 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFK-----PDDGTTPERIAQITGPPDR 58

Query: 408 ASSALSQVTLRLR 420
           A  A   +T  LR
Sbjct: 59  AQHAAEIITDLLR 71

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score =  128 bits (323), Expect = 3e-35
 Identities = 34/174 (19%), Positives = 65/174 (37%), Gaps = 17/174 (9%)

Query: 44  TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE--TVPGCDERIVTIYSSSEGTN 101
           TV   + P  K G +IGKGGE +KQL+      + + +  +     ++ + I        
Sbjct: 2   TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK-- 59

Query: 102 LFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQ 161
                   V  A + +  +            +E+G      + + VP   +G VIG+ G+
Sbjct: 60  --------VQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGE 111

Query: 162 VIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215
           +I+ I+ +   +I+              +++  + G P     A   I   L  
Sbjct: 112 MIKKIQNDAGVRIQF-----KQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score =  105 bits (263), Expect = 9e-27
 Identities = 37/163 (22%), Positives = 64/163 (39%), Gaps = 9/163 (5%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV--DSSGAEGDDCIIFIS-TKEFFED 319
              ++ PAG  G VIGKGG  IKQ+++ +G  + +  D S     D  + I       + 
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62

Query: 320 PSPTITAALRLQPRCSEKTERESG-DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA 378
               +   LR + +       E G        + VP   +G +IGR G +I ++++    
Sbjct: 63  ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGV 122

Query: 379 SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421
            I+              E++  I G  D    A   +   L++
Sbjct: 123 RIQFK-----QDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 160

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score =  100 bits (250), Expect = 4e-25
 Identities = 36/171 (21%), Positives = 70/171 (40%), Gaps = 32/171 (18%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
              +++PA + G VIGKGG+ I+ ++     ++ +++D          D+ L++ G+P  
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV---DKPLRIIGDPYK 59

Query: 202 VRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASARE 261
           V++A   +   L E                                G +  R +  S   
Sbjct: 60  VQQACEMVMDILRERDQ-----------------------------GGFGDRNEYGSRIG 90

Query: 262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
             + +  P  ++G VIG+ G +IK+I+ ++G  I+       G + I  I 
Sbjct: 91  GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 141

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 57.9 bits (140), Expect = 4e-10
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              I++P+ + G +IG+GG  I +++      + ++ + +        ++ ++I G    
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT---NVDKPLRIIGDPYK 59

Query: 408 ASSALSQVTLRLRAN 422
              A   V   LR  
Sbjct: 60  VQQACEMVMDILRER 74

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens} Length = 164

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 12/70 (17%), Positives = 26/70 (37%)

Query: 29  NPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDE 88
             G                   P   +G +IG+ GE++K+++++    I+  +      E
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 135

Query: 89  RIVTIYSSSE 98
           +I  I    +
Sbjct: 136 KIAHIMGPPD 145

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 75.8 bits (187), Expect = 2e-17
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 7/76 (9%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           +T+R+L+   ++G +IGK G+ ++ +R E+ A+I I  + + P      + ++ +AG   
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPTN 57

Query: 201 VVRKALVQIASRLHEN 216
            + KA   I  +L E+
Sbjct: 58  AIFKAFAMIIDKLEED 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 69.2 bits (170), Expect = 4e-15
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403
           +  +T R+L+   ++G +IG+ G  + +MR  + A I I +  N P      E ++ + G
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAG 54

Query: 404 SLDVASSALSQVTLRLRAN 422
             +    A + +  +L  +
Sbjct: 55  PTNAIFKAFAMIIDKLEED 73

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 2/59 (3%)

Query: 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          +     R L   +++GSIIGK GE VK++R E+ + I ISE    C ERI+T+   +  
Sbjct: 2  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNA 58

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Length = 73

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
              ++RL+     +G +IGK G  +K++R+ESGA I +        + II ++
Sbjct: 3   VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN--CPERIITLA 53

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 70.4 bits (173), Expect = 2e-15
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            V M VP + +G ++GKGG+ +   +  T A+I+I K         + +  + + G PA 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 202 VRKALVQIASRLHE 215
            + A   I+ R+  
Sbjct: 62  TQAAQYLISQRVTY 75

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 60.0 bits (146), Expect = 7e-12
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              + VP   +G ++G+GG  + E +  T A I+I  ++    +       V ITGS   
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI--SKKGEFLPGTRNRRVTITGSPAA 61

Query: 408 ASSALSQVTLRLRA 421
             +A   ++ R+  
Sbjct: 62  TQAAQYLISQRVTY 75

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 16/87 (18%)

Query: 44  TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGT 100
            +     P   +G+I+GKGG+ + + +  T + I+IS   E +PG   R VTI  S   T
Sbjct: 3   ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 101 NLFEDSGEFVSPAQDALFRVHDRIVAE 127
                        Q A + +  R+  E
Sbjct: 63  -------------QAAQYLISQRVTYE 76

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Length = 76

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 10/41 (24%), Positives = 23/41 (56%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG 301
           +  + +  P   +G ++GKGG  + + ++ +GA I++   G
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 69.7 bits (171), Expect = 4e-15
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            V + VP + +G ++GKGG+ +   +  T A+I+I K         + +  + + G PA 
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 202 VRKALVQIASRLHENPSRSQ 221
            + A   I+ R+        
Sbjct: 62  TQAAQYLISQRVTYEQGVRA 81

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              I VP   +G ++G+GG  + E +  T A I+I  ++    +       V ITGS   
Sbjct: 4   LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQI--SKKGEFLPGTRNRRVTITGSPAA 61

Query: 408 ASSALSQVTLRLRANTFEREG 428
             +A   ++ R+      R  
Sbjct: 62  TQAAQYLISQRVTYEQGVRAS 82

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 44  TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGT 100
            +     P   +G+I+GKGG+ + + +  T + I+IS   E +PG   R VTI  S   T
Sbjct: 3   ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62

Query: 101 N 101
            
Sbjct: 63  Q 63

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Length = 87

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 10/41 (24%), Positives = 23/41 (56%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG 301
           +  + +  P   +G ++GKGG  + + ++ +GA I++   G
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKG 42

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
               +++PA + G VIGKGG+ I+ ++     ++ +++D        + D+ L++ G+P 
Sbjct: 14  TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPY 70

Query: 201 VVRKALVQIASRLHE 215
            V++A   +   L E
Sbjct: 71  KVQQACEMVMDILRE 85

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 340 RESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMV 399
              G       I++P+ + G +IG+GG  I +++      + ++ + +        ++ +
Sbjct: 7   ANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT---NVDKPL 63

Query: 400 QITGSLDVASSALSQVTLRLR 420
           +I G       A   V   LR
Sbjct: 64  RIIGDPYKVQQACEMVMDILR 84

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 256 EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV--DSSGAEGDDCIIFIS 312
                     ++ PAG  G VIGKGG  IKQ+++ +G  + +  D S     D  + I 
Sbjct: 8   NGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII 66

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS--ETVPGCDERIVTIYSSS 97
          G   TV   + P  K G +IGKGGE +KQL+      + +    +     ++ + I    
Sbjct: 10 GQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP 69

Query: 98 E 98
           
Sbjct: 70 Y 70

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           IT ++ +P D  G +IGKGGQ I+ IR E+ A I+I  DE L       D ++ + G   
Sbjct: 7   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSE---DRIITITGTQD 61

Query: 201 VVRKALVQIASRLHENPSR 219
            ++ A   + + + +   +
Sbjct: 62  QIQNAQYLLQNSVKQYSGK 80

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 13/90 (14%)

Query: 38  GIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSS 97
           G        +   P    GSIIGKGG+ +KQ+R E+ ++I+I E + G ++RI+TI  + 
Sbjct: 1   GAMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60

Query: 98  EGTNLFEDSGEFVSPAQDALFRVHDRIVAE 127
           +               Q+A + + + +   
Sbjct: 61  DQI-------------QNAQYLLQNSVKQY 77

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 5/82 (6%)

Query: 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
           +  P+ITT++ +P    G +IG+GG  I ++R  + ASI+I  +E +      ++ ++ I
Sbjct: 2   AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLE---GSEDRIITI 56

Query: 402 TGSLDVASSALSQVTLRLRANT 423
           TG+ D   +A   +   ++  +
Sbjct: 57  TGTQDQIQNAQYLLQNSVKQYS 78

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Length = 82

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           + ++  P    G +IGKGG  IKQIR ESGASIK+D      +D II I+
Sbjct: 8   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 57

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 67.0 bits (164), Expect = 4e-14
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           IT ++ +P D  G +IGKGGQ I+ IR E+ A I+I  DE L       D ++ + G   
Sbjct: 14  ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSE---DRIITITGTQD 68

Query: 201 VVRKALVQIASRLHENPSR 219
            ++ A   + + + +   +
Sbjct: 69  QIQNAQYLLQNSVKQYSGK 87

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 65.8 bits (161), Expect = 9e-14
 Identities = 23/68 (33%), Positives = 38/68 (55%)

Query: 31 GDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERI 90
          G       +G      +   P    GSIIGKGG+ +KQ+R E+ ++I+I E + G ++RI
Sbjct: 1  GSHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRI 60

Query: 91 VTIYSSSE 98
          +TI  + +
Sbjct: 61 ITITGTQD 68

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 5/83 (6%)

Query: 341 ESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQ 400
           + G P+ITT++ +P    G +IG+GG  I ++R  + ASI+I  +E +      ++ ++ 
Sbjct: 8   DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLE---GSEDRIIT 62

Query: 401 ITGSLDVASSALSQVTLRLRANT 423
           ITG+ D   +A   +   ++  +
Sbjct: 63  ITGTQDQIQNAQYLLQNSVKQYS 85

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A Length = 89

 Score = 58.1 bits (141), Expect = 5e-11
 Identities = 27/68 (39%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 245 GSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG 304
           GS+ +Y            + ++  P    G +IGKGG  IKQIR ESGASIK+D      
Sbjct: 1   GSHMSYGD----LGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS 56

Query: 305 DDCIIFIS 312
           +D II I+
Sbjct: 57  EDRIITIT 64

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE 198
           +  T  + +P + IGC+IG+ G  I  IR  + AQI+I           S    + + G 
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGS 58

Query: 199 PAVVRKALVQIASRLHENPSRSQ 221
            A +  A   I +RL        
Sbjct: 59  AASISLAQYLINARLSSEKGMGC 81

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 13/92 (14%)

Query: 40  GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
               T +    P   IG IIG+ G  + ++R  + + I+I+  V G   R VTI  S+  
Sbjct: 2   LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61

Query: 100 TNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131
                           A + ++ R+ +E  + 
Sbjct: 62  I-------------SLAQYLINARLSSEKGMG 80

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS 404
              T  + +P+  IGC+IGR GA I+E+R  + A I+I        V       V ITGS
Sbjct: 4   SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIA-----NPVEGSSGRQVTITGS 58

Query: 405 LDVASSALSQVTLRLRA 421
               S A   +  RL +
Sbjct: 59  AASISLAQYLINARLSS 75

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Length = 82

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 17/50 (34%), Positives = 25/50 (50%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           +  L  P   IG +IG+ G  I +IRQ SGA IK+ +         + I+
Sbjct: 7   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 56

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 19/79 (24%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
               +++PA + G VIGKGG+ I+ ++     ++ +++D      A   D+ L++ G+P 
Sbjct: 15  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA---DKPLRITGDPY 71

Query: 201 VVRKALVQIASRLHENPSR 219
            V++A   +   + +  S 
Sbjct: 72  KVQQAKEMVLELIRDQGSG 90

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
            G       I++P+++ G +IG+GG  I +++      + ++ +          ++ ++I
Sbjct: 10  DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT---GADKPLRI 66

Query: 402 TGSLDVASSALSQVTLRLR 420
           TG       A   V   +R
Sbjct: 67  TGDPYKVQQAKEMVLELIR 85

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 52.4 bits (126), Expect = 5e-09
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 248 GNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV--DSSGAEGD 305
           G+  +             ++ PA   G VIGKGG  IKQ+++ +G  + +  D     G 
Sbjct: 1   GSSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA 60

Query: 306 DCIIFIS 312
           D  + I+
Sbjct: 61  DKPLRIT 67

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Length = 94

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 36 QRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE--TVPGCDERIVTI 93
            G G  + V   + P  K G +IGKGGE +KQL+      + + +        ++ + I
Sbjct: 7  GHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRI 66

Query: 94 YSSSEG 99
                
Sbjct: 67 TGDPYK 72

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
            +  + +P D IGC+IG+ G  I  IR  + AQI+I           S D  + + G  A
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV-----EGSTDRQVTITGSAA 59

Query: 201 VVRKALVQIASRLHE 215
            +  A   I  RL  
Sbjct: 60  SISLAQYLINVRLSS 74

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 60.0 bits (146), Expect = 8e-12
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
            +  + +P+  IGC+IGR GA I+E+R  + A I+I        V    +  V ITGS  
Sbjct: 5   TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKI-----ANPVEGSTDRQVTITGSAA 59

Query: 407 VASSALSQVTLRLRANT 423
             S A   + +RL + T
Sbjct: 60  SISLAQYLINVRLSSET 76

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 59.2 bits (144), Expect = 1e-11
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 13/87 (14%)

Query: 41  SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGT 100
           ++ T +    P   IG IIG+ G  + ++R  + + I+I+  V G  +R VTI  S+   
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASI 61

Query: 101 NLFEDSGEFVSPAQDALFRVHDRIVAE 127
                          A + ++ R+ +E
Sbjct: 62  -------------SLAQYLINVRLSSE 75

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 20/54 (37%), Positives = 28/54 (51%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           A+  S  L  P   IG +IG+ G  I +IRQ SGA IK+ +      D  + I+
Sbjct: 2   AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 61.0 bits (148), Expect = 7e-12
 Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 3/95 (3%)

Query: 134 EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL 193
              E T +  ++ VP   +G +IG+GG+ I++I   + A+I   K+    L       L+
Sbjct: 8   ILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL---SRLI 64

Query: 194 QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSS 228
           +++G    V  A   I  ++ E+    + +  S+S
Sbjct: 65  KISGTQKEVAAAKHLILEKVSEDEELRKRIAHSAS 99

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 335 SEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYE 394
           S  +   + +  +  ++ VP   +G +IGRGG  I  +  A+ A I     +   +    
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLL 59

Query: 395 DEEMVQITGSLDVASSALSQV 415
              +++I+G+    ++A   +
Sbjct: 60  LSRLIKISGTQKEVAAAKHLI 80

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 50.2 bits (120), Expect = 5e-08
 Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 248 GNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD--SSGAEGD 305
           G+  +            +L  P  ++G +IG+GG  I+ I + SGA I  D  S G    
Sbjct: 1   GSSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL 60

Query: 306 DCIIFIS 312
             +I IS
Sbjct: 61  SRLIKIS 67

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Length = 104

 Score = 49.8 bits (119), Expect = 7e-08
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 34  TEQRGIGSEDT--VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPG--CDER 89
           +   GI +E+T    +   P R +G IIG+GGE ++ +   + + I   +   G     R
Sbjct: 3   SGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSR 62

Query: 90  IVTIYSSSEGTN 101
           ++ I  + +   
Sbjct: 63  LIKISGTQKEVA 74

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 61.0 bits (148), Expect = 8e-12
 Identities = 19/102 (18%), Positives = 36/102 (35%), Gaps = 2/102 (1%)

Query: 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
           +  P       +P+ + G +IGRGG  +  +   T A + I  +  +P     + ++  I
Sbjct: 2   AMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFII 59

Query: 402 TGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMS 443
            GS      A   +  ++               P  P  P +
Sbjct: 60  RGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFN 101

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 59.9 bits (145), Expect = 2e-11
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            +   +P  + G VIG+GG+ ++ I  +T A + I     LP       +L  + G P  
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEI--SRQLPPNGDPNFKLFIIRGSPQQ 65

Query: 202 VRKALVQIASRLHENPSRSQ 221
           +  A   I  ++        
Sbjct: 66  IDHAKQLIEEKIEGPLCPVG 85

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 38 GIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVP---GCDERIVTIY 94
          G  +      +  P  K G +IG+GGE VK +  +T + + IS  +P     + ++  I 
Sbjct: 1  GAMAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR 60

Query: 95 SSSEG 99
           S + 
Sbjct: 61 GSPQQ 65

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 13/44 (29%), Positives = 21/44 (47%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDD 306
            +    P    G VIG+GG  +K I Q++GA +++        D
Sbjct: 8   EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGD 51

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 57.7 bits (139), Expect = 3e-10
 Identities = 33/155 (21%), Positives = 54/155 (34%), Gaps = 25/155 (16%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGA-SIKVDSSGAEGDDCIIFISTKEFF 317
           A  F  + +     +G  IG  G  I+Q R+  G  +I +D      D C   I      
Sbjct: 1   ASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIYG---- 51

Query: 318 EDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATR 377
            +    +  A              S        I VP   +G +IG+ G +I E+   + 
Sbjct: 52  -EDQDAVKKA-------------RSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSG 97

Query: 378 ASIRILTNENVPKVAYEDEEM-VQITGSLDVASSA 411
                +  EN   V  E+  +     G+ D  ++A
Sbjct: 98  VVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANA 132

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 53.5 bits (128), Expect = 8e-09
 Identities = 32/171 (18%), Positives = 55/171 (32%), Gaps = 37/171 (21%)

Query: 47  RYLCPLRKIGSIIGKGGEIVKQLRSETK-SNIRISETVPGCDERIVTIYSSSEGTNLFED 105
           +++     +G  IG  G  ++Q R     + I + E     D     IY           
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIY----------- 50

Query: 106 SGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQN 165
            GE     + A                     L      + VP + +G VIGK G++IQ 
Sbjct: 51  -GEDQDAVKKA------------------RSFLEFAEDVIQVPRNLVGKVIGKNGKLIQE 91

Query: 166 IRTETRA-QIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215
           I  ++   ++RI  +    +            G    +  A V +   L+ 
Sbjct: 92  IVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNY 142

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A Length = 144

 Score = 39.2 bits (91), Expect = 7e-04
 Identities = 10/43 (23%), Positives = 15/43 (34%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPL 184
             + +V  D +G  IG  G  IQ  R         L ++    
Sbjct: 5   HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTF 47

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            + + VP   +G VIG+ G++I+ I+ +   +I+  +D+         +++  + G P  
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD-----GTGPEKIAHIMGPPDR 66

Query: 202 VRKALVQIASRLHENPSRSQ 221
              A   I   L    S   
Sbjct: 67  CEHAARIINDLLQSLRSGPP 86

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 24/111 (21%), Positives = 42/111 (37%), Gaps = 12/111 (10%)

Query: 257 ASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS-TKE 315
            S     + +  P  ++G VIG+ G +IK+I+ ++G  I+       G + I  I    +
Sbjct: 6   GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 65

Query: 316 FFEDPSPTITAALRLQPRCSEK-TERESGDPVITTRILVPSAQIGCLIGRG 365
                      A R+    ++      SG P       +P    G   G+G
Sbjct: 66  -------RCEHAARI---INDLLQSLRSGPPGPPGGPGMPPGGRGRGRGQG 106

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 53.3 bits (128), Expect = 4e-09
 Identities = 11/51 (21%), Positives = 25/51 (49%)

Query: 49 LCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
            P   +G +IG+ GE++K+++++    I+  +      E+I  I    + 
Sbjct: 16 PVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDR 66

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              + VP   +G +IGR G +I ++++     I+   ++         E++  I G  D 
Sbjct: 12  GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT-----GPEKIAHIMGPPDR 66

Query: 408 ASSALSQVT 416
              A   + 
Sbjct: 67  CEHAARIIN 75

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 16/62 (25%), Positives = 27/62 (43%)

Query: 40  GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
                   Y  P   +G IIG+GGE + +++ E+   I+I+    G  ER   +  + E 
Sbjct: 11  QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES 70

Query: 100 TN 101
             
Sbjct: 71  VQ 72

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE 198
           +++T    VP   +G +IG+GG+ I  I+ E+  +I+I  D          +    + G 
Sbjct: 13  SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGT 67

Query: 199 PAVVRKALVQIASRLHENPSRSQ 221
           P  V+ A   +   + +  S   
Sbjct: 68  PESVQSAKRLLDQIVEKGRSGPS 90

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 15/65 (23%), Positives = 29/65 (44%)

Query: 248 GNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDC 307
           G+  +   +      +     P G +G +IG+GG  I +I+QESG  I++        + 
Sbjct: 1   GSSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPER 60

Query: 308 IIFIS 312
              ++
Sbjct: 61  SCMLT 65

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A Length = 92

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
               V+T    VP   +G +IGRGG  IS ++  +   I+I      P      E    +
Sbjct: 10  QQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCML 64

Query: 402 TGSLD 406
           TG+ +
Sbjct: 65  TGTPE 69

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 51.7 bits (124), Expect = 9e-09
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
            +  + +P +    VIGK G+ +Q++  +T  +I+I + +            +++ G   
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKE 69

Query: 201 VVRKALVQIASRLHENPSRS 220
            + KA  ++     E   RS
Sbjct: 70  GIEKARHEVLLISAEQDKRS 89

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          P      +IGK GE ++ L  +T + I+I    P      + I  + EG
Sbjct: 24 PKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEG 70

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 1/66 (1%)

Query: 245 GSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG 304
           GS G+          +  S  +  P  +   VIGK G  ++ +  ++   I++       
Sbjct: 1   GSSGSSGDIVARLQTQ-ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPS 59

Query: 305 DDCIIF 310
           +   I 
Sbjct: 60  NQIKIT 65

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 94

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
            +  + +P      +IG+ G  + ++   T   I+I   +       +    ++ITG+ +
Sbjct: 17  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKE 69

Query: 407 VASSALSQV 415
               A  +V
Sbjct: 70  GIEKARHEV 78

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
            T+++ VP   +G V+G  G  I+ I+  T   I     +  P+ A++        G P 
Sbjct: 10  TTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVT--------GMPE 61

Query: 201 VVRKALVQIASRLHENPSRS 220
            V +A  +I + +      S
Sbjct: 62  NVDRAREEIEAHITLRSGPS 81

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 11/35 (31%), Positives = 16/35 (45%)

Query: 269 PAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAE 303
           P   +G V+G  G  IK+I+Q +   I       E
Sbjct: 17  PYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKE 51

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 83

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 8/87 (9%)

Query: 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
           S     T ++ VP   +G ++G  GA I  ++  T   I             + E +  +
Sbjct: 5   SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAV 56

Query: 402 TGSLDVASSALSQVTLRLRANTFEREG 428
           TG  +    A  ++   +   +    G
Sbjct: 57  TGMPENVDRAREEIEAHITLRSGPSSG 83

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 38/201 (18%), Positives = 68/201 (33%), Gaps = 27/201 (13%)

Query: 33  ETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVT 92
           E E               P  +I  +IGK G+  K++   TK+ I I       +   V 
Sbjct: 23  EDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVW 77

Query: 93  IYSSSEGTNLFEDSGEFVSPAQD---ALFRVHDRIVAEDSLADDEFGEL-----TLITVR 144
           I S+ E  +        V  A+D   A+ R      A   L + E+ E+      +I   
Sbjct: 78  ITSTKETED-----PLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNE 132

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD--------EHLPLCALSFDELLQVA 196
                   G +IG+ G+  Q I   + A + +             + +   + ++L + +
Sbjct: 133 KNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQIEIAKTAIEKLARGS 192

Query: 197 GEPAVVRKALVQIASRLHENP 217
                V + L +    L    
Sbjct: 193 -PHGSVYRYLERRKKDLELEG 212

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 49.3 bits (117), Expect = 7e-07
 Identities = 28/154 (18%), Positives = 47/154 (30%), Gaps = 22/154 (14%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG--------AEGDDCIIFISTK 314
              +  P   I  +IGK G   K+I + +   I +DS           E +D +     +
Sbjct: 35  EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKAR 94

Query: 315 EFFEDPSP--TITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEM 372
           +         +   A RL             D +I           G +IGR G     +
Sbjct: 95  DIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQII 154

Query: 373 RSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
              + AS+ +              + V I G+  
Sbjct: 155 EEMSGASVSV------------YGKTVAIIGNPI 176

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B Length = 219

 Score = 46.6 bits (110), Expect = 6e-06
 Identities = 36/179 (20%), Positives = 58/179 (32%), Gaps = 28/179 (15%)

Query: 121 HDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI-LKD 179
           +     E    +DE+ E       + +P D+I  +IGK GQ  + I   T+ +I I  + 
Sbjct: 14  NVNKDGEIVEDEDEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSET 73

Query: 180 EHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYL 239
             +           +   +P  V KA   + +            LL+             
Sbjct: 74  GEVW------ITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNE------------ 115

Query: 240 SAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD 298
                G Y       D     E            G +IG+ G   + I + SGAS+ V 
Sbjct: 116 -----GEYLEIINLTDIIIGNE----KNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY 165

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 4/87 (4%)

Query: 129 SLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALS 188
           S  + E   L    + + V       +IG+ G VI  IR E    I+    +        
Sbjct: 5   SSGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----Q 60

Query: 189 FDELLQVAGEPAVVRKALVQIASRLHE 215
             + + + G       A   I   + E
Sbjct: 61  PQDQITITGYEKNTEAARDAILRIVGE 87

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 251 SARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS--GAEGDDCI 308
           S  +++ + R F L +         +IG+ G +I QIR E   +I+      G +  D I
Sbjct: 6   SGEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQI 65

Query: 309 IFISTKE 315
                ++
Sbjct: 66  TITGYEK 72

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 40.6 bits (95), Expect = 9e-05
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 51  PLRKIGSIIGKGGEIVKQLRSETKSNIRI-SETVPGCDERIVTIYSSSEGTN 101
             +    IIG+ G ++ Q+R E   NI+   +      +  +TI    + T 
Sbjct: 24  DPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTE 75

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 97

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
               + V       +IGR GA+I+++R     +I+    ++      + ++ + ITG   
Sbjct: 17  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----QPQDQITITGYEK 72

Query: 407 VASSA 411
              +A
Sbjct: 73  NTEAA 77

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 7/97 (7%)

Query: 131 ADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFD 190
             +    L  +T+ + VP D    VIG+ G  I+ +  E    I +   E          
Sbjct: 7   GKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQS 59

Query: 191 ELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSS 227
           +++ + G  A + +A   +  R+ E  +  +   L S
Sbjct: 60  DIIAITGLAANLDRAKAGLLERVKELQAEQEDRALRS 96

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 2/49 (4%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          P      +IG+ G  ++++  E + NI +    P     I+ I   +  
Sbjct: 24 PFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLAAN 70

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 12/59 (20%), Positives = 24/59 (40%)

Query: 251 SARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
           S +    +    ++ +  P      VIG+ G  I+++  E   +I V +   + D   I
Sbjct: 6   SGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAI 64

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 104

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 23/105 (21%), Positives = 38/105 (36%), Gaps = 10/105 (9%)

Query: 334 CSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAY 393
            S   E       +T  + VP      +IG+ G+ I +M      +I +   E       
Sbjct: 4   GSSGKEALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE------- 56

Query: 394 EDEEMVQITGS---LDVASSALSQVTLRLRANTFEREGALAAHPP 435
              +++ ITG    LD A + L +    L+A   +R        P
Sbjct: 57  LQSDIIAITGLAANLDRAKAGLLERVKELQAEQEDRALRSFKSGP 101

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 48.9 bits (116), Expect = 6e-07
 Identities = 23/134 (17%), Positives = 50/134 (37%), Gaps = 17/134 (12%)

Query: 50  CPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEF 109
               ++G++IG  GE+  ++   T + I +       +  +V +   +EG          
Sbjct: 10  VKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGI-----PPVN 59

Query: 110 VSPAQD---ALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQ----IGCVIGKGGQV 162
           +  A +   A+        A   L +D+   +  +   +    +      G +IG+GG+ 
Sbjct: 60  LMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRA 119

Query: 163 IQNIRTETRAQIRI 176
            + I   T   I +
Sbjct: 120 RRTIEEMTDTYINV 133

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1 Length = 191

 Score = 48.5 bits (115), Expect = 9e-07
 Identities = 28/162 (17%), Positives = 52/162 (32%), Gaps = 31/162 (19%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFE 318
           A +  + +      +G VIG  G +  +I + +G  I VD+     ++ ++ +  +    
Sbjct: 1   AMKPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGI 55

Query: 319 DPSPTITA-------ALRLQPRCSEKTERE-------SGDPVITTRILVPSAQIGCLIGR 364
            P   + A       +L   P  + +   E           V+           G +IG 
Sbjct: 56  PPVNLMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGE 115

Query: 365 GGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           GG     +   T   I +             E  V I G  +
Sbjct: 116 GGRARRTIEEMTDTYINV------------GEYEVAIIGDYE 145

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.0 bits (121), Expect = 7e-07
 Identities = 41/296 (13%), Positives = 79/296 (26%), Gaps = 87/296 (29%)

Query: 6   NINYG------KRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRY---------LC 50
            INY       K    Q    T    ++R+      Q  + ++  V R          L 
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ--VFAKYNVSRLQPYLKLRQALL 145

Query: 51  PLRKIGSII--GKGGEIVKQ-LRSETKSNIRISETVPG---------CD------ERIVT 92
            LR   +++  G  G   K  +  +   + ++   +           C+      E +  
Sbjct: 146 ELRPAKNVLIDGVLG-SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204

Query: 93  IYSSSEGTNLFEDSGEFVSPAQDALFRVHD------RIVAE----DSLA--DD------- 133
           +        +  +       + +   R+H       R++      + L    +       
Sbjct: 205 LL-----YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259

Query: 134 ---EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA---- 186
                    L+T R     D +         +  +  T T        DE   L      
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT-------PDEVKSLLLKYLD 312

Query: 187 LSFDELLQVAGEPAVVRK----ALVQIASRLHENPSRSQ---HLLLSSSSNIYQSS 235
               +L      P  V       L  IA  + +  +      H+     + I +SS
Sbjct: 313 CRPQDL------PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 27/119 (22%), Positives = 39/119 (32%), Gaps = 41/119 (34%)

Query: 53  RKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFV-- 110
            + G  IG+GG ++K LR     NI + E            YS         D    V  
Sbjct: 45  GEAGRAIGRGGRLIKLLREALGKNIEVVE------------YS--------SDLERIVKN 84

Query: 111 --SPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIR 167
                     ++    V       +  G      V + V  D  G  IGKGG   +N++
Sbjct: 85  LFPGV-----KIESINV------RERNGV---KQVVIKVSEDDKGAAIGKGG---KNVK 126

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 25/110 (22%), Positives = 39/110 (35%), Gaps = 20/110 (18%)

Query: 259 AREFSLRL--VCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEF 316
             E + RL  +   G  G  IG+GG +IK +R+  G +I+           ++     E+
Sbjct: 31  VDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIE-----------VV-----EY 74

Query: 317 FEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGG 366
             D    +           E       + V    I V     G  IG+GG
Sbjct: 75  SSDLERIVKNL--FPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGG 122

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
           +  V + +       +IGK G  I  I+ + +  +RI  D            L+++ G+P
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDP 56

Query: 200 AVVRKALVQI 209
             V++A  ++
Sbjct: 57  QGVQQAKREL 66

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 9/51 (17%), Positives = 20/51 (39%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
            R   + +         +IGK G  I +I+ +   S+++     + +   I
Sbjct: 2   NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRI 52

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A Length = 71

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
            +    +IGK G  + +++ + K ++RI       +   + I    +G
Sbjct: 12 DHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNL--IRIEGDPQG 58

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           ++  + +       +IG  G+ I+ I  E +  IR  +              + V G P 
Sbjct: 17  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD------PNCVTVTGLPE 70

Query: 201 VVRKALVQIASRLHENPSRSQH 222
            V +A+  I +   E  + S  
Sbjct: 71  NVEEAIDHILNLEEEYLADSGP 92

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 13/55 (23%), Positives = 20/55 (36%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
             S  +         +IG  G  I++I  E    I+   SGA   +C+      E
Sbjct: 16  MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE 70

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1 Length = 95

 Score = 37.8 bits (88), Expect = 9e-04
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 6/60 (10%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           ++  + +       +IG  G  I ++    +  IR       P+    D   V +TG  +
Sbjct: 17  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLPE 70

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans} Length = 376

 Score = 42.6 bits (99), Expect = 2e-04
 Identities = 26/206 (12%), Positives = 61/206 (29%), Gaps = 37/206 (17%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQV--IQNIRTETRAQIRILKDEHLPLCALSFDELLQVA 196
           T +T+ M   +     +    G    + +I  ET   I++            F + + + 
Sbjct: 28  TRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTIT 87

Query: 197 GEPAVVRKA----------------------LVQIASRLHENPSRSQHLLLSSS--SNIY 232
           G    V +A                      L ++ + + +NP ++  +    +   N  
Sbjct: 88  GYFGDVDRARMLMRRNCHFTVFMALSKMKMPLHELQAHVRQNPIQNVEMSFVDAPEKNGI 147

Query: 233 QSSGVYLSAPLVGSYG---------NYSARRDEASAREFSLRLVCPAGNIGGVIGKGGG- 282
            ++ + ++A     +              R   A    F+L        +  V+G     
Sbjct: 148 VTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYVDQVLGSSSTA 207

Query: 283 -IIKQIRQESGASIKVDSSGAEGDDC 307
            ++  I +E+   I         +  
Sbjct: 208 QLMPVIERETTTIISYPCYNNRNETR 233

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 42.9 bits (102), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 6/40 (15%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           I  VIG GG +I++I   +GA + ++      DD ++ +S
Sbjct: 581 IREVIGSGGKVIREIVATTGAKVDIN------DDGVVKVS 614

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 42.9 bits (102), Expect = 3e-04
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
           + +P D+I  VIG GG+VI+ I   T A++ I
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDI 605

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.5 bits (101), Expect = 3e-04
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
           + +  D+I  VIGKGG VI+ +  ET   I I
Sbjct: 564 IKINPDKIKDVIGKGGSVIRALTEETGTTIEI 595

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 42.1 bits (100), Expect = 4e-04
 Identities = 14/40 (35%), Positives = 25/40 (62%), Gaps = 6/40 (15%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           I  VIGKGG +I+ + +E+G +I+++      DD  + I+
Sbjct: 571 IKDVIGKGGSVIRALTEETGTTIEIE------DDGTVKIA 604

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 42.2 bits (100), Expect = 4e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 6/40 (15%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           IG VIG    +I QI++++GA I ++      DD  I+I 
Sbjct: 609 IGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIG 642

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 41.4 bits (98), Expect = 6e-04
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
           + +P D+IG VIG   Q+I  I+ +T A+I I
Sbjct: 602 VKIPVDKIGEVIGPKRQMINQIQEDTGAEITI 633

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 41.7 bits (99), Expect = 5e-04
 Identities = 8/32 (25%), Positives = 15/32 (46%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176
           + VP  +    +G GG  ++ ++ ET   I  
Sbjct: 571 VQVPLSKRAKFVGPGGYNLKKLQAETGVTISQ 602

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 41.4 bits (98), Expect = 6e-04
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 6/40 (15%)

Query: 273 IGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
               +G GG  +K+++ E+G +I         D+    + 
Sbjct: 578 RAKFVGPGGYNLKKLQAETGVTISQV------DEETFSVF 611

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	512
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.93
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.92
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.92
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.92
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.92
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.91
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.9
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.87
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.84
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.74
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.73
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.65
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.63
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.55
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.53
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.53
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.51
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.51
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.5
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.5
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.48
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.48
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.48
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.47
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.46
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.45
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.45
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.45
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.45
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.44
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.43
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.43
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.42
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.41
1we8_A	104	Tudor and KH domain containing protein; structural	99.4
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.39
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.38
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.38
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.38
1we8_A	104	Tudor and KH domain containing protein; structural	99.36
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.36
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.36
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.35
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.32
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.31
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.3
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.29
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.29
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.26
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.25
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.21
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.12
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.09
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.06
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.02
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.83
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.73
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.61
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.59
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.5
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.31
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.14
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.04
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.97
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.75
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.59
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.56
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.46
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.34
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.16
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.74
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.84
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.72
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.7
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.37
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.24
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.05
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.98
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	93.89
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	92.94
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.18

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.93  E-value=1.2e-26  Score=214.07  Aligned_cols=161  Identities=27%  Similarity=0.438  Sum_probs=130.4

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCC---CCCCCccEEEEEcCCCCcccccCCcccCcHHHHHH
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL  117 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~---~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~  117 (512)
                      +..++++|+||.+++|.||||+|++|++|+++|+|+|+|++.   .+++.+|+|+|+|+.++             +.+|.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~-------------v~~A~   69 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEA-------------LNAVH   69 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHH-------------HHHHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHH-------------HHHHH
Confidence            467999999999999999999999999999999999999864   46889999999998766             45666


Q ss_pred             HHHHHHHhhhcccCC-----------cccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCccc
Q 010374          118 FRVHDRIVAEDSLAD-----------DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA  186 (512)
Q Consensus       118 ~~i~~~i~~~~~~~~-----------~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~  186 (512)
                      .+|.+.+........           .........+++|+||.+++|+||||+|++|++|+++|||+|+|.++..   |.
T Consensus        70 ~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~---~~  146 (178)
T 2anr_A           70 GFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD---GI  146 (178)
T ss_dssp             HHHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC------
T ss_pred             HHHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCC---CC
Confidence            666665543211000           0001223578999999999999999999999999999999999987633   33


Q ss_pred             CCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          187 LSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       187 ~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                      .+.++.|+|+|++++|.+|+.+|.++|.++|
T Consensus       147 ~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          147 NLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             -CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            4678999999999999999999999999875

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.93  E-value=3e-26  Score=208.39  Aligned_cols=155  Identities=25%  Similarity=0.381  Sum_probs=131.2

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCC-CCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET-VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      +-+++|+||.+++|.||||+|++|++|+++|||+|+|++. .+++.+|+|+|+|++++             +.+|..+|+
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~-------------v~~A~~~I~   68 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA-------------QFKAQGRIY   68 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH-------------HHHHHHHHH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH-------------HHHHHHHHH
Confidence            4589999999999999999999999999999999999975 67899999999998766             677888888


Q ss_pred             HHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHH
Q 010374          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV  201 (512)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~  201 (512)
                      +.+.+.....   ......++++|+||.+++|+||||+|++|++|+++|||+|.|.++ ..|.  ...++.|+|+|++++
T Consensus        69 ~~~~e~~~~~---~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~-~~~~--~~~~~~v~I~G~~~~  142 (163)
T 3krm_A           69 GKLKEENFFG---PKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD-QTPD--ENDQVIVKIIGHFYA  142 (163)
T ss_dssp             HHHHHTTSSC---SSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTT-CCCC--TTSEEEEEEEECHHH
T ss_pred             HHHhcccccc---cccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCC-CCCC--CCCceEEEEEeCHHH
Confidence            7776543221   123346788999999999999999999999999999999999765 4454  134458999999999


Q ss_pred             HHHHHHHHHHHHhcC
Q 010374          202 VRKALVQIASRLHEN  216 (512)
Q Consensus       202 V~~A~~~I~~~l~~~  216 (512)
                      |.+|+.+|.+++.+.
T Consensus       143 v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          143 SQMAQRKIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999999874

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.93  E-value=5.6e-26  Score=205.94  Aligned_cols=155  Identities=35%  Similarity=0.515  Sum_probs=130.0

Q ss_pred             CCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        42 ~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|++.  ++++|+|+|+|+.++             +.+|..+|.
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~-------------v~~A~~~I~   67 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNA-------------IFKAFAMII   67 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHH-------------HHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHH-------------HHHHHHHHH
Confidence            56889999999999999999999999999999999999976  678999999998665             566777777


Q ss_pred             HHHhhhcccCCc--ccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010374          122 DRIVAEDSLADD--EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP  199 (512)
Q Consensus       122 ~~i~~~~~~~~~--~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~  199 (512)
                      +.+.+.....-.  .......++++|+||.+++|+||||+|.+|++|+++|||+|+|.++ .+|.   +.++.|+|+|++
T Consensus        68 ~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~-~~~~---~~~~~v~I~G~~  143 (160)
T 2jzx_A           68 DKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD-MLPN---STERAITIAGIP  143 (160)
T ss_dssp             HHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC-CSTT---CCEEEEEEEECH
T ss_pred             HHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC-CCCC---CCceEEEEEcCH
Confidence            666543221100  0112345899999999999999999999999999999999999765 4454   678999999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 010374          200 AVVRKALVQIASRLHE  215 (512)
Q Consensus       200 ~~V~~A~~~I~~~l~~  215 (512)
                      ++|.+|+.+|.+++.+
T Consensus       144 ~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          144 QSIIECVKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999999876

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.92  E-value=3.9e-25  Score=203.92  Aligned_cols=174  Identities=21%  Similarity=0.384  Sum_probs=134.2

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC-CCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE-HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|+|.++. ..|.   +.+|+|+|+|++++|.+|+.+|.+++.+.
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~---~~er~v~I~G~~~~v~~A~~~I~~~~~~~   79 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPG---TTERVCLIQGTIEALNAVHGFIAEKIREM   79 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTT---SSEEEEEEEECHHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCC---CCCceEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3568999999999999999999999999999999999998753 2343   67899999999999999999999999874


Q ss_pred             CCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEE
Q 010374          217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK  296 (512)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~  296 (512)
                      +....                                    ...  .                               +.
T Consensus        80 ~~~~~------------------------------------~~~--~-------------------------------~~   90 (178)
T 2anr_A           80 PQNVA------------------------------------KTE--P-------------------------------VS   90 (178)
T ss_dssp             CCC-----------------------------------------------------------------------------
T ss_pred             CCccc------------------------------------cCC--c-------------------------------cc
Confidence            22100                                    000  0                               00


Q ss_pred             ecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHh
Q 010374          297 VDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT  376 (512)
Q Consensus       297 v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~T  376 (512)
                      +..+.           .         .                 .......+.+|+||.+++|+||||+|++|++|+++|
T Consensus        91 ~~~~~-----------~---------~-----------------~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~t  133 (178)
T 2anr_A           91 ILQPQ-----------T---------T-----------------VNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQS  133 (178)
T ss_dssp             ----------------------------------------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHS
T ss_pred             ccCCc-----------c---------C-----------------CCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHH
Confidence            00000           0         0                 001123678999999999999999999999999999


Q ss_pred             CCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhch
Q 010374          377 RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (512)
Q Consensus       377 Ga~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~  423 (512)
                      ||+|+|.+....|   ..+++.|+|+|++++|+.|+.+|.++|++++
T Consensus       134 ga~I~i~~~~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          134 GAWVQLSQKPDGI---NLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             SCEEEECCCC-------CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             CCEEEEeCCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            9999997654333   4678999999999999999999999998753

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=99.92  E-value=4e-25  Score=203.09  Aligned_cols=156  Identities=23%  Similarity=0.357  Sum_probs=124.5

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~  122 (512)
                      ..+++|+||.+++|.||||+|++|++|+++|+|+|+|.+..+++.+|+|+|+|++++             +.+|+.+|.+
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~-------------v~~A~~~I~~   68 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR-------------AQHAAEIITD   68 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHH-------------HHHHHHHHHH
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHH-------------HHHHHHHHHH
Confidence            467999999999999999999999999999999999987667888999999999766             4556656655


Q ss_pred             HHhhhcccC-C-------------cc---cCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcc
Q 010374          123 RIVAEDSLA-D-------------DE---FGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLC  185 (512)
Q Consensus       123 ~i~~~~~~~-~-------------~~---~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  185 (512)
                      .+....... .             .+   ......++++|+||.+++|+||||+|++|++|+++|||+|+|.++.  +.|
T Consensus        69 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~  146 (174)
T 1j4w_A           69 LLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPN  146 (174)
T ss_dssp             HHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTT
T ss_pred             HHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCC
Confidence            544321000 0             00   0012246889999999999999999999999999999999998752  345


Q ss_pred             cCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          186 ALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       186 ~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      ..+.++.|+|+|++++|.+|+.+|.++|
T Consensus       147 ~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          147 ADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            5577899999999999999999998764

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=99.92  E-value=1.7e-24  Score=196.85  Aligned_cols=155  Identities=27%  Similarity=0.438  Sum_probs=129.8

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcc
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRS  220 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  220 (512)
                      .+++|+||.+.+|.||||+|++|++|+++|||+|+|.++ ..|   .+.+|+|+|+|+++++.+|+.+|.+++.+...  
T Consensus         3 ~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~-~~~---~~~~r~v~I~G~~e~v~~A~~~I~~~~~e~~~--   76 (163)
T 3krm_A            3 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPP-ETP---DSKVRMVIITGPPEAQFKAQGRIYGKLKEENF--   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCC-SST---TCSEEEEEEEECHHHHHHHHHHHHHHHHHTTS--
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCC-CCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcccc--
Confidence            488999999999999999999999999999999999875 233   37899999999999999999999999876210  


Q ss_pred             ccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCC
Q 010374          221 QHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS  300 (512)
Q Consensus       221 ~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~  300 (512)
                                 +                                   -|.                              
T Consensus        77 -----------~-----------------------------------~~~------------------------------   80 (163)
T 3krm_A           77 -----------F-----------------------------------GPK------------------------------   80 (163)
T ss_dssp             -----------S-----------------------------------CSS------------------------------
T ss_pred             -----------c-----------------------------------ccc------------------------------
Confidence                       0                                   000                              


Q ss_pred             CCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeE
Q 010374          301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI  380 (512)
Q Consensus       301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I  380 (512)
                                                                .....+.+|.||.+++|+||||+|++|++|++.|||+|
T Consensus        81 ------------------------------------------~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I  118 (163)
T 3krm_A           81 ------------------------------------------EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEV  118 (163)
T ss_dssp             ------------------------------------------CCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEE
T ss_pred             ------------------------------------------cCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeE
Confidence                                                      00135678999999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       381 ~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      +|++. ..|.  ..+++.|+|+|++++|+.|+.+|.++|++.
T Consensus       119 ~i~~~-~~~~--~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          119 VVPRD-QTPD--ENDQVIVKIIGHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             ECCTT-CCCC--TTSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             EECCC-CCCC--CCCceEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            99653 3443  344568999999999999999999999874

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.92  E-value=6.3e-25  Score=199.84  Aligned_cols=154  Identities=25%  Similarity=0.377  Sum_probs=125.1

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCC--CCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHH
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET--VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~--~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      ++++|+||.+++|.||||+|++|++|+++|+|+|+|.+.  .+++.+|+|+|+|++++             +..|+..|.
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~-------------v~~A~~~I~   68 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYK-------------VQQACEMVM   68 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHH-------------HHHHHHHHH
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHH-------------HHHHHHHHH
Confidence            689999999999999999999999999999999999754  35678999999998766             566777777


Q ss_pred             HHHhhhccc---CCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC
Q 010374          122 DRIVAEDSL---ADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE  198 (512)
Q Consensus       122 ~~i~~~~~~---~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~  198 (512)
                      +.+.+....   ...+......++++|+||.+++|+||||+|.+|++|+++|||+|.|.+.+  +   .+.++.|+|+|+
T Consensus        69 ~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~--~---~~~~~~v~I~G~  143 (164)
T 2jvz_A           69 DILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGP  143 (164)
T ss_dssp             HHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCC--T---TSSEEEEEEESC
T ss_pred             HHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCC--C---CCCcEEEEEEcC
Confidence            665432210   00011111235688999999999999999999999999999999998753  2   256899999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010374          199 PAVVRKALVQIASRLHE  215 (512)
Q Consensus       199 ~~~V~~A~~~I~~~l~~  215 (512)
                      +++|.+|+.+|.+++.+
T Consensus       144 ~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          144 PDRCEHAARIINDLLQS  160 (164)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999998875

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=99.91  E-value=6.8e-24  Score=193.01  Aligned_cols=160  Identities=23%  Similarity=0.392  Sum_probs=128.4

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcc
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRS  220 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  220 (512)
                      ++.+|+||.+.+|.||||+|++|++|+++|||+|+|.++...+   ...+|.|+|+|++++|.+|+.+|.+++.+.... 
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~ii~e~~~~-   77 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRERDQG-   77 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSS---SSSCEEEEEEECHHHHHHHHHHHHHHTTCSSSC-
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhccCC-
Confidence            5789999999999999999999999999999999998763222   367899999999999999999999988763110 


Q ss_pred             ccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCC
Q 010374          221 QHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS  300 (512)
Q Consensus       221 ~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~  300 (512)
                                .|.                                   |..                  .++.       
T Consensus        78 ----------~~~-----------------------------------~~~------------------~~~~-------   87 (164)
T 2jvz_A           78 ----------GFG-----------------------------------DRN------------------EYGS-------   87 (164)
T ss_dssp             ----------CCS-----------------------------------SCS------------------SCTT-------
T ss_pred             ----------CCC-----------------------------------Ccc------------------ccCC-------
Confidence                      000                                   000                  0000       


Q ss_pred             CCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeE
Q 010374          301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI  380 (512)
Q Consensus       301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I  380 (512)
                                                                 ....+.+|.||.+++|+||||+|++|++|+++|||+|
T Consensus        88 -------------------------------------------~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I  124 (164)
T 2jvz_A           88 -------------------------------------------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRI  124 (164)
T ss_dssp             -------------------------------------------SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEE
T ss_pred             -------------------------------------------CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeE
Confidence                                                       0013457889999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       381 ~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      +|.+.+  +   .+.++.|+|+|++++|+.|+.+|.++|++.
T Consensus       125 ~i~~~~--~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~  161 (164)
T 2jvz_A          125 QFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL  161 (164)
T ss_dssp             EECCCC--T---TSSEEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             EEeCCC--C---CCCcEEEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            997542  2   356799999999999999999999998763

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=99.90  E-value=9.2e-24  Score=193.99  Aligned_cols=173  Identities=20%  Similarity=0.333  Sum_probs=127.9

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCc
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSR  219 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~  219 (512)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+.+  +   ...+|+|+|+|++++|.+|+.+|.+++.+....
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~--~---~~~~r~v~I~G~~~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD--G---TTPERIAQITGPPDRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCT--T---SCSEEEEEEEECHHHHHHHHHHHHHHHHHHC--
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCC--C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhcccC
Confidence            35789999999999999999999999999999999998642  2   267899999999999999999999999873210


Q ss_pred             cccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEecC
Q 010374          220 SQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDS  299 (512)
Q Consensus       220 ~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~  299 (512)
                                 .+..                  +              -|..   .-.++       ...          
T Consensus        77 -----------~~~~------------------~--------------~p~~---~~~~~-------~~~----------   93 (174)
T 1j4w_A           77 -----------NPGG------------------P--------------GPGG---RGRGR-------GQG----------   93 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             -----------CCCC------------------C--------------CCCC---CCCCC-------CCC----------
Confidence                       0000                  0              0000   00000       000          


Q ss_pred             CCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCe
Q 010374          300 SGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS  379 (512)
Q Consensus       300 ~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~  379 (512)
                                      .+..                     .......+.+|.||.+++|+||||+|++|++|+++|||+
T Consensus        94 ----------------~~~~---------------------~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~  136 (174)
T 1j4w_A           94 ----------------NWNM---------------------GPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGAR  136 (174)
T ss_dssp             -----------------------------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCE
T ss_pred             ----------------cccc---------------------CCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCE
Confidence                            0000                     000123678999999999999999999999999999999


Q ss_pred             EEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          380 IRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       380 I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      |+|.+.  .+++.+++++.|+|+|++++|+.|+.+|.++|
T Consensus       137 I~i~~~--~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          137 IELQRN--PPPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEECC--CTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEECCC--CCCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            999764  23344577899999999999999999998864

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=99.90  E-value=5.4e-24  Score=192.83  Aligned_cols=157  Identities=27%  Similarity=0.520  Sum_probs=130.2

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS  218 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~  218 (512)
                      .+++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.+       ..+|.|+|+|++++|.+|+.+|.+++.+...
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~~-------~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~~   75 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTNAIFKAFAMIIDKLEEDIS   75 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECCT-------TTEEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCCC-------CCceEEEEEeCHHHHHHHHHHHHHHHHhhcc
Confidence            467899999999999999999999999999999999998651       4689999999999999999999998876210


Q ss_pred             ccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEEec
Q 010374          219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD  298 (512)
Q Consensus       219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~  298 (512)
                      .                                         .      .+.           +                
T Consensus        76 ~-----------------------------------------~------~~~-----------~----------------   81 (160)
T 2jzx_A           76 S-----------------------------------------S------MTN-----------S----------------   81 (160)
T ss_dssp             S-----------------------------------------C------CCS-----------S----------------
T ss_pred             c-----------------------------------------c------CCC-----------C----------------
Confidence            0                                         0      000           0                


Q ss_pred             CCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCC
Q 010374          299 SSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA  378 (512)
Q Consensus       299 ~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa  378 (512)
                        .           .                            ......+.+|.||.+++|+||||+|++|++|+++|||
T Consensus        82 --~-----------~----------------------------~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga  120 (160)
T 2jzx_A           82 --T-----------A----------------------------ASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGA  120 (160)
T ss_dssp             --S-----------C----------------------------CCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSS
T ss_pred             --c-----------c----------------------------CCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCC
Confidence              0           0                            0012367899999999999999999999999999999


Q ss_pred             eEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          379 SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       379 ~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      +|+|.+. ..|   .++++.|+|+|++++|+.|+.+|.+.|.+
T Consensus       121 ~I~i~~~-~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          121 QVQVAGD-MLP---NSTERAITIAGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EECCCCC-CST---TCCEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEECCC-CCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhc
Confidence            9999653 344   46789999999999999999999998876

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.87  E-value=9.6e-23  Score=204.45  Aligned_cols=231  Identities=13%  Similarity=0.120  Sum_probs=156.6

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCC--hhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGG--QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      .....+|+++.||..++++||||+|  ++|++|+++|||+|+|++.+.-..........|+|+|.+++|++|+.+|.+++
T Consensus        25 ~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~  104 (376)
T 3n89_A           25 INPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC  104 (376)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSC
T ss_pred             ecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcC
Confidence            3467899999999999999999999  99999999999999998763000011134568999999999999999887733


Q ss_pred             hcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCC
Q 010374          214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGA  293 (512)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga  293 (512)
                      .                                               +++.+.+|...+..  ......|.+ ++.+++
T Consensus       105 P-----------------------------------------------l~i~~elp~~~i~~--~~l~~~I~q-q~~y~V  134 (376)
T 3n89_A          105 H-----------------------------------------------FTVFMALSKMKMPL--HELQAHVRQ-NPIQNV  134 (376)
T ss_dssp             E-----------------------------------------------EEEEEECTTCSSCH--HHHHHHHHH-CCCTTC
T ss_pred             C-----------------------------------------------ceEEEEccccccCc--chhhhhhcc-ceeCce
Confidence            1                                               23444455432221  111223444 567999


Q ss_pred             eEEecCCCCCC--CCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCc--hhH
Q 010374          294 SIKVDSSGAEG--DDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGG--AII  369 (512)
Q Consensus       294 ~I~v~~~~~~~--~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG--~~I  369 (512)
                      +|.|+......  ....|+|.|.+.-  ...+.+|...+...+.+.  .......++..|.|+..+|..|||++|  ..|
T Consensus       135 ~I~Fp~~~~~~~~~sd~V~IrG~~~n--v~~akeA~~~Ll~~l~~~--e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~I  210 (376)
T 3n89_A          135 EMSFVDAPEKNGIVTTYLRITAREKN--QHELIEAAKRLNEILFRE--SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLM  210 (376)
T ss_dssp             EEEEEEEC-----CEEEEEEEEEGGG--HHHHHHHHHHHHHHHCC----CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHH
T ss_pred             EEEeCCcccccCCCCCEEEEEcChhh--HHHHHHHHHHHHHHHHhh--hcccccceEEEEEeCHHHHHHhhcCCCcchHH
Confidence            99997653221  3567888886410  012334444443333221  111234689999999999999999999  567


Q ss_pred             HHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          370 SEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       370 keI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ++|+++|||+|.++..++ +.....+...|+|+|++++|..|..+|+++|=-
T Consensus       211 kkIr~eTGv~I~FP~~~d-~~d~~~~~~~ItItGs~e~V~~Ark~I~~lLPv  261 (376)
T 3n89_A          211 PVIERETTTIISYPCYNN-RNETRGNIYEIKVVGNIDNVLKARRYIMDLLPI  261 (376)
T ss_dssp             HHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHhhCCEEECCCCCC-cccccCCceEEEEEeCHHHHHHHHHHHHhhCCE
Confidence            999999999999975432 111112456899999999999999999988754

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.84  E-value=6.5e-21  Score=191.21  Aligned_cols=287  Identities=11%  Similarity=0.055  Sum_probs=179.6

Q ss_pred             CCCCCeEEEEEecCCceeeeccCCc--hHHHHHHHhhCCeEEecCCC-----CCCCccEEEEEcCCCCcccccCCcccCc
Q 010374           39 IGSEDTVYRYLCPLRKIGSIIGKGG--EIVKQLRSETKSNIRISETV-----PGCDERIVTIYSSSEGTNLFEDSGEFVS  111 (512)
Q Consensus        39 ~~~~~~~~rilvp~~~~g~IIGk~G--~~I~~I~~~tga~I~i~~~~-----~~~~ervv~I~G~~e~~~~~~~~~~~~~  111 (512)
                      .....+++++-||..+|++||||+|  ++|++|+++|+|+|+|++..     +......|+|+|.+++|           
T Consensus        25 ~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enV-----------   93 (376)
T 3n89_A           25 INPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDV-----------   93 (376)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHH-----------
T ss_pred             ecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHH-----------
Confidence            4467899999999999999999999  99999999999999999764     12345789999998883           


Q ss_pred             HHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCc
Q 010374          112 PAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDE  191 (512)
Q Consensus       112 ~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr  191 (512)
                        .+|..+|.+.               ..+++.+-+|...+..  ..-...|.+ ++..+++|.|.......   .....
T Consensus        94 --E~AR~~I~~l---------------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~---~~~sd  150 (376)
T 3n89_A           94 --DRARMLMRRN---------------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKN---GIVTT  150 (376)
T ss_dssp             --HHHHHHHHHS---------------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC--------CEE
T ss_pred             --HHHHHHHHhc---------------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccccc---CCCCC
Confidence              4555555442               1335556666543322  111234554 67899999997652211   11244


Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCC
Q 010374          192 LLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAG  271 (512)
Q Consensus       192 ~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~  271 (512)
                      .|+|+|...+|.+|.+++..++.......                                   ......+++.+.|+..
T Consensus       151 ~V~IrG~~~nv~~akeA~~~Ll~~l~~~e-----------------------------------~~~~~~~s~~v~V~~~  195 (376)
T 3n89_A          151 YLRITAREKNQHELIEAAKRLNEILFRES-----------------------------------PAPENNFTLHFTLSTY  195 (376)
T ss_dssp             EEEEEEEGGGHHHHHHHHHHHHHHHCC-------------------------------------CCCSSCEEEEEEEEGG
T ss_pred             EEEEEcChhhHHHHHHHHHHHHHHHHhhh-----------------------------------cccccceEEEEEeCHH
Confidence            79999999777666555555443311100                                   0123457889999999


Q ss_pred             CCcccccCCCccc--cchhhhcCCeEEecCCCCC----CCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCc
Q 010374          272 NIGGVIGKGGGII--KQIRQESGASIKVDSSGAE----GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDP  345 (512)
Q Consensus       272 ~vg~IIGk~G~~I--k~I~~~tga~I~v~~~~~~----~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  345 (512)
                      +|..|||++|.++  ++|+++|||+|.||+..+.    .....|+|+|.+      ..+++|.+....+          -
T Consensus       196 ~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItItGs~------e~V~~Ark~I~~l----------L  259 (376)
T 3n89_A          196 YVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNI------DNVLKARRYIMDL----------L  259 (376)
T ss_dssp             GHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEEESCH------HHHHHHHHHHHHT----------S
T ss_pred             HHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEEEeCH------HHHHHHHHHHHhh----------C
Confidence            9999999999554  9999999999999975442    234578899865      3444444332222          2


Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCC---ceEEEEEcCHHHHHH
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYED---EEMVQITGSLDVASS  410 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~---~r~V~I~G~~~~v~~  410 (512)
                      .+...|.++.+-.-.-.-.--..|..+.++.++.|.|.++...|..--++   -..|.|+.-.-++..
T Consensus       260 Pv~l~Fd~~~~d~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~s~e~n~~~  327 (376)
T 3n89_A          260 PISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVPLNCASLRSKEFNIKK  327 (376)
T ss_dssp             EEEEEEEEEGGGBC--------CBEEEECTTSCEEEEEEEEECCSSSSCCCEEEEEEEEEEEGGGHHH
T ss_pred             CEEEEEecCCcccccccccchhHHHHHHHhcCeEEEEeecCCCchhhcccccccceEEEEEEeccHHH
Confidence            36666766654333323333334445668889999997753323100011   135778875555444

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.74  E-value=3.3e-18  Score=151.24  Aligned_cols=139  Identities=19%  Similarity=0.242  Sum_probs=100.6

Q ss_pred             cceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccC
Q 010374          261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTER  340 (512)
Q Consensus       261 ~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~  340 (512)
                      .++.++.||.+.+|.+||++|++|++|++++|+.|...+..   .+.++......      ..+..+..+..        
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~~---~~~~i~~~~~p------~~v~~~~~~l~--------   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDED---TCTFHIYGEDQ------DAVKKARSFLE--------   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEETT---TTEEEEEESSH------HHHHHHHHHHC--------
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCCC---chheeeccCCH------HHHHHHHHhhh--------
Confidence            46789999999999999999999999999999444333322   33333333211      23333322211        


Q ss_pred             CCCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCC-eEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          341 ESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA-SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       341 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa-~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                           ..+.++.||.+++|++|||+|++|++|++.||| +|+|.+.++......+..+.|+|+|++++|+.|+.+|.++|
T Consensus        66 -----~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vtI~G~~~~v~~Ak~li~~~l  140 (144)
T 2qnd_A           66 -----FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHL  140 (144)
T ss_dssp             -----EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEEEEEEHHHHHHHHHHHHHHH
T ss_pred             -----cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEEEEeCHHHHHHHHHHHHHHH
Confidence                 124889999999999999999999999999997 99998754321111112246899999999999999999998


Q ss_pred             hh
Q 010374          420 RA  421 (512)
Q Consensus       420 ~~  421 (512)
                      ..
T Consensus       141 ~~  142 (144)
T 2qnd_A          141 NY  142 (144)
T ss_dssp             HT
T ss_pred             Hh
Confidence            64

>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains, type I domains, fragIle X mental retardation protein, RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A

Probab=99.73  E-value=7.8e-18  Score=148.85  Aligned_cols=136  Identities=19%  Similarity=0.258  Sum_probs=100.3

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEc-CCCCcccccCCcccCcHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS-SSEGTNLFEDSGEFVSPAQDALFRVH  121 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G-~~e~~~~~~~~~~~~~~a~~a~~~i~  121 (512)
                      .++.+|+||.+.+|++||++|++|++|+++++  |++.+.. ..+++ +++.+ +++.             +.++. .++
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~-~i~~~~~p~~-------------v~~~~-~~l   64 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCT-FHIYGEDQDA-------------VKKAR-SFL   64 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTE-EEEEESSHHH-------------HHHHH-HHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchh-eeeccCCHHH-------------HHHHH-Hhh
Confidence            56789999999999999999999999999999  5443221 12334 44444 3332             12221 111


Q ss_pred             HHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCc-eEEEeecCCCCcccCCCCc--eEEEecC
Q 010374          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRA-QIRILKDEHLPLCALSFDE--LLQVAGE  198 (512)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga-~I~i~~~~~~p~~~~~~dr--~v~I~G~  198 (512)
                      .      +           .++++.||.+++|++|||+|++|+.|++.||| +|+|.++++...  ...++  .|+|+|+
T Consensus        65 ~------~-----------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~  125 (144)
T 2qnd_A           65 E------F-----------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGT  125 (144)
T ss_dssp             C------E-----------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEE
T ss_pred             h------c-----------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeC
Confidence            1      0           13789999999999999999999999999997 999998643211  12344  4899999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010374          199 PAVVRKALVQIASRLHE  215 (512)
Q Consensus       199 ~~~V~~A~~~I~~~l~~  215 (512)
                      +++|++|..+|.++|.+
T Consensus       126 ~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          126 KDSIANATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999999865

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.65  E-value=1.5e-16  Score=149.51  Aligned_cols=150  Identities=19%  Similarity=0.141  Sum_probs=105.5

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~  122 (512)
                      .-..++.||.+.++.|||++|++|++|+++|||+|+|+..     ++.|+|+++...-        ....++.|...|.+
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~--------d~~~i~kA~~~I~~   99 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETE--------DPLAVWKARDIVLA   99 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCC--------SHHHHHHHHHHHHH
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCC--------CHHHHHHHHHHHHH
Confidence            3456999999999999999999999999999999999743     6779999864210        01125566666555


Q ss_pred             HHhhhcccCCcccCCCcceEEEEEee-----C------CceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCc
Q 010374          123 RIVAEDSLADDEFGELTLITVRMLVP-----A------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDE  191 (512)
Q Consensus       123 ~i~~~~~~~~~~~~~~~~~~~~llVP-----~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr  191 (512)
                      .+.....+....-.........+-++     .      ..+|+||||+|.+|+.|++.|||+|.|..            +
T Consensus       100 i~rg~~~e~g~~ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~------------~  167 (219)
T 2e3u_A          100 IGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG------------K  167 (219)
T ss_dssp             HHTTCCHHHHGGGGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET------------T
T ss_pred             HhccCCccccceeccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC------------e
Confidence            43110000000000001111112222     1      26899999999999999999999999953            4


Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          192 LLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       192 ~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                      .|.|.|+.++|+.|..+|.+++...+
T Consensus       168 ~v~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          168 TVAIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             EEEEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             EEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence            69999999999999999999996643

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.63  E-value=1.1e-15  Score=143.53  Aligned_cols=154  Identities=21%  Similarity=0.222  Sum_probs=109.1

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-----HHHHHHHHHHHHHHHh
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-----PAVVRKALVQIASRLH  214 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-----~~~V~~A~~~I~~~l~  214 (512)
                      ....++.||.+.++.|||++|++|+.|+++|||+|.|..+          ++.|+|.++     ++++.+|..+|..+..
T Consensus        33 P~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~----------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~r  102 (219)
T 2e3u_A           33 KQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE----------TGEVWITSTKETEDPLAVWKARDIVLAIGR  102 (219)
T ss_dssp             CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT----------TCEEEEEECTTCCSHHHHHHHHHHHHHHHT
T ss_pred             CEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC----------CCEEEEecCCCCCCHHHHHHHHHHHHHHhc
Confidence            3467899999999999999999999999999999999633          456888875     6999999999999875


Q ss_pred             cCCCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCe
Q 010374          215 ENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGAS  294 (512)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~  294 (512)
                      .........++                                 .++..+.                            .
T Consensus       103 g~~~e~g~~ll---------------------------------~dd~~~e----------------------------~  121 (219)
T 2e3u_A          103 GFSPERAFRLL---------------------------------NEGEYLE----------------------------I  121 (219)
T ss_dssp             TCCHHHHGGGG---------------------------------STTCEEE----------------------------E
T ss_pred             cCCccccceec---------------------------------cCCccce----------------------------e
Confidence            31100000000                                 0000000                            0


Q ss_pred             EEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHH
Q 010374          295 IKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRS  374 (512)
Q Consensus       295 I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~  374 (512)
                      +.+..-                                             .+...-..+...+|+||||+|++|+.|++
T Consensus       122 i~i~~~---------------------------------------------~v~~~~~~~~r~~GriIGk~G~tik~ie~  156 (219)
T 2e3u_A          122 INLTDI---------------------------------------------IIGNEKNALPRVRGRIIGRKGRTRQIIEE  156 (219)
T ss_dssp             EEGGGC---------------------------------------------C------CHHHHHHHHHCGGGHHHHHHHH
T ss_pred             EEcccc---------------------------------------------cccCCchhhhhhhheeECCCchHHHHHHH
Confidence            000000                                             00000011234789999999999999999


Q ss_pred             HhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          375 ATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       375 ~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .|||+|.|..            +.|+|.|++++++.|..+|+++|..
T Consensus       157 ~Tg~~I~v~~------------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          157 MSGASVSVYG------------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHCCEEEEET------------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             HhCceEEECC------------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            9999999952            3799999999999999999999965

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=5.8e-15  Score=123.52  Aligned_cols=74  Identities=20%  Similarity=0.286  Sum_probs=64.5

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      .+.+|+||.+++|+||||+|++|++|+++|||+|+|.+.. .| ..+.++++|+|+|++++|++|+.+|.++|.+.
T Consensus         7 ~~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~-~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            7 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CCEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             CeEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            3789999999999999999999999999999999997542 22 23457899999999999999999999998663

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.53  E-value=1.4e-14  Score=113.66  Aligned_cols=73  Identities=25%  Similarity=0.357  Sum_probs=63.9

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..+..  .++.++.|+|+|++++|+.|+.+|.++|.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCC--CCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999999999997653322  246789999999999999999999998754

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.53  E-value=9.3e-15  Score=113.53  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=64.2

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ..++.+|+||.+++|+||||+|++|++|+++|||+|+|.+.       +..+|.|+|+|++++|..|+.+|.++|++
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            35789999999999999999999999999999999999653       24689999999999999999999999976

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.51  E-value=3.9e-14  Score=112.73  Aligned_cols=73  Identities=29%  Similarity=0.514  Sum_probs=65.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+++++.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            45889999999999999999999999999999999999642  22   467899999999999999999999999874

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=99.51  E-value=1.2e-14  Score=112.84  Aligned_cols=70  Identities=29%  Similarity=0.571  Sum_probs=65.0

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+++       ..+|+|+|+|++++|.+|+.+|.++|.+
T Consensus         3 ~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~~-------~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecCC-------CCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            457999999999999999999999999999999999998751       4689999999999999999999999986

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.50  E-value=2e-14  Score=112.72  Aligned_cols=73  Identities=34%  Similarity=0.528  Sum_probs=65.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.++|++.
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP--VE---GSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC--CT---TCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC--CC---CCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            35789999999999999999999999999999999999652  22   578999999999999999999999998763

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.50  E-value=2.9e-14  Score=113.52  Aligned_cols=73  Identities=36%  Similarity=0.500  Sum_probs=64.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .   .+++++.|+|+|++++|+.|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--V---EGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--C---TTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--C---CCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            35789999999999999999999999999999999999652  2   2567999999999999999999999998775

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.48  E-value=1.2e-13  Score=126.46  Aligned_cols=151  Identities=19%  Similarity=0.223  Sum_probs=110.2

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----cCHHHHHHHHHHHHHHHhcC
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA-----GEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~-----G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ..+++||...+|.|||++|++++.|+++++++|++...          ++.|+|.     |++.++.+|..+|..+.+..
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~----------~~~V~i~t~~~t~dp~~i~KA~dlI~ai~rgf   74 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   74 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC----------CCeEEEEeCCCCCCHHHHHHHHHHHHHHHcCC
Confidence            46899999999999999999999999999999999643          5678888     99999999999999888753


Q ss_pred             CCccccccccCCCCccCCCCcccCCCCcCCCCCCCcccCccccccceEEEecCCCCCcccccCCCccccchhhhcCCeEE
Q 010374          217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK  296 (512)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~  296 (512)
                      +......+                                 ..+++.+.                               
T Consensus        75 ~~e~A~~L---------------------------------l~Dd~~~e-------------------------------   90 (191)
T 1tua_A           75 PPEKAFRL---------------------------------LEEDQILV-------------------------------   90 (191)
T ss_dssp             CHHHHGGG---------------------------------GSTTEEEE-------------------------------
T ss_pred             CHHHhhhc---------------------------------ccCcceeE-------------------------------
Confidence            21100000                                 00000000                               


Q ss_pred             ecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEEEEecCCceeeeecCCchhHHHHHHHh
Q 010374          297 VDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT  376 (512)
Q Consensus       297 v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~T  376 (512)
                                 ++.+.             .....            . .      ..+..+.|+||||+|.+|+.|+..|
T Consensus        91 -----------~i~i~-------------~~~~~------------~-~------~~~~r~~GrIIGk~G~tik~iE~~T  127 (191)
T 1tua_A           91 -----------VVDLK-------------QVVGD------------S-Q------NHLKRIKGRIIGEGGRARRTIEEMT  127 (191)
T ss_dssp             -----------EEETH-------------HHHTT------------C-H------HHHHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             -----------EEEcc-------------ccccc------------C-c------hhHHHHhhheeCCCccHHHHHHHHH
Confidence                       00000             00000            0 0      0124578999999999999999999


Q ss_pred             CCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          377 RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       377 Ga~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ||+|.|..            ..|.|.|++++++.|...|+.++..
T Consensus       128 g~~I~v~~------------~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          128 DTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             TCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEcC------------CEEEEEeChHHHHHHHHHHHHHHcC
Confidence            99999942            2899999999999999999998864

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.48  E-value=2.7e-14  Score=114.97  Aligned_cols=77  Identities=25%  Similarity=0.318  Sum_probs=67.1

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchhc
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFE  425 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~~  425 (512)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+..  .++.++.|+|+|++++|+.|+.+|.++|.+....
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~   79 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTYEQGV   79 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS--TTSCEEEEEEESSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhccccc
Confidence            5789999999999999999999999999999999997643221  2467899999999999999999999999885543

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=5.4e-14  Score=117.03  Aligned_cols=71  Identities=21%  Similarity=0.351  Sum_probs=63.3

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      .+.+|.||.+++|+||||+|++||+|+++|||+|+|.+++  +   ...+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C---CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            4789999999999999999999999999999999996532  1   356899999999999999999999999874

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.47  E-value=4.3e-14  Score=129.43  Aligned_cols=143  Identities=16%  Similarity=0.140  Sum_probs=102.9

Q ss_pred             EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHh
Q 010374           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV  125 (512)
Q Consensus        46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~  125 (512)
                      ++++||...+|.|||++|++++.|+++++++|.++..     ++.|+|+.+.+...        ...++.|...|.+...
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~~-----~~~V~i~t~~~t~d--------p~~i~KA~dlI~ai~r   72 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAEGIP--------PVNLMKAAEVVKAISL   72 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESSTTSC--------HHHHHHHHHHHHHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEcC-----CCeEEEEeCCCCCC--------HHHHHHHHHHHHHHHc
Confidence            6899999999999999999999999999999999754     78899985433210        1124455544433222


Q ss_pred             hhcccCCcc-cCCCcceEEE-EEee----------CCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010374          126 AEDSLADDE-FGELTLITVR-MLVP----------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (512)
Q Consensus       126 ~~~~~~~~~-~~~~~~~~~~-llVP----------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v  193 (512)
                        .+..++. .-..+.+.+. +-++          ...+|+||||+|.+|+.|+..|||+|.|..            +.|
T Consensus        73 --gf~~e~A~~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~------------~~v  138 (191)
T 1tua_A           73 --GFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE------------YEV  138 (191)
T ss_dssp             --TCCHHHHGGGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEE
T ss_pred             --CCCHHHhhhcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC------------CEE
Confidence              1111000 0001122233 3344          236899999999999999999999999953            369


Q ss_pred             EEecCHHHHHHHHHHHHHHHhc
Q 010374          194 QVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .|.|+.++++.|...|.+++..
T Consensus       139 ~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          139 AIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             EEEEEHHHHHHHHHHHHHHHTT
T ss_pred             EEEeChHHHHHHHHHHHHHHcC
Confidence            9999999999999999999965

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.46  E-value=6e-14  Score=113.41  Aligned_cols=75  Identities=29%  Similarity=0.530  Sum_probs=66.9

Q ss_pred             CCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       343 ~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+++.+.
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~--~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--CS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--CC---CCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            3457899999999999999999999999999999999999642  22   467899999999999999999999999874

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=109.38  Aligned_cols=74  Identities=19%  Similarity=0.333  Sum_probs=64.6

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|.|.+....+   ...+|.|+|+|++++++.|+.+|.+++++
T Consensus        12 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~---~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           12 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS---TTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            346789999999999999999999999999999999997643222   46789999999999999999999998753

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.45  E-value=8.5e-14  Score=109.15  Aligned_cols=72  Identities=31%  Similarity=0.499  Sum_probs=64.1

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .+++|+||.+.+|+||||+|++|++|+++|||+|+|.++++ .|   .+.++.|+|+|++++|.+|+.+|.+++.+
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST---TCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCC---CCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            58899999999999999999999999999999999987632 23   36789999999999999999999998764

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=99.45  E-value=7.2e-14  Score=111.19  Aligned_cols=74  Identities=30%  Similarity=0.446  Sum_probs=65.5

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ...++++|+||.+++|+||||+|++|++|+++|||+|+|.+.     +..+.++.|+|+|++++|.+|+.+|.+++.++
T Consensus         3 g~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~-----~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            3 GSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TTCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CCcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC-----CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            356789999999999999999999999999999999999864     22367999999999999999999999999875

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.45  E-value=1.2e-13  Score=112.39  Aligned_cols=73  Identities=26%  Similarity=0.388  Sum_probs=65.6

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..  +   +..++.|+|+|++++|+.|+.+|.++|++.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~--~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           13 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            457899999999999999999999999999999999997532  2   457899999999999999999999999874

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.44  E-value=6.6e-14  Score=109.74  Aligned_cols=73  Identities=32%  Similarity=0.490  Sum_probs=66.0

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|.+.     +..+.++.|+|+|++++|.+|+.+|.+++.++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~-----~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~E   75 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-----VEGSTDRQVTITGSAASISLAQYLINVRLSSE   75 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC-----CTTCSEEEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC-----CCCCCeEEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            45789999999999999999999999999999999999863     22477999999999999999999999998763

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=99.43  E-value=2e-13  Score=108.60  Aligned_cols=73  Identities=32%  Similarity=0.524  Sum_probs=63.7

Q ss_pred             CCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHH
Q 010374           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFR  119 (512)
Q Consensus        40 ~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~  119 (512)
                      +...++++|+||.+++|.||||+|++|++|+++|+|+|+|++..++..+|+|+|+|++++             +..|..+
T Consensus         3 ~g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G~~~~-------------v~~A~~~   69 (82)
T 1zzk_A            3 MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ-------------IQNAQYL   69 (82)
T ss_dssp             CCCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTSCSSEEEEEEEECHHH-------------HHHHHHH
T ss_pred             CCCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCCCCCCceEEEEEeCHHH-------------HHHHHHH
Confidence            456789999999999999999999999999999999999998878889999999998766             4666666


Q ss_pred             HHHHHh
Q 010374          120 VHDRIV  125 (512)
Q Consensus       120 i~~~i~  125 (512)
                      |.+.+.
T Consensus        70 I~~~i~   75 (82)
T 1zzk_A           70 LQNSVK   75 (82)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666554

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=7.6e-14  Score=110.71  Aligned_cols=69  Identities=20%  Similarity=0.315  Sum_probs=61.7

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|+|++.        ++++.|+|+|++++|+.|+.+|.+.+..
T Consensus         8 ~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~--------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            8 GQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS--------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC--------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            45788999999999999999999999999999999999643        2357899999999999999999997654

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.42  E-value=1.5e-13  Score=112.20  Aligned_cols=74  Identities=19%  Similarity=0.354  Sum_probs=65.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ..++.+|+||.+++|+||||+|++|++|+++|||+|+|.+... +.  ..++|.|+|+|++++|+.|+.+|.++|++
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   86 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QN--TGADKPLRITGDPYKVQQAKEMVLELIRD   86 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCC-CS--SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCC-CC--CCCceEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            5688999999999999999999999999999999999975432 11  34789999999999999999999999976

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.41  E-value=4e-13  Score=107.60  Aligned_cols=75  Identities=25%  Similarity=0.476  Sum_probs=66.0

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ....+.+|.||.+.+|+||||+|++|++|+++|||+|.|.++...+   .+.+|.|+|+|++++|.+|+.+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~---~~~er~v~I~G~~~~v~~A~~~I~~i~~e   85 (85)
T 2opv_A           11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQN---TNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSS---TTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            3456889999999999999999999999999999999998763222   36799999999999999999999998864

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.40  E-value=6.2e-13  Score=110.66  Aligned_cols=77  Identities=19%  Similarity=0.322  Sum_probs=66.6

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~  424 (512)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|.+... +  ...+++.|+|+|++++|+.|+.+|.++|.+...
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~-~--~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~~   89 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE-G--TLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE   89 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC-C--SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC-C--CCCCcceEEEEcCHHHHHHHHHHHHHHHhhChH
Confidence            4578999999999999999999999999999999999975422 1  124689999999999999999999999977543

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.39  E-value=2.1e-13  Score=110.22  Aligned_cols=74  Identities=31%  Similarity=0.504  Sum_probs=66.8

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ....++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.  .|   .+.++.|+|+|++++|.+|+.+|.+++.+
T Consensus        10 ~~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~--~~---~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CCCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSC--CS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCC--CC---CCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            4567899999999999999999999999999999999999753  23   36789999999999999999999999987

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.38  E-value=2.5e-13  Score=110.87  Aligned_cols=77  Identities=22%  Similarity=0.436  Sum_probs=68.0

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ....++++|+||.+.+|+||||+|++|++|+++|||+|+|.++....   ...+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        11 ~p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            34678999999999999999999999999999999999998763221   257899999999999999999999999773

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.4e-13  Score=109.22  Aligned_cols=70  Identities=24%  Similarity=0.341  Sum_probs=63.4

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ...++++|.||.+++|+||||+|++||+|+++|||+|+|++.        ..+++|+|+|++++|++|+.+|.+++..
T Consensus         7 ~~~~~~~i~VP~~~vG~IIGkgG~tIk~Iqe~Tga~I~I~~~--------~~~~~v~ItG~~e~v~~A~~~I~~~i~~   76 (83)
T 2dgr_A            7 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR--------DKEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCS--------SSCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCC--------CCCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            456789999999999999999999999999999999999865        2368899999999999999999998764

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=99.38  E-value=2.4e-13  Score=109.43  Aligned_cols=73  Identities=29%  Similarity=0.488  Sum_probs=65.7

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      .+++|+||.+.+|+||||+|++|++|+++|||+|.|.++++ .|   .+.++.|+|+|++++|.+|+.+|.+++.+.
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~---g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBST---TSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCC---CCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999999987632 33   367899999999999999999999999874

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=99.36  E-value=3.6e-13  Score=112.09  Aligned_cols=86  Identities=24%  Similarity=0.372  Sum_probs=71.9

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (512)
                      ....+++|+||.+.+|+||||+|++|++|+++|||+|+|.+...  .+ .+.++.|+|+|+.++|.+|+.+|.+++.+++
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--GT-LLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--CS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC--CC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            45678999999999999999999999999999999999987532  11 2468999999999999999999999998876


Q ss_pred             Ccccccccc
Q 010374          218 SRSQHLLLS  226 (512)
Q Consensus       218 ~~~~~~~~~  226 (512)
                      ...+++..+
T Consensus        89 ~~~~~~~~~   97 (104)
T 1we8_A           89 ELRKRIAHS   97 (104)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHhccC
Confidence            655444333

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.36  E-value=6.1e-13  Score=111.20  Aligned_cols=73  Identities=23%  Similarity=0.401  Sum_probs=64.8

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      +++|+||.+++|+||||+|++|++|+++|||+|+|.++. .| +....++.|+|+|++++|++|+.+|.+++.+.
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~-~~-~~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~   80 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQL-PP-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCC-CT-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCcc-CC-CCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            789999999999999999999999999999999998762 22 22356899999999999999999999999874

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=99.36  E-value=9.1e-13  Score=107.07  Aligned_cols=72  Identities=25%  Similarity=0.369  Sum_probs=63.1

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHH
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV  120 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i  120 (512)
                      ...++++|+||.+++|.||||+|++|++|+++|+|+|+|.+..++..+|+|+|+|++++             +..|..+|
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G~~e~-------------v~~A~~~I   78 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPES-------------VQSAKRLL   78 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCTTCSEEEEEEEECHHH-------------HHHHHHHH
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCCCCCccEEEEEeCHHH-------------HHHHHHHH
Confidence            46789999999999999999999999999999999999998877888999999999766             46666666


Q ss_pred             HHHHh
Q 010374          121 HDRIV  125 (512)
Q Consensus       121 ~~~i~  125 (512)
                      .+.+.
T Consensus        79 ~~~i~   83 (92)
T 1x4n_A           79 DQIVE   83 (92)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=8.2e-13  Score=109.87  Aligned_cols=71  Identities=23%  Similarity=0.426  Sum_probs=63.7

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      .+++|+||.+++++||||+|++|++|+++|+|+|+|.++.  +   .+.+|.|+|+|++++|++|+.+|.+++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C---CCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3789999999999999999999999999999999998652  2   256899999999999999999999999873

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.32  E-value=1.4e-12  Score=100.54  Aligned_cols=67  Identities=21%  Similarity=0.287  Sum_probs=59.5

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|.|++..       +.++.|+|+|++++++.|+.+|.+.+
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            46889999999999999999999999999999999996532       35679999999999999999988753

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.31  E-value=2.8e-12  Score=104.61  Aligned_cols=74  Identities=15%  Similarity=0.196  Sum_probs=64.9

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhchh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~~  424 (512)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|+++.      +.+++.|+|+|++++|+.|+.+|..++++...
T Consensus        15 ~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g------~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~~   88 (95)
T 2ctm_A           15 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYLA   88 (95)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCC------CCCCcEEEEEcCHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999996432      13467899999999999999999998887543

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.30  E-value=2.3e-12  Score=105.06  Aligned_cols=71  Identities=18%  Similarity=0.325  Sum_probs=63.3

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|.|||++|++|++|+++|||+|+|++.+       +.++.|+|+|++++|+.|+.+|.+++.+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            458999999999999999999999999999999999996431       23568999999999999999999998774

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=6e-12  Score=103.09  Aligned_cols=72  Identities=18%  Similarity=0.271  Sum_probs=63.5

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .++..|.||.++++.|||++|++|++|+++|||+|+|++... |   ...++.|+|+|+++++..|+.+|...+.+
T Consensus        16 ~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999975432 2   23678999999999999999999988876

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=2.6e-12  Score=105.23  Aligned_cols=74  Identities=20%  Similarity=0.234  Sum_probs=65.2

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ...+++.|.||.+.++.||||+|++|++|+++|||+|.|+++.. |   ...++.|+|+|+.++|.+|+.+|..++.+
T Consensus        14 ~~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~---~~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           14 LRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             HTTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ccceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34579999999999999999999999999999999999987632 2   14678999999999999999999998865

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.26  E-value=4.1e-12  Score=103.60  Aligned_cols=73  Identities=21%  Similarity=0.326  Sum_probs=65.0

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ....++.+|.||.+.+|.|||++|.+|++|+++|||+|+|++.+       ..++.|+|+|++++|.+|+.+|.+++.+.
T Consensus        13 l~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           13 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             hCCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            34568999999999999999999999999999999999997642       23578999999999999999999998774

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.25  E-value=5.7e-12  Score=102.73  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=65.1

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ....++..|.||.++++.|||++|++|++|+++|||+|+|+++..      ..++.|+|+|.+++|++|+.+|..++.+
T Consensus        13 l~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   85 (95)
T 2ctm_A           13 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEE   85 (95)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC------CCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            355679999999999999999999999999999999999976521      3467899999999999999999998876

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.25  E-value=3.5e-12  Score=98.28  Aligned_cols=67  Identities=22%  Similarity=0.359  Sum_probs=60.0

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      ..+..|.||.++++.|||++|++|++|+++|||+|.|++++       ..++.|+|+|+.++|.+|+.+|.+++
T Consensus         4 ~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999998762       35679999999999999999998753

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.21  E-value=1.3e-11  Score=102.45  Aligned_cols=71  Identities=21%  Similarity=0.263  Sum_probs=62.7

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhch
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~  423 (512)
                      ..+..|.||.+++|.|||++|++|++|+++|||+|.|++..       +..+.|+|+|++++|+.|+.+|.+++++..
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~e   86 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            47899999999999999999999999999999999996532       234589999999999999999999887744

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.12  E-value=4.2e-11  Score=99.26  Aligned_cols=69  Identities=25%  Similarity=0.374  Sum_probs=62.2

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..+..|.||.+.++.|||++|.+|++|+++|||+|.|+++.       ...+.|+|+|+.++|.+|+.+|..++.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            46889999999999999999999999999999999998652       2345899999999999999999998876

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.09  E-value=1e-10  Score=95.11  Aligned_cols=70  Identities=17%  Similarity=0.223  Sum_probs=62.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHh-CCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSAT-RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~T-Ga~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ..++..|.||.++++.|||++|.+|++|+++| ||+|.|+..       ++..+.|+|.|+.++|+.|+.+|.+++.+
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999999999 999999643       23455899999999999999999998876

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.06  E-value=3.2e-10  Score=93.48  Aligned_cols=67  Identities=16%  Similarity=0.278  Sum_probs=59.7

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      .++.+|.||..+|++|||++|++|++|+++ ++++|.+++          +++.|+|+|+++.|..|..+|...+++.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            378999999999999999999999999997 589999853          2348999999999999999999988764

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.04  E-value=1.5e-10  Score=94.19  Aligned_cols=73  Identities=23%  Similarity=0.301  Sum_probs=65.0

Q ss_pred             CCCcceEEEEEeeCCceeEEecCCChhHHHHHhhc-CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHh
Q 010374          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET-RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLH  214 (512)
Q Consensus       136 ~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~  214 (512)
                      +..+.++..|.||.++++.|||++|.+|++|+++| ||+|.|+++.       +..+.|+|.|+.++|++|+.+|.+++.
T Consensus        12 e~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~iv~   84 (95)
T 2ctj_A           12 DLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAE   84 (95)
T ss_dssp             CCCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             HHhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHh
Confidence            34567789999999999999999999999999999 9999997652       345679999999999999999999987


Q ss_pred             c
Q 010374          215 E  215 (512)
Q Consensus       215 ~  215 (512)
                      +
T Consensus        85 e   85 (95)
T 2ctj_A           85 E   85 (95)
T ss_dssp             H
T ss_pred             h
Confidence            6

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.02  E-value=3.5e-10  Score=93.25  Aligned_cols=65  Identities=20%  Similarity=0.309  Sum_probs=59.5

Q ss_pred             eEEEEEeeCCceeEEecCCChhHHHHHhh-cCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTE-TRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       141 ~~~~llVP~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ++.+|.||..+++.|||++|++|++|+++ ++++|.|++.          ++.|+|+|+++.|.+|..+|..++.+
T Consensus        27 ~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~~----------~~~ItI~G~~~~V~~a~~~I~~~v~e   92 (102)
T 2ctf_A           27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----------EDKITLEGPTEDVSVAQEQIEGMVKD   92 (102)
T ss_dssp             EEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCCC----------CCEEEEECCHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999997 5999998652          46899999999999999999998876

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.83  E-value=2.3e-09  Score=85.55  Aligned_cols=65  Identities=22%  Similarity=0.287  Sum_probs=56.6

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRL  419 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~-I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l  419 (512)
                      ..+...|.||.+++|.|||++|++|++|+++|||+ |.|..          ++..|+|.| +.+++++|+.+|...-
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e----------ddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            45788999999999999999999999999999998 99952          346899999 8999999988875443

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.73  E-value=8.2e-09  Score=82.32  Aligned_cols=65  Identities=23%  Similarity=0.288  Sum_probs=57.2

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCce-EEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHH
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIAS  211 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~  211 (512)
                      ....+...|.||.+.++.|||++|.+|++|+++|||+ |.|..+          +..|+|.| +.+++++|+.+|..
T Consensus        11 ~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~ed----------dG~V~I~g~~~ea~~~A~~~I~~   77 (91)
T 2cpq_A           11 LAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDED----------TGTFRIYGESADAVKKARGFLEF   77 (91)
T ss_dssp             SSCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEETT----------TTEEEEEESSHHHHHHHHHHHSC
T ss_pred             ccCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEcC----------CCEEEEEECCHHHHHHHHHHHHh
Confidence            4456788999999999999999999999999999998 999643          46899999 89999999887754

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.61  E-value=1.2e-07  Score=81.51  Aligned_cols=76  Identities=18%  Similarity=0.332  Sum_probs=61.8

Q ss_pred             eeEEEEEecCC------ceeeeecCCchhHHHHHHHhCCeEEEecCCCC-----------CCCCCCCceEEEEEc-CHHH
Q 010374          346 VITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PKVAYEDEEMVQITG-SLDV  407 (512)
Q Consensus       346 ~~t~~l~VP~~------~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~-----------p~~~~~~~r~V~I~G-~~~~  407 (512)
                      .++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+...           +.....++-.|.|++ +.+.
T Consensus         6 k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~   85 (131)
T 1k1g_A            6 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   85 (131)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             eEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH
Confidence            47889999987      88999999999999999999999999764211           111123466788999 7899


Q ss_pred             HHHHHHHHHHHHhh
Q 010374          408 ASSALSQVTLRLRA  421 (512)
Q Consensus       408 v~~A~~~I~~~l~~  421 (512)
                      ++.|+.+|..+|..
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999966

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.59  E-value=1.8e-07  Score=78.77  Aligned_cols=76  Identities=11%  Similarity=0.074  Sum_probs=58.1

Q ss_pred             eeEEEEEecCC-------ceeeeecCCchhHHHHHHHhCCeEEEecCCC-----CCCCCCCCceEEEEEc-CHHHHHHHH
Q 010374          346 VITTRILVPSA-------QIGCLIGRGGAIISEMRSATRASIRILTNEN-----VPKVAYEDEEMVQITG-SLDVASSAL  412 (512)
Q Consensus       346 ~~t~~l~VP~~-------~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~-----~p~~~~~~~r~V~I~G-~~~~v~~A~  412 (512)
                      ..+.+|.||.+       ++|.|||++|.+||+|+++|||+|.|..+..     ....+..++-.|.|.+ +++++++|+
T Consensus        11 ~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A~   90 (119)
T 2yqr_A           11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAK   90 (119)
T ss_dssp             CEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHHH
T ss_pred             EEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHHH
Confidence            46778888754       7899999999999999999999999964321     0011122344677776 799999999


Q ss_pred             HHHHHHHhh
Q 010374          413 SQVTLRLRA  421 (512)
Q Consensus       413 ~~I~~~l~~  421 (512)
                      .+|.++|..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999998875

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=98.50  E-value=2.6e-07  Score=79.39  Aligned_cols=77  Identities=26%  Similarity=0.322  Sum_probs=61.3

Q ss_pred             cceEEEEEeeCC------ceeEEecCCChhHHHHHhhcCceEEEeecCCCCc-----------ccCCCCceEEEec-CHH
Q 010374          139 TLITVRMLVPAD------QIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPL-----------CALSFDELLQVAG-EPA  200 (512)
Q Consensus       139 ~~~~~~llVP~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~-----------~~~~~dr~v~I~G-~~~  200 (512)
                      ..++.+|.||.+      .+|.|||++|.+||+|+++|||+|.|........           .....+--|.|++ +.+
T Consensus         5 ~k~~~kv~IP~~~~P~~n~iG~IIGP~G~tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e   84 (131)
T 1k1g_A            5 TRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTME   84 (131)
T ss_dssp             CCEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHH
T ss_pred             ceEEEEEEECCccccCcceeeeEECCCcHHHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHH
Confidence            457899999988      7889999999999999999999999987421110           0012355688888 588


Q ss_pred             HHHHHHHHHHHHHhc
Q 010374          201 VVRKALVQIASRLHE  215 (512)
Q Consensus       201 ~V~~A~~~I~~~l~~  215 (512)
                      .+.+|+.+|..+|.+
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            899999999999976

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.31  E-value=1.1e-06  Score=74.02  Aligned_cols=77  Identities=17%  Similarity=0.129  Sum_probs=57.8

Q ss_pred             cceEEEEEeeCC-------ceeEEecCCChhHHHHHhhcCceEEEeecCCC---C--cccCCCCceEEEec-CHHHHHHH
Q 010374          139 TLITVRMLVPAD-------QIGCVIGKGGQVIQNIRTETRAQIRILKDEHL---P--LCALSFDELLQVAG-EPAVVRKA  205 (512)
Q Consensus       139 ~~~~~~llVP~~-------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---p--~~~~~~dr~v~I~G-~~~~V~~A  205 (512)
                      ..++.+|.||-+       .++.|||++|.+||+|+++|||+|.|..+...   +  ......+-.|.|++ +.+++++|
T Consensus        10 ~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e~i~~A   89 (119)
T 2yqr_A           10 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA   89 (119)
T ss_dssp             SCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHHHHHHH
T ss_pred             eEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHHHHHHH
Confidence            456888998865       68999999999999999999999999744210   0  00011233566765 69999999


Q ss_pred             HHHHHHHHhc
Q 010374          206 LVQIASRLHE  215 (512)
Q Consensus       206 ~~~I~~~l~~  215 (512)
                      +.+|.+++.+
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999999876

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.14  E-value=1.7e-06  Score=74.62  Aligned_cols=76  Identities=18%  Similarity=0.352  Sum_probs=56.6

Q ss_pred             eEEEEEeeCCc------eeEEecCCChhHHHHHhhcCceEEEeecCCC------------Cccc-CCCCceEEEecC-HH
Q 010374          141 ITVRMLVPADQ------IGCVIGKGGQVIQNIRTETRAQIRILKDEHL------------PLCA-LSFDELLQVAGE-PA  200 (512)
Q Consensus       141 ~~~~llVP~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~dr~v~I~G~-~~  200 (512)
                      ++.+|.||.+.      +|.|||++|.++|+|+++|||+|.|..+...            |... ...+--|.|+++ .+
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            57789999655      8999999999999999999999999875321            1100 112235778884 32


Q ss_pred             -----HHHHHHHHHHHHHhcC
Q 010374          201 -----VVRKALVQIASRLHEN  216 (512)
Q Consensus       201 -----~V~~A~~~I~~~l~~~  216 (512)
                           .+.+|+.+|..+|...
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p~  102 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVPA  102 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             hhHHHHHHHHHHHHHHHCCCC
Confidence                 7899999999988653

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.04  E-value=4.6e-06  Score=72.00  Aligned_cols=74  Identities=19%  Similarity=0.304  Sum_probs=54.5

Q ss_pred             eEEEEEecCC------ceeeeecCCchhHHHHHHHhCCeEEEecCCCC------------CC-CCCCCceEEEEEc-CHH
Q 010374          347 ITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNENV------------PK-VAYEDEEMVQITG-SLD  406 (512)
Q Consensus       347 ~t~~l~VP~~------~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~------------p~-~~~~~~r~V~I~G-~~~  406 (512)
                      ++.+|.||.+      ++|.|||++|.++|+|+++|||+|.|-.+...            |. ...+++--|.|++ +++
T Consensus         2 ~~~Ki~IP~~~~P~~NfiG~IiGPrG~t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~   81 (140)
T 2bl5_A            2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (140)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             ceeEEEcCcccCCCCCeeeEEECCCcchHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCch
Confidence            4677888854      49999999999999999999999999764311            00 0012333688888 343


Q ss_pred             -----HHHHHHHHHHHHHh
Q 010374          407 -----VASSALSQVTLRLR  420 (512)
Q Consensus       407 -----~v~~A~~~I~~~l~  420 (512)
                           .++.|+.+|..+|.
T Consensus        82 ~~~~~~l~~A~~~I~~lL~  100 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLV  100 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             hhHHHHHHHHHHHHHHHCC
Confidence                 78899999988875

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.97  E-value=4.4e-06  Score=90.01  Aligned_cols=95  Identities=19%  Similarity=0.185  Sum_probs=71.3

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++...|++.+.+.......+-.........|.||.+.++.|||++|.+||.|+++|||+|.|.++        
T Consensus       534 ~aL~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d~--------  605 (630)
T 3u1k_A          534 EAIQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDE--------  605 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS--------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcCC--------
Confidence            346667888888887765443322222223345578899999999999999999999999999999999643        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHH
Q 010374          188 SFDELLQVAGE-PAVVRKALVQIASRL  213 (512)
Q Consensus       188 ~~dr~v~I~G~-~~~V~~A~~~I~~~l  213 (512)
                         -.|.|.+. .+++.+|+.+|..++
T Consensus       606 ---G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          606 ---ETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             ---SEEEEEESSHHHHHHHHHHTTC--
T ss_pred             ---cEEEEEeCCHHHHHHHHHHHHHHh
Confidence               46999886 678999998887654

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.75  E-value=6.2e-05  Score=63.54  Aligned_cols=69  Identities=16%  Similarity=0.137  Sum_probs=59.5

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ...|.|...+++.|+|++|+.|++|+..|++.|+|..-+      .+....|+|.|++..-..|+.+|.....-+
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~~h  125 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAHYC  125 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999997532      235678999999999999999998776543

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.59  E-value=3.6e-05  Score=82.93  Aligned_cols=64  Identities=19%  Similarity=0.267  Sum_probs=54.3

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRL  419 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l  419 (512)
                      ......|.||.+.+|.|||+||++||+|+++|||+|.|.           ++..|.|.++ .+++++|+.+|.+.+
T Consensus       565 ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~-----------d~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          565 GPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQV-----------DEETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             CCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEEC-----------SSSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEc-----------CCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            456788999999999999999999999999999999994           2358999995 688999998886554

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.56  E-value=8e-06  Score=70.96  Aligned_cols=109  Identities=23%  Similarity=0.304  Sum_probs=74.9

Q ss_pred             CCCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHH
Q 010374           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFR  119 (512)
Q Consensus        40 ~~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~  119 (512)
                      |++.-.+.++|+...+|..||++|++|+.|+++.|-+|+|-+-..+           +                .+   .
T Consensus        32 d~~~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d-----------~----------------~~---f   81 (144)
T 2cxc_A           32 DEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSD-----------L----------------ER---I   81 (144)
T ss_dssp             EGGGTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSS-----------H----------------HH---H
T ss_pred             eCCCCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCC-----------H----------------HH---H
Confidence            3444678899999999999999999999999999999988543111           0                00   0


Q ss_pred             HHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEee
Q 010374          120 VHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILK  178 (512)
Q Consensus       120 i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  178 (512)
                      +...+.......-.-...+....+.+.||..+.+..|||+|++++-..+-||.+|.|..
T Consensus        82 I~naLsPA~V~~V~i~~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A           82 VKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             HHHHSTTSCEEEEEEEEETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             HHHhcCCceEEEEEEeecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence            11111111000000000023457889999999999999999999999999999887753

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.46  E-value=5e-05  Score=82.76  Aligned_cols=97  Identities=24%  Similarity=0.354  Sum_probs=28.8

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++...|++.+.........+-.........|.||.+.++.|||++|.+||+|+++|||+|.|..+        
T Consensus       537 ~aL~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~dd--------  608 (726)
T 4aid_A          537 QALAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDINDD--------  608 (726)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC----------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEECC--------
Confidence            446678888888887765433222222122234467899999999999999999999999999999998643        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010374          188 SFDELLQVAGE-PAVVRKALVQIASRLHE  215 (512)
Q Consensus       188 ~~dr~v~I~G~-~~~V~~A~~~I~~~l~~  215 (512)
                         ..|.|.+. .+++++|+..|..++.+
T Consensus       609 ---G~v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          609 ---GVVKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             --------CCSCHHHHHHHHHC-------
T ss_pred             ---ceEEEEeCCHHHHHHHHHHHHHHhhh
Confidence               34677665 88899999999887754

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.34  E-value=5.3e-05  Score=65.76  Aligned_cols=104  Identities=22%  Similarity=0.322  Sum_probs=74.1

Q ss_pred             ceEEEecCCCCCcccccCCCccccchhhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCC
Q 010374          262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE  341 (512)
Q Consensus       262 ~~~~v~vP~~~vg~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~  341 (512)
                      -.+.+.++...+|..||++|++|+.|.++.|-+|.+-.-+.+                +..-+..+  +.|.-...+.-.
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d----------------~~~fI~na--LsPA~V~~V~i~   97 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSD----------------LERIVKNL--FPGVKIESINVR   97 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSS----------------HHHHHHHH--STTSCEEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCC----------------HHHHHHHh--cCCceEEEEEEe
Confidence            467889999999999999999999999999999887654321                11112222  222111111100


Q ss_pred             CCCceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEe
Q 010374          342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (512)
Q Consensus       342 ~~~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~  383 (512)
                      ..+......+.||.+..+..|||+|.+++-..+-||.+|.|.
T Consensus        98 ~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           98 ERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             EETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             ecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence            002346678899999999999999999999999999988874

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.16  E-value=0.00063  Score=57.44  Aligned_cols=68  Identities=16%  Similarity=0.187  Sum_probs=59.5

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .+.+.|.+..++.|+|++|+.|+.|+..|+|.|+|..-+.      +..--|+|.|.+..-.+|+.+|..+...
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s------~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP------ERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT------TSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC------CCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            5679999999999999999999999999999999986521      3355699999999999999999887765

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.74  E-value=0.0003  Score=76.70  Aligned_cols=66  Identities=23%  Similarity=0.343  Sum_probs=12.1

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhhc
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~  422 (512)
                      .....+.||.+.++.|||+||.+||+|+++||++|.|.           ++..|.|.+ +.++++.|+.+|...+.+.
T Consensus       569 p~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-----------ddG~v~I~~~~~~~~~~A~~~i~~i~~~~  635 (726)
T 4aid_A          569 PKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-----------DDGVVKVSASDGAKIKAAIDWIKSITDEA  635 (726)
T ss_dssp             CC------------------------------------------------------CCSCHHHHHHHHHC--------
T ss_pred             CeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-----------CCceEEEEeCCHHHHHHHHHHHHHHhhhh
Confidence            45678999999999999999999999999999999984           234677777 5889999999888877653

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.84  E-value=0.0068  Score=57.12  Aligned_cols=97  Identities=23%  Similarity=0.216  Sum_probs=64.5

Q ss_pred             CceeeeccCCchHHHHH-HHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQL-RSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I-~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|++|+.| ++-.|=+|+|-.-..+           +                .   ..|...+.......
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-----------p----------------~---~fi~nalsPA~V~~  175 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-----------P----------------A---RFVANALSPAKVVS  175 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-----------H----------------H---HHHHHHTTTSCCSE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC-----------H----------------H---HHHHhccCCcceEE
Confidence            46899999999999999 5666888887432111           0                0   01111111111100


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (512)
                      -.- .....-.+.+.||..+.+..|||+|++++--..-||.+|.|....
T Consensus       176 V~i-~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  223 (251)
T 2asb_A          176 VSV-IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  223 (251)
T ss_dssp             EEE-EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             EEE-EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHH
Confidence            000 000123788999999999999999999999999999999998763

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.72  E-value=0.0038  Score=62.20  Aligned_cols=97  Identities=25%  Similarity=0.226  Sum_probs=66.0

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|..||++|++|+.|.++. |=+|+|-+-..              +                ....|...+.......
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~--------------d----------------p~~fi~nalsPA~V~~  298 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDD--------------D----------------PARFVANALSPAKVVS  298 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCS--------------S----------------HHHHHHHHTTTSCCSE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCC--------------C----------------HHHHHHHhcCCcceeE
Confidence            468999999999999999998 88888743211              1                0001111111111100


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecC
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (512)
                      -.. -......+.+.||..+.+..|||+|++++-...-||.+|.|....
T Consensus       299 V~~-~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          299 VSV-IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             EEE-EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             EEE-EcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            000 001134788999999999999999999999999999999998763

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=95.70  E-value=0.0062  Score=57.43  Aligned_cols=97  Identities=22%  Similarity=0.275  Sum_probs=65.8

Q ss_pred             CCCcccccCCCccccch-hhhcCCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCccccccc-CCCCCceeE
Q 010374          271 GNIGGVIGKGGGIIKQI-RQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT  348 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I-~~~tga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~t  348 (512)
                      +-+|..||++|++|+.| ++-.|-+|.+-.-+.+                  +.....-.+.+.-...+. .+.  ....
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d------------------p~~fi~nalsPA~V~~V~i~~~--~~~~  185 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD------------------PARFVANALSPAKVVSVSVIDQ--TARA  185 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS------------------HHHHHHHHTTTSCCSEEEEEET--TTTE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC------------------HHHHHHhccCCcceEEEEEEcC--CCcE
Confidence            34799999999999999 6666777777553311                  122111222221111111 011  1246


Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCC
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN  387 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~  387 (512)
                      ..+.||.++.+.-|||+|.+|+--.+.||.+|.|....+
T Consensus       186 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          186 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             EEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence            789999999999999999999999999999999976543

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=95.37  E-value=0.0083  Score=59.77  Aligned_cols=96  Identities=22%  Similarity=0.271  Sum_probs=66.5

Q ss_pred             CCCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccc-cCCCCCceeE
Q 010374          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT-ERESGDPVIT  348 (512)
Q Consensus       271 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~t  348 (512)
                      +-+|..||++|.+|+.|.++- |-+|.+-.-+.+                  +.....-.+.|.-...+ ..+.  ....
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d------------------p~~fi~nalsPA~V~~V~~~~~--~~~~  308 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD------------------PARFVANALSPAKVVSVSVIDQ--TARA  308 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS------------------HHHHHHHHTTTSCCSEEEEEET--TTTE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhcCCcceeEEEEEcC--CCcE
Confidence            347999999999999999998 777777543311                  12222222222111111 0001  1346


Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCC
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNE  386 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~  386 (512)
                      ..+.||.+..+..|||+|.+++-..+.||.+|.|....
T Consensus       309 a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~  346 (366)
T 1k0r_A          309 ARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA  346 (366)
T ss_dssp             EEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESS
T ss_pred             EEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHH
Confidence            88999999999999999999999999999999997654

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.24  E-value=0.0047  Score=67.56  Aligned_cols=96  Identities=22%  Similarity=0.287  Sum_probs=13.9

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++...|++.+.........+-.........+.||.+.++.|||++|.+|+.|.++||+.|.|..+        
T Consensus       527 ~~l~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~d--------  598 (723)
T 3cdi_A          527 VALNQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDD--------  598 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCC----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecCC--------
Confidence            455667777777877665433221111122234456788999999999999999999999999999988543        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHHh
Q 010374          188 SFDELLQVAGE-PAVVRKALVQIASRLH  214 (512)
Q Consensus       188 ~~dr~v~I~G~-~~~V~~A~~~I~~~l~  214 (512)
                         ..|.|.+. .+.+++|...|..++.
T Consensus       599 ---g~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          599 ---GTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------------
T ss_pred             ---ccEEEecCCHHHHHHHHHHHHHHhh
Confidence               34666554 5567778777766554

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.05  E-value=0.052  Score=53.82  Aligned_cols=95  Identities=31%  Similarity=0.364  Sum_probs=64.1

Q ss_pred             CCcccccCCCccccchhhhc-CCeEEecCCCCCCCCeEEEecCCcccCCCchhHHHHHhhCCcccccccCCCCCceeEEE
Q 010374          272 NIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTR  350 (512)
Q Consensus       272 ~vg~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~t~~  350 (512)
                      -+|..||.+|.+|+.+.++- |-+|.+-.-+.                +  +...-.-.+.|.-...+... ........
T Consensus       246 pvGacvg~~G~ri~~i~~el~ge~Idii~~s~----------------d--~~~fi~nal~Pa~v~~v~~~-d~~~~~~~  306 (344)
T 1hh2_P          246 PIGACIGEGGSRIAAILKELKGEKLDVLKWSD----------------D--PKQLIANALAPATVIEVEIL-DKENKAAR  306 (344)
T ss_dssp             HHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS----------------S--HHHHHHHHTCSSCCSEEEEE-ETTTTEEE
T ss_pred             ccceeeccCCcEeHHHHHHhCCCeeeEEecCC----------------C--HHHHHHHhcCccEEEEEEEE-cCCCCEEE
Confidence            47999999999999999888 56666544221                1  12211112222111111110 01134688


Q ss_pred             EEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       351 l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      +.||.++.+.-|||+|.+++--.+.||.+|.|...
T Consensus       307 v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          307 VLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            99999999999999999999999999999999653

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=93.98  E-value=0.047  Score=54.18  Aligned_cols=96  Identities=22%  Similarity=0.279  Sum_probs=64.2

Q ss_pred             CceeeeccCCchHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHHHHhhhcccC
Q 010374           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (512)
Q Consensus        53 ~~~g~IIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~~i~~~~~~~  131 (512)
                      +-+|+.||.+|+.|+.|.++. |-+|.|-.-.              ++                ....|...+.......
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s--------------~d----------------~~~fi~nal~Pa~v~~  294 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWS--------------DD----------------PKQLIANALAPATVIE  294 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECC--------------SS----------------HHHHHHHHTCSSCCSE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecC--------------CC----------------HHHHHHHhcCccEEEE
Confidence            468999999999999999998 6777764321              01                0011111111110000


Q ss_pred             CcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeec
Q 010374          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (512)
Q Consensus       132 ~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (512)
                      -.- ..+..-.+.+.||..+.+..|||+|++++--..-||.+|.|...
T Consensus       295 v~~-~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          295 VEI-LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEE-EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEE-EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            000 00122378899999999999999999999999999999999765

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=93.89  E-value=0.0051  Score=67.55  Aligned_cols=94  Identities=24%  Similarity=0.325  Sum_probs=36.7

Q ss_pred             ccCcHHHHHHHHHHHHHhhhcccCCcccCCCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccC
Q 010374          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (512)
Q Consensus       108 ~~~~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (512)
                      +.+..|.++...|++.+....... .+-.........|.||.+.++.+||++|.+|++|+++||+.|.|..+        
T Consensus       566 ~aL~~A~~~~~~I~~~m~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~d--------  636 (757)
T 1e3p_A          566 AALKQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD--------  636 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSC-CCCCTTSCBCCCC------------------CTTCCCCCSCC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccc-ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecCC--------
Confidence            456667778888877765433222 21112223345688999999999999999999999999999988643        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHH
Q 010374          188 SFDELLQVAGE-PAVVRKALVQIASRL  213 (512)
Q Consensus       188 ~~dr~v~I~G~-~~~V~~A~~~I~~~l  213 (512)
                         ..|.|+.. .+.+++|...|..+.
T Consensus       637 ---G~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          637 ---GTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             ------CCCBSSHHHHCC---------
T ss_pred             ---ceEEEecCCHHHHHHHHHHHHHhc
Confidence               34666553 556666766665543

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=92.94  E-value=0.018  Score=62.93  Aligned_cols=64  Identities=22%  Similarity=0.322  Sum_probs=0.0

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHh
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR  420 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~  420 (512)
                      .....+.||.+.++.|||++|.+|+.|.++||+.|.|..           +..|.|.+ +.+.+++|..+|...+.
T Consensus       559 p~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-----------dg~v~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          559 PRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-----------DGTVKIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             ceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-----------CccEEEecCCHHHHHHHHHHHHHHhh
Confidence            456788999999999999999999999999999998842           34677766 45677777776665543

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=90.18  E-value=0.016  Score=63.73  Aligned_cols=63  Identities=21%  Similarity=0.252  Sum_probs=21.7

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRL  419 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l  419 (512)
                      .....|.||.+.+|.|||++|.+||+|++.||+.|.|..           +..|.|.. +.+.++.|..+|....
T Consensus       597 p~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          597 PRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CBCCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             ceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            344578899999999999999999999999999999842           34677776 4566666765555443

---

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	512
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-15
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	6e-13
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-10
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	6e-14
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	2e-09
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	8e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	6e-06
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	7e-14
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-11
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-07
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-13
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-11
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	5e-13
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-11
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-10
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	5e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	1e-09
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	7e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	1e-11
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-10
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	8e-09
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-06
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-11
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-10
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	3e-09
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-06
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	1e-10
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	7e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-10
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	8e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	5e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	7e-08
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	1e-06
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	7e-10
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	9e-09
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	5e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	8e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	9e-08
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	1e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	2e-08
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-05
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	1e-04
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	0.001
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	3e-08
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-06
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	5e-05
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	9e-07
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-06
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	4e-05
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	3e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	3e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	4e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	7e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	8e-05
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	2e-04
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	2e-05
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.001
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.002
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.003
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	3e-04
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.001
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.004
d2je6i3	69	d.51.1.1 (I:153-221) Exosome complex RNA-binding p	0.004
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	3e-04
d2z0sa2	87	d.51.1.1 (A:148-234) Exosome complex RNA-binding p	0.002

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.0 bits (169), Expect = 2e-15
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           +T+R+L+   ++G +IGK G+ ++ +R E+ A+I I +           + ++ +AG   
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTN 56

Query: 201 VVRKALVQIASRLHE 215
            + KA   I  +L E
Sbjct: 57  AIFKAFAMIIDKLEE 71

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.7 bits (150), Expect = 6e-13
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403
           +  +T R+L+   ++G +IG+ G  + +MR  + A I I             E ++ + G
Sbjct: 1   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC-------PERIITLAG 53

Query: 404 SLDVASSALSQVTLRLR 420
             +    A + +  +L 
Sbjct: 54  PTNAIFKAFAMIIDKLE 70

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (132), Expect = 2e-10
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
             R L   +++GSIIGK GE VK++R E+ + I ISE    C ERI+T+   +  
Sbjct: 4  LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNA 57

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (126), Expect = 1e-09
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           ++RL+     +G +IGK G  +K++R+ESGA I +        + II ++
Sbjct: 5   TIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN--CPERIITLA 52

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.8 bits (160), Expect = 6e-14
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 6/96 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           +  ++ VP   +G +IG+GG+ I++I   + A+I   K+       L    L++++G   
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE---SEGTLLLSRLIKISGTQK 71

Query: 201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSG 236
            V  A   I  ++ E+    + +  S+S     SSG
Sbjct: 72  EVAAAKHLILEKVSEDEELRKRIAHSAS---GPSSG 104

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.1 bits (127), Expect = 2e-09
 Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           +  ++ VP   +G +IGRGG  I  +  A+ A I     +   +       +++I+G+  
Sbjct: 15  VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKISGTQK 71

Query: 407 VASSALSQVTLRLR 420
             ++A   +  ++ 
Sbjct: 72  EVAAAKHLILEKVS 85

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.4 bits (107), Expect = 8e-07
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 37 RGIGSEDT--VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCD--ERIVT 92
           GI +E+T    +   P R +G IIG+GGE ++ +   + + I   +   G     R++ 
Sbjct: 6  SGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIK 65

Query: 93 IYSSSEG 99
          I  + + 
Sbjct: 66 ISGTQKE 72

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV--DSSGAEGDDCIIFIS 312
             +L  P  ++G +IG+GG  I+ I + SGA I    +S G      +I IS
Sbjct: 16  FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKIS 67

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.5 bits (157), Expect = 7e-14
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            V M VP + +G ++GKGG+ +   +  T A+I+I K         + +  + + G PA 
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPAA 61

Query: 202 VRKALVQIASRL 213
            + A   I+ R+
Sbjct: 62  TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.3 bits (141), Expect = 1e-11
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              + VP   +G ++G+GG  + E +  T A I+I                V ITGS   
Sbjct: 4   LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAA 61

Query: 408 ASSALSQVTLRL 419
             +A   ++ R+
Sbjct: 62  TQAAQYLISQRV 73

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEG 99
          +     P   +G+I+GKGG+ + + +  T + I+IS   E +PG   R VTI  S   
Sbjct: 4  LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAA 61

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG---AEGDDCIIFIS 312
           + +  P   +G ++GKGG  + + ++ +GA I++   G       +  + I+
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.9 bits (153), Expect = 3e-13
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           +T    VP   +G +IG+GG+ I  I+ E+  +I+I  D          +    + G P 
Sbjct: 8   MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD-----SGGLPERSCMLTGTPE 62

Query: 201 VVRKALVQIASRLHEN 216
            V+ A   +   + + 
Sbjct: 63  SVQSAKRLLDQIVEKG 78

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.5 bits (139), Expect = 2e-11
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 35 EQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY 94
          +QR + +E     Y  P   +G IIG+GGE + +++ E+   I+I+    G  ER   + 
Sbjct: 3  QQRSVMTE----EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLT 58

Query: 95 SSSEG 99
           + E 
Sbjct: 59 GTPES 63

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.4 bits (136), Expect = 5e-11
 Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
           V+T    VP   +G +IGRGG  IS ++  +   I+I      P      E    +TG+ 
Sbjct: 7   VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA-----PDSGGLPERSCMLTGTP 61

Query: 406 DVASSALSQVTLRLR 420
           +   SA   +   + 
Sbjct: 62  ESVQSAKRLLDQIVE 76

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (125), Expect = 2e-09
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           +     P G +G +IG+GG  I +I+QESG  I++        +    ++
Sbjct: 9   TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLT 58

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.8 bits (150), Expect = 5e-13
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
            T  + +P + IGC+IG+ G  I  IR  + AQI+I           S    + + G  A
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP-----VEGSSGRQVTITGSAA 56

Query: 201 VVRKALVQIASRL 213
            +  A   I +RL
Sbjct: 57  SISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 3e-11
 Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
            T  + +P+  IGC+IGR GA I+E+R  + A I+I        V       V ITGS  
Sbjct: 2   TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI-----ANPVEGSSGRQVTITGSAA 56

Query: 407 VASSALSQVTLRL 419
             S A   +  RL
Sbjct: 57  SISLAQYLINARL 69

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (133), Expect = 1e-10
 Identities = 18/56 (32%), Positives = 28/56 (50%)

Query: 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          T +    P   IG IIG+ G  + ++R  + + I+I+  V G   R VTI  S+  
Sbjct: 2  TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 57

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 17/50 (34%), Positives = 25/50 (50%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           +  L  P   IG +IG+ G  I +IRQ SGA IK+ +         + I+
Sbjct: 3   THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTIT 52

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.3 bits (146), Expect = 2e-12
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           IT ++ +P D  G +IGKGGQ I+ IR E+ A I+I +         S D ++ + G   
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-----LEGSEDRIITITGTQD 58

Query: 201 VVRKALVQIASRLHE 215
            ++ A   + + + +
Sbjct: 59  QIQNAQYLLQNSVKQ 73

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (143), Expect = 5e-12
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS 404
           P+ITT++ +P    G +IG+GG  I ++R  + ASI+I        +   ++ ++ ITG+
Sbjct: 2   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-----DEPLEGSEDRIITITGT 56

Query: 405 LDVASSALSQVTLRLR 420
            D   +A   +   ++
Sbjct: 57  QDQIQNAQYLLQNSVK 72

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 21/53 (39%), Positives = 35/53 (66%)

Query: 47 RYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          +   P    GSIIGKGG+ +KQ+R E+ ++I+I E + G ++RI+TI  + + 
Sbjct: 7  QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ 59

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 7e-08
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
           + ++  P    G +IGKGG  IKQIR ESGASIK+D      +D II I+
Sbjct: 5   TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 54

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 1e-11
 Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
               +++PA + G VIGKGG+ I+ ++     ++ +++D      A   D+ L++ G+P 
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA---DKPLRITGDPY 64

Query: 201 VVRKALVQIASRLHE 215
            V++A   +   + +
Sbjct: 65  KVQQAKEMVLELIRD 79

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT 402
           G       I++P+++ G +IG+GG  I +++      + ++ +          ++ ++IT
Sbjct: 4   GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT---GADKPLRIT 60

Query: 403 GSLDVASSALSQVTLRLR 420
           G       A   V   +R
Sbjct: 61  GDPYKVQQAKEMVLELIR 78

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.3 bits (120), Expect = 8e-09
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 38 GIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE--TVPGCDERIVTIYS 95
          G G  + V   + P  K G +IGKGGE +KQL+      + + +        ++ + I  
Sbjct: 2  GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG 61

Query: 96 SSEG 99
              
Sbjct: 62 DPYK 65

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.8 bits (103), Expect = 2e-06
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG--AEGDDCIIFIS 312
                ++ PA   G VIGKGG  IKQ+++ +G  + +   G    G D  + I+
Sbjct: 7   NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 60

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.0 bits (140), Expect = 1e-11
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
               +VP  + G +IGKGG+ I++I  ++ A+I +    + P  A    +L  + G P  
Sbjct: 2   EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQ 59

Query: 202 VRKALVQIASRL 213
           +  A   I  ++
Sbjct: 60  IDYARQLIEEKI 71

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (129), Expect = 4e-10
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVAS 409
             +VP+ + G +IG+GG  I  +   + A I +  N   P  A  + ++  I G+     
Sbjct: 4   NFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLFTIRGTPQQID 61

Query: 410 SALSQV 415
            A   +
Sbjct: 62  YARQLI 67

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.1 bits (122), Expect = 3e-09
 Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEG 99
          + ++ P  K G IIGKGGE +K +  ++ + I +          + ++ TI  + + 
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQ 59

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (98), Expect = 6e-06
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD---SSGAEGDDCIIFIS 312
              + P G  G +IGKGG  IK I Q+SGA I++       A+ +  +  I 
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIR 54

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (134), Expect = 1e-10
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 7/95 (7%)

Query: 133 DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL 192
           +    L  +T+ + VP D    VIG+ G  I+ +  E    I +   E          ++
Sbjct: 2   EALEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDI 54

Query: 193 LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSS 227
           + + G  A + +A   +  R+ E  +  +   L S
Sbjct: 55  IAITGLAANLDRAKAGLLERVKELQAEQEDRALRS 89

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 3e-07
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
           +T  + VP      +IG+ G+ I +M      +I +   E          +++ ITG   
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAA 62

Query: 407 VASSALSQVTLRLR 420
               A + +  R++
Sbjct: 63  NLDRAKAGLLERVK 76

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 5e-07
 Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
           ++ +  P      VIG+ G  I+++  E   +I V +      D I       
Sbjct: 11  TIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-LQSDIIAITGLAA 62

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (107), Expect = 7e-07
 Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 2/49 (4%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
          P      +IG+ G  ++++  E + NI +    P     I+ I   +  
Sbjct: 17 PFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGLAAN 63

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (132), Expect = 2e-10
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE 198
           T  +  + +P +    VIGK G+ +Q++  +T  +I+I + +            +++ G 
Sbjct: 8   TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGT 60

Query: 199 PAVVRKALVQIASRLHENPSR 219
              + KA  ++     E   R
Sbjct: 61  KEGIEKARHEVLLISAEQDKR 81

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (114), Expect = 5e-08
 Identities = 9/49 (18%), Positives = 20/49 (40%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
           + S  +  P  +   VIGK G  ++ +  ++   I++       +   I
Sbjct: 9   QASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKI 57

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (113), Expect = 8e-08
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
            +  + +P      +IG+ G  + ++   T   I+I   +       +    ++ITG+ +
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKE 62

Query: 407 VASSALSQV 415
               A  +V
Sbjct: 63  GIEKARHEV 71

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 50 CPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
           P      +IGK GE ++ L  +T + I+I    P      + I  + EG
Sbjct: 16 IPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGTKEG 63

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.1 bits (130), Expect = 5e-10
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 4/79 (5%)

Query: 137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA 196
            L    + + V       +IG+ G VI  IR E    I+    +          + + + 
Sbjct: 6   ALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----QPQDQITIT 61

Query: 197 GEPAVVRKALVQIASRLHE 215
           G       A   I   + E
Sbjct: 62  GYEKNTEAARDAILRIVGE 80

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEG--DDCIIFISTKE 315
           R F L +         +IG+ G +I QIR E   +I+           D I     ++
Sbjct: 8   RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEK 65

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 7e-08
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 4/69 (5%)

Query: 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406
               + V       +IGR GA+I+++R     +I+    ++      + ++ + ITG   
Sbjct: 10  FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGN----QPQDQITITGYEK 65

Query: 407 VASSALSQV 415
              +A   +
Sbjct: 66  NTEAARDAI 74

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (104), Expect = 1e-06
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRIS-ETVPGCDERIVTIYSSSEG 99
            +    IIG+ G ++ Q+R E   NI+   +      +  +TI    + 
Sbjct: 17 DPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKN 66

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 7e-10
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV 201
            + + +P   +G VIG+ G++I+ I+ +   +I+   D        + + + Q+ G P  
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD-----DGTTPERIAQITGPPDR 58

Query: 202 VRKALVQIASRLHE 215
            + A   I   L  
Sbjct: 59  AQHAAEIITDLLRS 72

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (121), Expect = 5e-09
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
           +     P   +G +IG+ GE++K+++++    I+         ERI  I    + 
Sbjct: 3  HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDR 58

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (119), Expect = 9e-09
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407
              + +P   +G +IGR G +I ++++     I+   ++         E + QITG  D 
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDR 58

Query: 408 ASSALSQVTLRLR 420
           A  A   +T  LR
Sbjct: 59  AQHAAEIITDLLR 71

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 5e-08
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
            + +  P   +G VIG+ G +IK+I+ ++G  I+         + I  I+
Sbjct: 4   MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT 53

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 15/38 (39%), Positives = 23/38 (60%)

Query: 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
            + + +P D+IG VIG   Q+I  I+ +T A+I I  D
Sbjct: 4   IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDD 41

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 46.6 bits (111), Expect = 8e-08
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 265 RLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
            +  P   IG VIG    +I QI++++GA I ++      DD  I+I   +
Sbjct: 6   TVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAAD 50

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 46.6 bits (111), Expect = 9e-08
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 6/54 (11%)

Query: 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98
          +     P+ KIG +IG   +++ Q++ +T + I I       D+  + I ++  
Sbjct: 4  IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE------DDGTIYIGAADG 51

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]} Length = 54

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 43.1 bits (102), Expect = 1e-06
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 12/60 (20%)

Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS 404
           P I T + +P  +IG +IG    +I++++  T A I I           ED+  + I  +
Sbjct: 2   PRIIT-VKIPVDKIGEVIGPKRQMINQIQEDTGAEITI-----------EDDGTIYIGAA 49

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTE-TRAQIRILKDEHLPLCALSFDELLQVAG 197
            +  V + +PA     +IG  G++I++I  E     I    +           + + + G
Sbjct: 8   NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-------GSDTVVIRG 60

Query: 198 EPAVVRKALVQIASRLHENPSR 219
             + V KA  Q+     E  ++
Sbjct: 61  PSSDVEKAKKQLLHLAEEKQTK 82

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 50 CPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
           P +   S+IG  G +++ +  E    + I   V G     V I   S  
Sbjct: 16 IPAKLHNSLIGTKGRLIRSIMEE-CGGVHIHFPVEGSGSDTVVIRGPSSD 64

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCII 309
           A    + +  PA     +IG  G +I+ I +E  G  I     G+  D  +I
Sbjct: 7   ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVI 58

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 8/71 (11%)

Query: 346 VITTRILVPSAQIGCLIGRGGAIISE-MRSATRASIRILTNENVPKVAYEDEEMVQITGS 404
           +    + +P+     LIG  G +I   M       I      +         + V I G 
Sbjct: 9   IAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS-------GSDTVVIRGP 61

Query: 405 LDVASSALSQV 415
                 A  Q+
Sbjct: 62  SSDVEKAKKQL 72

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (115), Expect = 3e-08
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199
           +  V + +       +IGK G  I  I+ + +  +RI  D            L+++ G+P
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDP 56

Query: 200 AVVRKALVQI 209
             V++A  ++
Sbjct: 57  QGVQQAKREL 66

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
            +    +IGK G  + +++ + K ++RI          ++ I    +G
Sbjct: 12 DHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGDPQG 58

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 7/70 (10%)

Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
           +    I +       LIG+ GA I+ ++   + S+RI           E   +++I G  
Sbjct: 4   MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRI-------PPDSEKSNLIRIEGDP 56

Query: 406 DVASSALSQV 415
                A  ++
Sbjct: 57  QGVQQAKREL 66

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 8/47 (17%), Positives = 19/47 (40%)

Query: 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309
            + +         +IGK G  I +I+ +   S+++     + +   I
Sbjct: 6   YVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRI 52

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPA 200
           ++  + +       +IG  G+ I+ I  E +  IR  +              + V G P 
Sbjct: 10  VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPD------PNCVTVTGLPE 63

Query: 201 VVRKALVQIASRLHE 215
            V +A+  I +   E
Sbjct: 64  NVEEAIDHILNLEEE 78

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 9e-07
 Identities = 13/55 (23%), Positives = 20/55 (36%)

Query: 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
             S  +         +IG  G  I++I  E    I+   SGA   +C+      E
Sbjct: 9   MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPE 63

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL 405
           +++  + +       +IG  G  I ++    +  IR       P+    D   V +TG  
Sbjct: 9   MVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRF------PQSGAPDPNCVTVTGLP 62

Query: 406 DVASSALSQV 415
           +    A+  +
Sbjct: 63  ENVEEAIDHI 72

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
            R    IIG  G+ ++++  E K +IR  ++    D   VT+    E 
Sbjct: 17 DHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP-DPNCVTVTGLPEN 64

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 43.2 bits (102), Expect = 3e-06
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180
           + V  +++G VIG  G+V   I   T   I +  + 
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN 42

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 5/50 (10%)

Query: 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIST 313
           + +      +G VIG  G +  +I + +G  I VD+     ++ ++ +  
Sbjct: 5   IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEP 49

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 12/51 (23%), Positives = 24/51 (47%)

Query: 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
           + V   ++G +IG  G + +E+   T   I + T  ++  V  E E +  +
Sbjct: 7   VKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPV 57

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 17/76 (22%)

Query: 51  PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFV 110
              ++G++IG  GE+  ++   T + I +       +  +V +   +E            
Sbjct: 10  KPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAE------------ 52

Query: 111 SPAQDALFRVHDRIVA 126
                 L +  + + A
Sbjct: 53  GIPPVNLMKAAEVVKA 68

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 17/75 (22%)

Query: 135 FGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ 194
           FG +      + +   ++  VIGK G +I+ +++E   QI + +           + L+ 
Sbjct: 1   FGRI------VAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIW 43

Query: 195 VAGEPAVVRKALVQI 209
           V G+   V  A   I
Sbjct: 44  VNGDRRKVSIAEEAI 58

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.3 bits (92), Expect = 7e-05
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
             ++  +IGK G ++K L+SE    I +          ++ +      
Sbjct: 8  NPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVNGDRRK 50

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.3 bits (92), Expect = 8e-05
 Identities = 10/65 (15%), Positives = 25/65 (38%), Gaps = 11/65 (16%)

Query: 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASS 410
           + +  A++  +IG+ G++I  ++S     I +               ++ + G     S 
Sbjct: 5   VAINPARVPRVIGKKGSMIKLLKSELDVQIVV-----------GQNGLIWVNGDRRKVSI 53

Query: 411 ALSQV 415
           A   +
Sbjct: 54  AEEAI 58

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)

Query: 269 PAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
               +  VIGK G +IK ++ E    I V        + +I+++
Sbjct: 8   NPARVPRVIGKKGSMIKLLKSELDVQIVVG------QNGLIWVN 45

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 10/50 (20%), Positives = 14/50 (28%)

Query: 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFD 190
                +V  D +G  IG  G  IQ  R         L ++          
Sbjct: 8   FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGES 57

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 2/57 (3%)

Query: 259 AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKE 315
           A  F    V     +G  IG  G  I+Q R+  G +              I+  + +
Sbjct: 5   AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTG--TFRIYGESAD 59

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 1/57 (1%)

Query: 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN-VPKVAYEDEEMVQ 400
                  +V    +G  IG  G+ I + R     +   L  +    ++  E  + V+
Sbjct: 6   AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVK 62

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 10/47 (21%), Positives = 14/47 (29%), Gaps = 4/47 (8%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSS 97
              +G  IG  G  ++Q R          +   G       IY  S
Sbjct: 15 REDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTG----TFRIYGES 57

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 5/35 (14%), Positives = 17/35 (48%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
           + +   ++  VIGK   + + + +++   I +  +
Sbjct: 5   IDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN 39

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 269 PAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG 301
               +  VIGK   + + +  +SG SI V ++G
Sbjct: 8   MPVKVPRVIGKNKSMYETLTSKSGCSIFVANNG 40

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 8/53 (15%), Positives = 20/53 (37%), Gaps = 1/53 (1%)

Query: 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQI 401
             I +   ++  +IG+  ++   + S +  SI +  N  +           +I
Sbjct: 3   IVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRI-WATCPSRFSEEI 54

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 69

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 6/48 (12%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98
             K+  +IGK   + + L S++  +I ++      +   +     S 
Sbjct: 8  MPVKVPRVIGKNKSMYETLTSKSGCSIFVA------NNGRIWATCPSR 49

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 7/44 (15%), Positives = 17/44 (38%), Gaps = 6/44 (13%)

Query: 269 PAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFIS 312
               +  VIG+   ++K + +++   I V        +  I + 
Sbjct: 8   SPAKVPRVIGRKMSMLKTLEEKTECKIFVA------RNGRIHLE 45

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 5/35 (14%), Positives = 19/35 (54%)

Query: 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179
           + +   ++  VIG+   +++ +  +T  +I + ++
Sbjct: 5   VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN 39

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	512
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.58
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.57
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.57
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.57
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.57
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.56
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.55
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.54
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.53
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.52
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.51
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.49
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.49
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.48
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.47
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.43
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.43
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.3
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.21
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.21
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.19
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.13
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.1
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.09
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.78
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.78
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.72
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.68
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.67
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.62
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.57
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.55
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.43
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.36
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.12
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.97
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.74
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.61
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.57
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.57
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.28
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.13
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	81.47

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.2e-15  Score=116.02  Aligned_cols=72  Identities=28%  Similarity=0.467  Sum_probs=65.2

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      .+|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..     ..+++++|+|+|++++|+.|+.+|.++|+++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~-----~~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT-----SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999999996432     2467899999999999999999999999874

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.6e-15  Score=115.44  Aligned_cols=70  Identities=23%  Similarity=0.414  Sum_probs=61.6

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      +.+|.||.+++|+||||+|++|++|++.|||+|+|++... + ..++++|.|+|+|++++|+.|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~-~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-P-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-T-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-C-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            4689999999999999999999999999999999976432 2 23567899999999999999999998874

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.1e-15  Score=116.17  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=63.6

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ..++.+|+||.+++|+||||+|++|++|+++|||+|+|++.       ...+|+|+|+|++++|..|+.+|.++|++
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCC-------CCCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            35789999999999999999999999999999999999643       24579999999999999999999999874

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.5e-15  Score=115.13  Aligned_cols=68  Identities=37%  Similarity=0.507  Sum_probs=61.6

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      .|.+|.||.+++|+||||+|++|++|+++|||+|+|.+..     .+.++|.|+|+|++++|+.|+.+|.++|
T Consensus         2 ~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           2 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC-----CCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5889999999999999999999999999999999996432     2467899999999999999999999876

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.1e-15  Score=115.72  Aligned_cols=71  Identities=25%  Similarity=0.374  Sum_probs=62.7

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l  419 (512)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|.+.++..+  ++++|.|+|+|++++|+.|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP--GTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST--TCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            35789999999999999999999999999999999977544322  467899999999999999999998876

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.2e-15  Score=116.11  Aligned_cols=70  Identities=29%  Similarity=0.571  Sum_probs=64.3

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|++..       ..||+|+|+|++++|.+|+.+|.++|+|
T Consensus         2 ~~vt~~i~vp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~-------~~er~v~I~G~~~~v~~A~~~I~~~l~E   71 (71)
T d2axya1           2 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTNAIFKAFAMIIDKLEE   71 (71)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSSC-------CSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             ccEEEEEEECHHHcCeEECCCChhHHHHHHHhCCEEEEcCCC-------CCcceEEEEECHHHHHHHHHHHHHHhcC
Confidence            357999999999999999999999999999999999997651       4589999999999999999999999875

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=2.3e-15  Score=117.61  Aligned_cols=74  Identities=19%  Similarity=0.341  Sum_probs=66.4

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      ..++.+|+||.+++|+||||+|++|++|+++|||+|+|.+.+..+   .+.+|.|+|+|++++|..|+.+|.++|++
T Consensus         6 ~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           6 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             ccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999997653333   36789999999999999999999999865

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=3.4e-15  Score=114.61  Aligned_cols=70  Identities=27%  Similarity=0.435  Sum_probs=63.6

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .+.+|.||.+++|+||||+|++|++|+++|||+|+|...+.     +..++.|+|+|++++|+.|+.+|.++|++
T Consensus         3 ~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-----SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-----CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999999976432     45789999999999999999999999976

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=3e-15  Score=116.97  Aligned_cols=75  Identities=23%  Similarity=0.448  Sum_probs=68.0

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ...++.+|+||.+++|+||||+|++|++|+++|||+|.|.+++..+   .+.+|.|+|+|++++|.+|..+|.++|.+
T Consensus         5 ~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           5 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999999999998764333   36789999999999999999999999976

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=6e-15  Score=113.10  Aligned_cols=70  Identities=29%  Similarity=0.473  Sum_probs=62.7

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      .++|+||.+++|+||||+|++|++|+++|||+|+|.++++...  .+.+|+|+|+|++++|.+|+.+|.++|
T Consensus         4 ~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~--~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP--GTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCST--TCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCC--CCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            6899999999999999999999999999999999988744222  367999999999999999999998875

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=7.3e-15  Score=111.67  Aligned_cols=70  Identities=27%  Similarity=0.513  Sum_probs=61.7

Q ss_pred             EEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010374          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (512)
Q Consensus       142 ~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l  213 (512)
                      +++|+||++++|+||||+|++|++|+++|||+|+|.++.. + +..+.+|+|+|+|++++|.+|..+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~-~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-P-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-T-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-C-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            5689999999999999999999999999999999987632 2 23467899999999999999999998864

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.7e-14  Score=110.96  Aligned_cols=71  Identities=31%  Similarity=0.518  Sum_probs=64.7

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .+|.+|+||.+++|+||||+|++|++|+++|||+|+|.+..  +   .+.+|+|+|+|++++|.+|+.+|.++|++
T Consensus         3 ~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~--~---~~~~r~i~I~G~~~~v~~A~~~I~~~i~e   73 (75)
T d1zzka1           3 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL--E---GSEDRIITITGTQDQIQNAQYLLQNSVKQ   73 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT--S---CSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999997542  2   36789999999999999999999999986

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=1.9e-14  Score=111.85  Aligned_cols=73  Identities=26%  Similarity=0.397  Sum_probs=65.8

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||.+++|+|||++|.+|++|++.|||+|.|++.+     .+++++.|+|+|++++|+.|+.+|.+.|.++
T Consensus         6 ~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~-----~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           6 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----GGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            468899999999999999999999999999999999996532     2467899999999999999999999999864

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1e-14  Score=110.41  Aligned_cols=69  Identities=29%  Similarity=0.455  Sum_probs=62.6

Q ss_pred             CeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCcccCcHHHHHHHHHHH
Q 010374           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (512)
Q Consensus        43 ~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~a~~~i~~  122 (512)
                      +++.+|+||.+++|+||||+|++|++|+++|||+|.|++..+++++|+|+|+|++++             +..|..+|.+
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G~~~~-------------v~~A~~~I~~   67 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS-------------ISLAQYLINA   67 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCTTCSEEEEEEEECHHH-------------HHHHHHHHHH
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCCCCCcEEEEEEeCHHH-------------HHHHHHHHHH
Confidence            478999999999999999999999999999999999998888999999999999887             5677777776


Q ss_pred             HH
Q 010374          123 RI  124 (512)
Q Consensus       123 ~i  124 (512)
                      ++
T Consensus        68 ~i   69 (70)
T d1wvna1          68 RL   69 (70)
T ss_dssp             HT
T ss_pred             Hc
Confidence            54

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.48  E-value=3.7e-14  Score=116.13  Aligned_cols=77  Identities=19%  Similarity=0.341  Sum_probs=67.2

Q ss_pred             CceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhch
Q 010374          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (512)
Q Consensus       344 ~~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~  423 (512)
                      ...++.+|.||..++|+||||+|.+|++|+++|||+|.|.+....   ....+|.|+|+|++++|..|+.+|.++|++..
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCcH
Confidence            356889999999999999999999999999999999999765332   23568999999999999999999999997643

>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=1.7e-14  Score=110.63  Aligned_cols=71  Identities=23%  Similarity=0.426  Sum_probs=64.2

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..+++|+||.+++|+||||+|++|++|+++|||+|+|.+.+.     .+.+|+|+|+|++++|.+|..+|.++|.+
T Consensus         2 ~~~~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i~~   72 (74)
T d1j4wa1           2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDG-----TTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTT-----SCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccCCC-----CCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999987632     25689999999999999999999999875

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=7.6e-14  Score=108.75  Aligned_cols=73  Identities=15%  Similarity=0.210  Sum_probs=64.2

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhch
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~~  423 (512)
                      ..++..+.||..++++|||++|++|++|+++|||+|+|++.+      +.+.+.|+|+|++++|+.|+.+|.+++++++
T Consensus         8 ~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~------~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           8 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSG------APDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTT------CSCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCcc------CCCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            457889999999999999999999999999999999996542      2234589999999999999999999998753

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=7.2e-14  Score=114.37  Aligned_cols=77  Identities=27%  Similarity=0.430  Sum_probs=68.0

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ....++.+|+||..++|+||||+|.+|++|+++|||+|.|.+.+..   ....+|+|+|+|++++|.+|+.+|.++|.+.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4456889999999999999999999999999999999999876322   2356899999999999999999999999874

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=6e-14  Score=108.90  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=66.8

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ...++.+|+||.+++|+|||++|.+|++|+++|||+|.|.+.+  +   .+.+++|+|+|++++|.+|+.+|.++|.++
T Consensus         5 ~~~~t~~i~IP~~~~g~iIG~~G~~i~~I~~~tg~~I~i~~~~--~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   78 (79)
T d1x4na1           5 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCC--C---CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            4568999999999999999999999999999999999998652  2   367899999999999999999999999874

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1.9e-13  Score=106.39  Aligned_cols=71  Identities=18%  Similarity=0.299  Sum_probs=63.7

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||..++|+|||++|++|++|+++|||+|.+++.       ++.++.|+|+|++++|..|..+|.+++++.
T Consensus         8 ~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           8 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999643       245678999999999999999999998773

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.1e-13  Score=106.06  Aligned_cols=72  Identities=18%  Similarity=0.271  Sum_probs=64.0

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .++.+|.||..++++|||++|++|++|+++|||+|++++.+. +   ...++.|+|+|++++|..|..+|.+.+++
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C---CCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999999999999965422 2   45677999999999999999999999876

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=1.6e-13  Score=107.78  Aligned_cols=73  Identities=19%  Similarity=0.219  Sum_probs=65.2

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..++++|.||..++++|||++|++|++|+++|||+|+|++.+. +   ...++.|+|+|+.++|.+|..+|.+++.+
T Consensus         8 ~~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           8 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C---CCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            4568899999999999999999999999999999999976522 2   36788999999999999999999999876

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=3.1e-13  Score=102.35  Aligned_cols=66  Identities=21%  Similarity=0.286  Sum_probs=59.3

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLR  418 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~  418 (512)
                      ..+.+|.||..++++|||++|++|++|+++|||+|+|++.       .++++.|+|+|++++|+.|+.+|+++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999643       34567899999999999999999875

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=4.3e-13  Score=104.40  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=64.4

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ....++..+.||..++++|||++|.+|++|+++|||+|+|++.+.      ..++.|+|+|++++|.+|+.+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~~e   78 (81)
T d2ctma1           6 LEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEE   78 (81)
T ss_dssp             TTTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hhcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHH
Confidence            345668899999999999999999999999999999999976632      2356899999999999999999999876

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=4.7e-13  Score=104.48  Aligned_cols=71  Identities=17%  Similarity=0.221  Sum_probs=62.4

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++.+|.||..+||+|||++|++|++|+++ ++|+|++++.       ++.++.|+|+|++++|+.|+.+|++++++.
T Consensus         8 ~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           8 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            3578999999999999999999999999987 5899988543       345679999999999999999999999863

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=4e-13  Score=104.60  Aligned_cols=72  Identities=21%  Similarity=0.327  Sum_probs=65.0

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ....++.+|.||..++++|||++|.+|++|+++|||+|.|++.+       +.++.|+|+|++++|.+|..+|.+++.+
T Consensus         6 ~~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-------~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           6 LQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CCSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             hcCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCCC-------CCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34567999999999999999999999999999999999997652       4567899999999999999999999876

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=1e-12  Score=104.65  Aligned_cols=69  Identities=20%  Similarity=0.254  Sum_probs=62.7

Q ss_pred             eeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       346 ~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .++..|.||..++++|||++|++|++|+++|||+|.+++.       ++.+..|+|+|++++|+.|+.+|.+++.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999653       34556899999999999999999998876

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=7.8e-13  Score=103.22  Aligned_cols=73  Identities=23%  Similarity=0.302  Sum_probs=64.3

Q ss_pred             CCcceEEEEEeeCCceeEEecCCChhHHHHHhh-cCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE-TRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       137 ~~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..+.++.+|.||..++++||||+|++|++|+++ ++|+|.++..+       +.++.|+|+|++++|.+|..+|.+++++
T Consensus         6 ~~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~~v~e   78 (82)
T d2ctja1           6 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-------SGSDTVVIRGPSSDVEKAKKQLLHLAEE   78 (82)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCTT-------TTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             hcCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCCC-------CCCceEEEeCCHHHHHHHHHHHHHHHhh
Confidence            345678999999999999999999999999987 59999987652       5578999999999999999999999987


Q ss_pred             C
Q 010374          216 N  216 (512)
Q Consensus       216 ~  216 (512)
                      .
T Consensus        79 ~   79 (82)
T d2ctja1          79 K   79 (82)
T ss_dssp             H
T ss_pred             h
Confidence            4

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=1.5e-12  Score=98.54  Aligned_cols=66  Identities=23%  Similarity=0.370  Sum_probs=59.7

Q ss_pred             ceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHH
Q 010374          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASR  212 (512)
Q Consensus       140 ~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~  212 (512)
                      ..+++|.||..++++|||++|++|++|+++|||+|+|++++       +.++.|+|+|++++|++|..+|.++
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCCC-------CCCCEEEEECCHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999999999997652       5567899999999999999999875

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.4e-12  Score=102.47  Aligned_cols=70  Identities=24%  Similarity=0.369  Sum_probs=63.8

Q ss_pred             cceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       139 ~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ..++..|.||.+++++|||++|.+|++|+++|||+|.|++.+       +.++.|+|+|++++|.+|..+|.+++.+
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~-------~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCCC-------CCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            367999999999999999999999999999999999997652       4567899999999999999999998876

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2.9e-12  Score=98.32  Aligned_cols=63  Identities=24%  Similarity=0.304  Sum_probs=56.0

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHH
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVT  416 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~  416 (512)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|.+..         ++++.|+|.| ++++|+.|+.+|.
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~---------~~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHS
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec---------CCCceEEEEECCHHHHHHHHHHHH
Confidence            3578999999999999999999999999999999999854         2346899999 7999999999884

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.21  E-value=6e-12  Score=97.86  Aligned_cols=63  Identities=17%  Similarity=0.260  Sum_probs=57.1

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..+.||.+++|.|||++|++|++|+++|||+|.|.+           +..|+|+|++++++.|+.+|...+++.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            568999999999999999999999999999999942           348999999999999999998888764

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=2.3e-11  Score=96.16  Aligned_cols=68  Identities=16%  Similarity=0.276  Sum_probs=60.5

Q ss_pred             ceeEEEEEecCCceeeeecCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhhc
Q 010374          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       345 ~~~t~~l~VP~~~vG~IIGkgG~~IkeI~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..++..|.||..+|++|||++|++|++|+++ ++++|.+++          +...|+|+|++++|+.|..+|.+++++.
T Consensus        19 ~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          19 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999 589999953          2347999999999999999999998763

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=3.7e-11  Score=94.92  Aligned_cols=68  Identities=19%  Similarity=0.295  Sum_probs=61.3

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhc-CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTET-RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      ...++..|.||..+++.|||++|++|++|++++ +++|.++.+          +..|+|+|++++|++|..+|.+++.+
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~~----------~~~v~i~G~~~~ve~Ak~~I~~iv~e   86 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----------EDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----------SCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC----------CceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            456799999999999999999999999999995 899999644          45799999999999999999999876

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=3.6e-11  Score=92.04  Aligned_cols=64  Identities=22%  Similarity=0.257  Sum_probs=56.9

Q ss_pred             CcceEEEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHH
Q 010374          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIA  210 (512)
Q Consensus       138 ~~~~~~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~  210 (512)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.+..+         .++.|+|.| ++++|++|..+|.
T Consensus         5 ~~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---------~~g~v~I~g~~~eav~~A~~~Ie   69 (78)
T d2cpqa1           5 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLE   69 (78)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHS
T ss_pred             cCCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---------CCceEEEEECCHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999988654         246799999 6999999998884

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.09  E-value=3.4e-11  Score=93.54  Aligned_cols=63  Identities=25%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             EEEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010374          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (512)
Q Consensus       143 ~~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~  216 (512)
                      ..+.||.+.++.||||+|++|++|+++|||+|.|.++           ..|+|+|++++|.+|..+|..++.+.
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~-----------g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQN-----------GLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTT-----------SEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCC-----------CEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3588999999999999999999999999999999543           47999999999999999999988773

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.78  E-value=3.5e-09  Score=81.66  Aligned_cols=64  Identities=20%  Similarity=0.170  Sum_probs=52.2

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEE-----cCHHHHHHHHHHHHHHHhhc
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT-----GSLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~-----G~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..+.||.+.+|.|||++|++|++|+++|||+|+|..+          +..|.+.     |.+.+++.|..+|.+..+..
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d----------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE----------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT----------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC----------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            3589999999999999999999999999999999643          2245554     57888999988888776543

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.78  E-value=9.9e-11  Score=87.35  Aligned_cols=61  Identities=11%  Similarity=0.086  Sum_probs=46.4

Q ss_pred             EEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhh
Q 010374          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRA  421 (512)
Q Consensus       350 ~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~~  421 (512)
                      .+.||.+.+|.||||+|++|++|+++|||+|.|.+           +..|+|+|. ++.++.|..+|....++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----------~g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----------NGRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----------TSEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----------CCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999999942           237999995 77899999988765554

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.72  E-value=8.6e-09  Score=79.61  Aligned_cols=63  Identities=13%  Similarity=0.227  Sum_probs=54.8

Q ss_pred             EEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhhc
Q 010374          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRAN  422 (512)
Q Consensus       349 ~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~~~  422 (512)
                      ..+.||.+.+|.|||++|++|+.|+++|||+|.|..           +-.|.|.| +.+.+..|+.+|....++.
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea   66 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999999999952           23799999 5889999999988877654

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.68  E-value=2.8e-10  Score=84.82  Aligned_cols=61  Identities=11%  Similarity=0.098  Sum_probs=46.6

Q ss_pred             EEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010374          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (512)
Q Consensus       144 ~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I~~~l~~  215 (512)
                      .+.||.+.+|.||||+|++|++|+++|||+|.|.++           ..|+|+|. .+++.+|..+|..+.++
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~-----------g~v~I~g~~~~~v~~A~~~I~~i~~e   65 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANN-----------GRIWATCPSRFSEEILIEAIRKIENE   65 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTT-----------SEEEC-----CTTCCTHHHHTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcCC-----------CEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999999999533           36999996 67899999999765554

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.67  E-value=9.7e-09  Score=79.12  Aligned_cols=48  Identities=19%  Similarity=0.355  Sum_probs=41.0

Q ss_pred             EEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010374           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (512)
Q Consensus        46 ~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (512)
                      +.+.||.+++|.||||+|++|++|+++|||+|+|++.     +..+.+.+..+
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-----~g~v~i~~~~~   52 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-----NSMVIVEPEAE   52 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-----TTEEEEEESST
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-----CCeEEEecCCc
Confidence            3589999999999999999999999999999999754     45677776544

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.62  E-value=1.9e-08  Score=77.62  Aligned_cols=61  Identities=13%  Similarity=0.209  Sum_probs=54.2

Q ss_pred             EEEeeCCceeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010374          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (512)
Q Consensus       144 ~llVP~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I~~~l~~  215 (512)
                      .+.||.+.++.|||++|++|+.|+++|||+|.|.++           -.|.|.|+ .+.+.+|+.+|..+..+
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~-----------G~V~I~g~~~~~~~~A~~~I~~I~~e   65 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN-----------GRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT-----------TEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC-----------cEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999999999999643           26999995 88899999999887765

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.57  E-value=2.6e-09  Score=74.79  Aligned_cols=48  Identities=23%  Similarity=0.475  Sum_probs=16.1

Q ss_pred             EEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010374           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (512)
Q Consensus        45 ~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (512)
                      ..+|.||.+++|.|||++|++||+|+++|||+|.|.+      +..|+|++..+
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d------dg~v~I~a~~~   51 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED------DGTIYIGAADG   51 (54)
T ss_dssp             CC---------------------CHHHHSCCCC--------------CCCCBSS
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC------CeEEEEEecCc
Confidence            3578999999999999999999999999999999974      56799988654

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.55  E-value=2.5e-09  Score=74.87  Aligned_cols=46  Identities=26%  Similarity=0.445  Sum_probs=14.2

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS  404 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~  404 (512)
                      ..+|.||.+.+|.|||++|++||+|+++|||+|.|.           ++..|+|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~-----------ddg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIE-----------DDGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC-------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEe-----------CCeEEEEEec
Confidence            356889999999999999999999999999999994           2457777764

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.43  E-value=6.6e-08  Score=77.12  Aligned_cols=54  Identities=22%  Similarity=0.275  Sum_probs=47.7

Q ss_pred             CceeeeecCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhh
Q 010374          356 AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (512)
Q Consensus       356 ~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~~  421 (512)
                      .+.|.|||++|.+|+.|++.|||+|.|..            ..|.|.|++++++.|+.+|..++..
T Consensus        22 R~~GrIIG~gGktik~Ie~~Tg~~I~I~d------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          22 RIKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HHhcceeCCCcHHHHHHHHHHCCeEEEeC------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            34799999999999999999999999942            2588889999999999999988865

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.36  E-value=8.6e-08  Score=76.44  Aligned_cols=52  Identities=21%  Similarity=0.240  Sum_probs=46.8

Q ss_pred             eeEEecCCChhHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010374          152 IGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (512)
Q Consensus       152 vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~  215 (512)
                      .|+|||++|.+|+.|++.|||+|.|..+            .|.|.|+++++..|..+|..++.+
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d~------------~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGEY------------EVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECSS------------EEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeCC------------eEEEEECchhHHHHHHHHHHHHcC
Confidence            5899999999999999999999999533            477889999999999999999965

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.12  E-value=4.6e-06  Score=68.46  Aligned_cols=75  Identities=19%  Similarity=0.373  Sum_probs=57.7

Q ss_pred             eEEEEEecCC------ceeeeecCCchhHHHHHHHhCCeEEEecCCCC----------CCCC-CCCceEEEEEc-CHHHH
Q 010374          347 ITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNENV----------PKVA-YEDEEMVQITG-SLDVA  408 (512)
Q Consensus       347 ~t~~l~VP~~------~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~----------p~~~-~~~~r~V~I~G-~~~~v  408 (512)
                      ++..|.||-+      ++|.|||.+|+++|+|+++|||+|.|-.+...          +... .+..--|.|++ +++.+
T Consensus         3 ~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~~   82 (122)
T d1k1ga_           3 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENV   82 (122)
T ss_dssp             EEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHH
T ss_pred             eeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhhH
Confidence            5778889865      48999999999999999999999999764320          1000 12233577888 67899


Q ss_pred             HHHHHHHHHHHhh
Q 010374          409 SSALSQVTLRLRA  421 (512)
Q Consensus       409 ~~A~~~I~~~l~~  421 (512)
                      ..|+.+|...|..
T Consensus        83 ~~A~~~i~~ll~~   95 (122)
T d1k1ga_          83 KKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999965

>d1k1ga_ d.51.1.1 (A:) RNA splicing factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: RNA splicing factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=1e-05  Score=66.37  Aligned_cols=76  Identities=25%  Similarity=0.360  Sum_probs=57.0

Q ss_pred             ceEEEEEeeCCc------eeEEecCCChhHHHHHhhcCceEEEeecCCC----------CcccCCC-CceEEEecC-HHH
Q 010374          140 LITVRMLVPADQ------IGCVIGKGGQVIQNIRTETRAQIRILKDEHL----------PLCALSF-DELLQVAGE-PAV  201 (512)
Q Consensus       140 ~~~~~llVP~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~~~~~-dr~v~I~G~-~~~  201 (512)
                      .++.+|+||-+.      +|.|||.+|.++|+|+++|||+|.|-.....          +...... +--|.|+++ .+.
T Consensus         2 k~~~Ki~iP~~~~P~fNfvG~IlGPrG~t~K~Le~eTgckI~IrGrGS~kd~~~~~~~~~~~~~~~epLHv~I~a~~~~~   81 (122)
T d1k1ga_           2 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN   81 (122)
T ss_dssp             CEEEEEECCTTTCCSHHHHHHHHCSSSHHHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH
T ss_pred             ceeEEEecCCccCCCCCeeeeEeCCCCchHHHHHHHHCCEEEEEecCCcccccccccCCCCCCCCCCCceEEEecCChhh
Confidence            367889999765      8999999999999999999999999764221          1011111 223667775 668


Q ss_pred             HHHHHHHHHHHHhc
Q 010374          202 VRKALVQIASRLHE  215 (512)
Q Consensus       202 V~~A~~~I~~~l~~  215 (512)
                      +.+|+.+|..+|.+
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999965

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.74  E-value=8.9e-06  Score=67.47  Aligned_cols=76  Identities=18%  Similarity=0.332  Sum_probs=55.5

Q ss_pred             eEEEEEeeC------CceeEEecCCChhHHHHHhhcCceEEEeecCCC------------Cccc-CCCCceEEEecCH--
Q 010374          141 ITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL------------PLCA-LSFDELLQVAGEP--  199 (512)
Q Consensus       141 ~~~~llVP~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~dr~v~I~G~~--  199 (512)
                      ++.+|+||.      +.+|.|||++|.++|+|+++|||+|.|-.....            |... ...+--|.|+++.  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            467889994      478999999999999999999999999875321            0000 1223347787752  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 010374          200 ----AVVRKALVQIASRLHEN  216 (512)
Q Consensus       200 ----~~V~~A~~~I~~~l~~~  216 (512)
                          ..+.+|+.+|..+|...
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p~  102 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVPA  102 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCC
Confidence                35888999999888653

>d2bl5a1 d.51.1.1 (A:1-134) Quaking protein A (Xqua) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Quaking protein A (Xqua)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=97.61  E-value=4.3e-05  Score=63.23  Aligned_cols=74  Identities=19%  Similarity=0.269  Sum_probs=53.1

Q ss_pred             eEEEEEecC------CceeeeecCCchhHHHHHHHhCCeEEEecCCCC------------CC-CCCCCceEEEEEcCH--
Q 010374          347 ITTRILVPS------AQIGCLIGRGGAIISEMRSATRASIRILTNENV------------PK-VAYEDEEMVQITGSL--  405 (512)
Q Consensus       347 ~t~~l~VP~------~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~~~~------------p~-~~~~~~r~V~I~G~~--  405 (512)
                      ++.+|.||.      +++|.|||.+|.++|+|+++|||+|.|-.+...            |. ...+++--|.|++.-  
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~IrGrGS~k~~~~~~~~~~~~~~~~~~epLHv~I~a~~~~   81 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQ   81 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCC
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEEecCCCcCccccccccCCCCCcCCCCCCEEEEEecCcH
Confidence            456778873      578999999999999999999999999775421            00 001234457888742  


Q ss_pred             ----HHHHHHHHHHHHHHh
Q 010374          406 ----DVASSALSQVTLRLR  420 (512)
Q Consensus       406 ----~~v~~A~~~I~~~l~  420 (512)
                          ..+..|+.+|...|.
T Consensus        82 ~~a~~kl~~A~~~I~~lL~  100 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLV  100 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcC
Confidence                357788888887774

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.57  E-value=0.013  Score=41.90  Aligned_cols=38  Identities=32%  Similarity=0.408  Sum_probs=35.2

Q ss_pred             EEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       348 t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      ...+.||.+..+..|||+|.+|+-..+.||.+|.|...
T Consensus        28 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~   65 (68)
T d1hh2p3          28 AARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI   65 (68)
T ss_dssp             EEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEc
Confidence            57789999999999999999999999999999999654

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.57  E-value=0.0087  Score=42.69  Aligned_cols=42  Identities=21%  Similarity=0.201  Sum_probs=37.3

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecCC
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET   82 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~~   82 (512)
                      .+.-.+.+.||.+..+..|||+|.+++-..+-||.+|.|-.+
T Consensus        23 e~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          23 QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CCCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            344578899999999999999999999999999999999643

>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.28  E-value=0.012  Score=42.07  Aligned_cols=41  Identities=29%  Similarity=0.385  Sum_probs=36.5

Q ss_pred             CCCeEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEecC
Q 010374           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (512)
Q Consensus        41 ~~~~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i~~   81 (512)
                      .+.-.+.+.||.+..+..|||+|.+++-..+-||.+|.|..
T Consensus        24 e~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          24 KENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            34446889999999999999999999999999999999964

>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Transcription factor NusA, C-terminal domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.13  E-value=0.016  Score=41.30  Aligned_cols=39  Identities=26%  Similarity=0.298  Sum_probs=35.7

Q ss_pred             eEEEEEecCCceeeeecCCchhHHHHHHHhCCeEEEecC
Q 010374          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (512)
Q Consensus       347 ~t~~l~VP~~~vG~IIGkgG~~IkeI~~~TGa~I~i~~~  385 (512)
                      -...+.||.+.....|||+|.+|+-..+.||.+|.|..+
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            367789999999999999999999999999999999754

>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.47  E-value=0.23  Score=37.43  Aligned_cols=36  Identities=11%  Similarity=0.269  Sum_probs=29.3

Q ss_pred             eEEEEEecCCceeeeccCCchHHHHHHHhhCCeEEe
Q 010374           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI   79 (512)
Q Consensus        44 ~~~rilvp~~~~g~IIGk~G~~I~~I~~~tga~I~i   79 (512)
                      ..++|.|....-|.|||++|+.|++|+++..-++.+
T Consensus        35 ~~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~   70 (92)
T d1wh9a_          35 TRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF   70 (92)
T ss_dssp             SCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCC
T ss_pred             CeEEEEEEeCCCceeeccCchhHHHHHHHHHHHHCC
Confidence            346788899999999999999999998876544433