Citrus Sinensis ID: 010746

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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--
Protein Sequence
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGRG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccEEEEEccccHHHHHHHHHHcccEEEcccccccccEEEEEEccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccEEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEEcccccccccccccEEEEEEcHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccHHHHHHHcccccccccccccccccEEEEccccccccccHHHHHHHHcccccccccccccccccEEEEEEEccccEEEEEccccccHHHHHHHHccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEccccccccccEEEEEccHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEEccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHcccEEEEccccccccccEEEEEcccccccHHHHHHHHHHHHHHHccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
magqsninygkrthfqsdaatnggskrrnpgdeteqrgigsedtVYRYLCplrkigsiigkGGEIVKQLRSETksnirisetvpgcdeRIVTIYsssegtnlfedsgefvspaQDALFRVHDrivaedsladdefgeLTLITVRMlvpadqigcvigkggqVIQNIRTETRAQIRILkdehlplcaLSFDELLQVAGEPAVVRKALVQIASRlhenpsrsqhLLLSsssniyqssgvylsaplvgsygnysarrdeasAREFSLRlvcpagniggvigkggGIIKQIRQesgasikvdssgaegddciifistkeffedpsptiTAALrlqprcsekteresgdpvittrilvpsaqigcligrgGAIISEMRSATRASIRIltnenvpkvayedeeMVQITGSLDVASSALSQVTLRLRANTFeregalaahppvlpyvpmslditdgskygnrdnqsrgrgnsyatgnlpgrdsygsyggslsgggnaygaygdhssgrg
Flexible Loop (DISEMBL)
magqsninygkrthfqsdaatnggskrrnpgdeteqrgigsedtvYRYLCPLRkigsiigkggeIVKQLrsetksnirisetvpgcderIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAedsladdefGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPagniggvigkGGGIIKQIRQESGAsikvdssgaegDDCIIFIStkeffedpsPTITAAlrlqprcsekteresgdpvittrilvpsaqiGCLIGRGGAIISEMRSATRasiriltnenvpkvaYEDEEMVQITGSLDVASSALSQVTLRLRANTFERegalaahppvlpyvpMSLDITDGSkygnrdnqsrgrgnsyatgnlpgRDSYGSYGGSLSgggnaygaygdhssgrg
Low Complexity Region (SEG)
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRkigsiigkggeivkQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPsrsqhlllssssNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAgniggvigkgggiikqiRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDsygsyggslsgggnaygaygDHSSGRG
Disordered region (IsUnstruct)
******************************************DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASR******************IYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQ*************EGDDCIIFISTKEFFEDP**TITAA******************VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDI********************************************************
Disordered Region (DISOPRED)
*********************************************YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRV**********************VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP************************************************************************************************************************************RILVPSAQIGCLIGRGGAIISEMRSATRASIR***********YEDEEMVQITGSLDVASSALSQVTLR************************************************************************************
Disordered Region (DISEMBL)
MAGQSNINYGKRTHFQSD*******************GIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQE***********AEGDDCIIFISTKEFFEDPSPTITAALRLQP************PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGRG
Disordered Region (DISPRO)
****************************************SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSL******ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS*SQH************************************AREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF*********PPVLPYVPMSLDITDGSK**************YATGN*P*RDSY*SY*GS*******************
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)
MAGQSNINYGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNRDNQSRGRGNSYATGNLPGRDSYGSYGGSLSGGGNAYGAYGDHSSGRG
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	502	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.904	0.749	0.301	8e-50
Q5RB68	556	Insulin-like growth facto	no	no	0.681	0.615	0.261	2e-16
Q9CPN8	579	Insulin-like growth facto	no	no	0.745	0.645	0.243	8e-15
Q0VCU0	403	Poly(rC)-binding protein	no	no	0.476	0.593	0.299	1e-14
P57724	403	Poly(rC)-binding protein	no	no	0.480	0.598	0.297	1e-14
Q9Y6M1	599	Insulin-like growth facto	no	no	0.693	0.580	0.250	1e-14
P57722	371	Poly(rC)-binding protein	no	no	0.298	0.404	0.312	1e-14
P57721	371	Poly(rC)-binding protein	no	no	0.298	0.404	0.312	2e-14
P57723	403	Poly(rC)-binding protein	no	no	0.462	0.575	0.292	2e-14
O00425	579	Insulin-like growth facto	no	no	0.743	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 = 8e-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 = 87.8 bits (216), Expect = 2e-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 = 8e-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 = 85/284 (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 QNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE-------- 215
           + IR  T AQ+++  D    L   S +  + V+G P  +   + QI + + E        
Sbjct: 125 KEIRETTGAQVQVAGD----LLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATI 180

Query: 216 --NPSRSQHLLLSSSSNIYQSSGVY-------------LSAPLVGSYGNYSARRDEASAR 260
             +PS S   +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 = 81.6 bits (200), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 84/282 (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 IRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE---------- 215
           IR  T AQ+++  D    L   S +  + V+G P  +   + QI + + E          
Sbjct: 127 IRETTGAQVQVAGD----LLPNSTERAVTVSGVPDAIILCVRQICAVILESPPKGATIPY 182

Query: 216 NPSRSQHLLLSSSSNIYQSSGVY-------------LSAPLVGSYGNYSARRDEASAREF 262
           +PS S   +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|Q9Y6M1|IF2B2_HUMAN Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2 PE=1 SV=2

 Score = 81.6 bits (200), 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 IEIMKKLRE-AFENDMLAVNQQANLI--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|P57722|PCBP3_MOUSE Poly(rC)-binding protein 3 OS=Mus musculus GN=Pcbp3 PE=2 SV=3

 Score = 81.3 bits (199), 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|P57721|PCBP3_HUMAN Poly(rC)-binding protein 3 OS=Homo sapiens GN=PCBP3 PE=2 SV=2

 Score = 81.3 bits (199), Expect = 2e-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|P57723|PCBP4_HUMAN Poly(rC)-binding protein 4 OS=Homo sapiens GN=PCBP4 PE=2 SV=1

 Score = 81.3 bits (199), Expect = 2e-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|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	502
296086352	583	unnamed protein product [Vitis vinifera]	0.904	0.778	0.784	0.0
359473301	517	PREDICTED: KH domain-containing protein	0.904	0.878	0.784	0.0
147853553	543	hypothetical protein VITISV_009249 [Viti	0.918	0.848	0.742	0.0
224112243	553	predicted protein [Populus trichocarpa]	0.972	0.882	0.678	0.0
53749469	533	KH domain containing protein [Solanum de	0.994	0.936	0.634	1e-178
356550877	561	PREDICTED: KH domain-containing protein	0.994	0.889	0.618	1e-176
356572762	548	PREDICTED: KH domain-containing protein	0.994	0.910	0.615	1e-175
113205451	600	KH domain containing protein, putative [	0.996	0.833	0.634	1e-175
449527609	546	PREDICTED: KH domain-containing protein	0.932	0.857	0.633	1e-174
449447377	545	PREDICTED: KH domain-containing protein	0.932	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 (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: 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 (1757), 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 (1674), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/532 (67%), Positives = 424/532 (79%), Gaps = 44/532 (8%)

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 DGSKYGSRDSQSRGRGYTSSSSGYGSRDVHPSDSYGSNGGSLIGGESSYGAY 526

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 =  630 bits (1625), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 327/515 (63%), Positives = 398/515 (77%), Gaps = 16/515 (3%)

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 501
           G     D     SYGGS  GGG  Y  YG +SSGR
Sbjct: 479 GGHDYNDLSPSDSYGGSQVGGGGNYAPYGVYSSGR 513

Source: Solanum demissum

Species: Solanum demissum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  624 bits (1608), 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|356572762|ref|XP_003554535.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  622 bits (1603), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 326/530 (61%), Positives = 395/530 (74%), Gaps = 31/530 (5%)

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 501
            +  GRG+        + +L   D YGSYGGS  G  +AYGAYG +S GR
Sbjct: 479 GKRHGRGHSYSSGYGGSSDLAAGDIYGSYGGSQLGSNSAYGAYGSYSLGR 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 (1598), 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 =  619 bits (1595), 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 =  619 bits (1595), 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

---

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	502
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.912	0.956	0.542	2.9e-126
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.619	0.567	0.468	1.2e-72
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.406	0.316	0.341	4e-45
TAIR|locus:2056951	153	AT2G03110 "AT2G03110" [Arabido	0.278	0.915	0.556	3e-37
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.420	0.323	0.297	4.6e-35
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.396	0.328	0.315	6.8e-33
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.352	0.285	0.345	2.1e-29
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.354	0.308	0.346	1.6e-18
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.336	0.267	0.301	1.3e-14
RGD|1307430	319	Pcbp3 "poly(rC) binding protei	0.264	0.416	0.306	2.1e-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 = 4.0e-45, Sum P(2) = 4.0e-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 = 4.6e-35, Sum P(2) = 4.6e-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 = 6.8e-33, Sum P(2) = 6.8e-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 = 2.1e-29, Sum P(2) = 2.1e-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 = 1.6e-18, Sum P(2) = 1.6e-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 = 1.3e-14, Sum P(2) = 1.3e-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 = 2.1e-12, Sum P(2) = 2.1e-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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 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.

---

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	502
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-18
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-17
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-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	9e-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	9e-09
pfam13014	42	pfam13014, KH_3, KH domain	5e-08
smart00322	68	smart00322, KH, K homology RNA-binding domain	6e-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	9e-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	6e-04
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	6e-04
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.001
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.001
cd02394	62	cd02394, vigilin_like_KH, K homology RNA-binding d	0.002
COG0195	190	COG0195, NusA, Transcription elongation factor [Tr	0.002
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	0.002
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	0.004
cd02393	61	cd02393, PNPase_KH, Polynucleotide phosphorylase (	0.004

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

 Score = 77.9 bits (193), 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 = 75.6 bits (187), Expect = 3e-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 = 3e-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 = 9e-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 = 51.8 bits (125), 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 = 9e-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|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 = 49.2 bits (118), Expect = 6e-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|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 = 43.1 bits (102), Expect = 9e-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 = 40.7 bits (96), Expect = 6e-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 = 37.5 bits (88), 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|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

 Score = 36.7 bits (86), 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|223273 COG0195, NusA, Transcription elongation factor [Transcription]

 Score = 39.5 bits (93), Expect = 0.002
 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|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|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

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

 Score = 35.6 bits (83), Expect = 0.004
 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	502
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	99.96
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	99.91
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.89
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.83
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.62
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.6
PRK13763	180	putative RNA-processing protein; Provisional	99.59
PRK13763	180	putative RNA-processing protein; Provisional	99.56
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	99.35
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.27
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.24
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.23
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.23
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.22
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.19
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.17
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.15
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.14
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.1
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	99.05
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.04
PF13014	43	KH_3: KH domain	98.98
PF13014	43	KH_3: KH domain	98.9
smart00322	69	KH K homology RNA-binding domain.	98.88
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.83
smart00322	69	KH K homology RNA-binding domain.	98.76
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.74
KOG2113	394	consensus Predicted RNA binding protein, contains	98.4
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.32
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.28
PRK08406	140	transcription elongation factor NusA-like protein;	98.13
KOG2113	394	consensus Predicted RNA binding protein, contains	98.12
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.98
PRK08406	140	transcription elongation factor NusA-like protein;	97.75
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.61
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.59
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.59
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.52
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.44
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.41
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.3
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.3
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.08
COG0195	190	NusA Transcription elongation factor [Transcriptio	97.01
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.01
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.8
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.79
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.74
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.71
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.71
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.7
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.67
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.59
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.46
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.37
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.2
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.06
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.05
PRK00468	75	hypothetical protein; Provisional	96.03
TIGR01953	341	NusA transcription termination factor NusA. This m	95.96
TIGR01953	341	NusA transcription termination factor NusA. This m	95.94
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.92
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.83
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.73
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	95.72
PRK00106	535	hypothetical protein; Provisional	95.72
PRK02821	77	hypothetical protein; Provisional	95.72
PRK12704	520	phosphodiesterase; Provisional	95.61
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.61
PRK02821	77	hypothetical protein; Provisional	95.53
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.48
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	95.43
PRK00468	75	hypothetical protein; Provisional	95.42
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.4
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.32
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.26
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.25
COG1837	76	Predicted RNA-binding protein (contains KH domain)	95.24
PRK01064	78	hypothetical protein; Provisional	95.21
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.09
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.05
PRK09202	470	nusA transcription elongation factor NusA; Validat	94.82
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	94.8
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	94.78
PRK01064	78	hypothetical protein; Provisional	94.62
PRK12704	520	phosphodiesterase; Provisional	94.5
PRK00106	535	hypothetical protein; Provisional	94.41
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.38
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	93.45
PRK12705	508	hypothetical protein; Provisional	92.95
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	91.75
COG5166	657	Uncharacterized conserved protein [Function unknow	91.09
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	90.98
PRK12705	508	hypothetical protein; Provisional	90.84
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	90.77
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	90.6
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	89.45
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	88.89
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	88.73
COG5166	657	Uncharacterized conserved protein [Function unknow	88.5
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	87.86
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	87.61
KOG3875	362	consensus Peroxisomal biogenesis protein peroxin [	87.56
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	87.44
COG1855	604	ATPase (PilT family) [General function prediction	87.29
KOG3875	362	consensus Peroxisomal biogenesis protein peroxin [	87.22
KOG2874	356	consensus rRNA processing protein [Translation, ri	87.06
COG1782	637	Predicted metal-dependent RNase, consists of a met	87.01
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	86.76
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	86.56
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	86.52
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.98
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.9
KOG2874	356	consensus rRNA processing protein [Translation, ri	84.19
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	83.64
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.24
PRK13764	602	ATPase; Provisional	83.17
cd02413	81	40S_S3_KH K homology RNA-binding (KH) domain of th	82.58
PRK13764	602	ATPase; Provisional	82.54
COG1855	604	ATPase (PilT family) [General function prediction	82.34
PRK06418	166	transcription elongation factor NusA-like protein;	81.2
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	80.89

>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=6.5e-47  Score=389.42  Aligned_cols=398  Identities=42%  Similarity=0.609  Sum_probs=314.9

Q ss_pred             CCCccCCCCCcccCCCCCCCCCCCCCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCc
Q 010746            9 YGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDE   88 (502)
Q Consensus         9 ~~kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~e   88 (502)
                      ..++.........++..+++...+. .+....+...++||||+.+.+|.||||+|.+|++|+++|.++|+|.+..++|+|
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~e   87 (485)
T KOG2190|consen    9 PRPKNSTTSNVGDNGSIKRPSLGDP-VISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPE   87 (485)
T ss_pred             ccccCCCcccccCCCcccccCCCCC-cccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCc
Confidence            3445555566655555555555554 344455566669999999999999999999999999999999999999999999


Q ss_pred             cEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCC---Cc---CCCCccEEEEEEeeCCceeeeecCCChH
Q 010746           89 RIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLAD---DE---FGELTLITVRMLVPADQIGCVIGKGGQV  162 (502)
Q Consensus        89 rvv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~---~~---~~~~~~~~~~llVp~~~vg~IIGk~G~~  162 (502)
                      |+|+|+|...+        ..++++++|++++++.++......+   ++   +....++++|||||.+++|+||||+|+.
T Consensus        88 RIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~  159 (485)
T KOG2190|consen   88 RIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSL  159 (485)
T ss_pred             ceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHH
Confidence            99999997222        2788899999999999987422111   11   1122268999999999999999999999


Q ss_pred             HHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCC---CCccc
Q 010746          163 IQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQS---SGVYL  239 (502)
Q Consensus       163 Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~---gg~~~  239 (502)
                      ||+|+++|||+|+|.++ ++|.   +++|.|+|.|.+++|.+|+..|+.+|++++.+......+  +..|.+   .+...
T Consensus       160 Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~s--t~~y~P~~~~~~~~  233 (485)
T KOG2190|consen  160 IKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVS--TIPYRPSASQGGPV  233 (485)
T ss_pred             HHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCC--cccCCCcccccCcc
Confidence            99999999999999999 8998   578999999999999999999999999976542211111  111211   01111


Q ss_pred             cCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCC
Q 010746          240 SAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFED  319 (502)
Q Consensus       240 ~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~  319 (502)
                      .+.+......+........+.++.+++.+|...++.|+|+++..|+.|+.++++.|.+.....+   |+++++..+.+++
T Consensus       234 ~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~~  310 (485)
T KOG2190|consen  234 LPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPED  310 (485)
T ss_pred             ccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCccc
Confidence            1111111111122333345677888999999999999999999999999999999999988754   9999999999988


Q ss_pred             C-chhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceE
Q 010746          320 P-SPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEM  398 (502)
Q Consensus       320 ~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~  398 (502)
                      . +.++++++..++.+.+....+. ...++.+|+||.+++||||||+|++|.+||+.|||.|+|...++.   ...++++
T Consensus       311 ~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~~~~e~~  386 (485)
T KOG2190|consen  311 RYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---SGVREAL  386 (485)
T ss_pred             ccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---CCcceeE
Confidence            7 8899999999999988777655 788999999999999999999999999999999999999887653   2468899


Q ss_pred             EEEEcCHHHHHHHHHHHHHHHHhchhcccC
Q 010746          399 VQITGSLDVASSALSQVTLRLRANTFEREG  428 (502)
Q Consensus       399 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~  428 (502)
                      ++|+|+..+...|+.++..++.......++
T Consensus       387 ~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~  416 (485)
T KOG2190|consen  387 VQITGMLREDLLAQYLIRARLSAPKSSMGG  416 (485)
T ss_pred             EEecchhHHHHhhhhhcccccccCccCCCC
Confidence            999999999999999998888776544333

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

Probab=100.00  E-value=3.3e-44  Score=362.45  Aligned_cols=328  Identities=23%  Similarity=0.375  Sum_probs=254.6

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      ...+.++.||.+++++||||+|+.|..|..++||+|+|+....+..+|.+.++|.+++++.          |+..+..+.
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~----------aK~li~evv  121 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV----------AKQLIGEVV  121 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH----------HHHhhhhhh
Confidence            5667899999999999999999999999999999999988777889999999999999532          333333333


Q ss_pred             HHHhhhcccCC--CcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010746          122 DRIVAEDSLAD--DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP  199 (502)
Q Consensus       122 ~~i~~~~~~~~--~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~  199 (502)
                      ++..    ...  .+......++.+|+||.+.+|.||||+|++||.|++++||++.+..+.....   ..++.+.|+|++
T Consensus       122 ~r~~----~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp  194 (600)
T KOG1676|consen  122 SRGR----PPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP  194 (600)
T ss_pred             hccC----CCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence            3322    110  1112245679999999999999999999999999999999999999854432   478899999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCcccccccc
Q 010746          200 AVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGK  279 (502)
Q Consensus       200 ~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk  279 (502)
                      +.|+.|..+|.++|.+....           .+..++.         +++       ..-...+++|.||...||.||||
T Consensus       195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~---------~g~-------~~g~~~~~~V~VPr~~VG~IIGk  247 (600)
T KOG1676|consen  195 DKVEQAKQLVADILREEDDE-----------VPGSGGH---------AGV-------RGGGSATREVKVPRSKVGIIIGK  247 (600)
T ss_pred             HHHHHHHHHHHHHHHhcccC-----------CCccccc---------cCc-------CccccceeEEeccccceeeEEec
Confidence            99999999999999963211           0111000         000       11123378999999999999999


Q ss_pred             CcccccchhhhcCCeEEecCCCC-CCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC------CCCcee--EEE
Q 010746          280 GGGIIKQIRQESGASIKVDSSGA-EGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE------SGDPVI--TTR  350 (502)
Q Consensus       280 ~G~~Ik~i~~~sga~I~v~~~~~-~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~--~~~  350 (502)
                      +|++||+|+.+||++|+|.+++. ...+|++.|.|..      ..++.+.+++..+.+.....      ......  ...
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            99999999999999999998766 5789999988864      23444444433332221111      011222  788


Q ss_pred             EEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       351 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      |.||.+.||.||||+|++||.|..+|||++.+.+.   |+..+..+++|+|+|++.+|+.|..||.+++...
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=2e-42  Score=333.24  Aligned_cols=353  Identities=25%  Similarity=0.357  Sum_probs=274.3

Q ss_pred             CCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHH
Q 010746           39 IGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL  117 (502)
Q Consensus        39 ~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al  117 (502)
                      ....+.++|+|||-.++|.||||.|+|||.|.+.|.|+|+|.. +..|..|+.|+|.+++|.             +.+|+
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            4467899999999999999999999999999999999999984 456889999999999998             57788


Q ss_pred             HHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec
Q 010746          118 FRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG  197 (502)
Q Consensus       118 ~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G  197 (502)
                      .+|++-+..+...    +.....+.++++.++..||+||||.|.+||+|+.+||++|.|++-.++..+  +.||.|++.|
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            8888877654421    234467889999999999999999999999999999999999987666553  6799999999


Q ss_pred             CHHHHHHHHHHHHHHHhcCCCccccccccCCC---------CccCCCCcc--ccCCCcCCCC-CCCccc--Cccccccce
Q 010746          198 EPAVVRKALVQIASRLHENPSRSQHLLLSSSS---------NIYQSSGVY--LSAPLVGSYG-NYSARR--DEASAREFS  263 (502)
Q Consensus       198 ~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~---------~~~~~gg~~--~~~p~~~~~~-~~~~~~--~~~~~~~~~  263 (502)
                      ..++|..|..+|..+|++..+.+-  ...+..         +.++.+.+.  +++|..-+.. .|..|.  .....+.-.
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            999999999999999999755441  111110         011111110  1112111000 111111  112234557


Q ss_pred             EEEeccCCccccccccCcccccchhhhcCCeEEecCCC-CCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC-
Q 010746          264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG-AEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE-  341 (502)
Q Consensus       264 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~-~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~-  341 (502)
                      ++|.||...+|+|||++|.+||.|...+|+.|++..+. .+..+|+|+|+|..         ++.++.|.++..++..+ 
T Consensus       413 V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp---------eaqfKAQgrifgKikEen  483 (584)
T KOG2193|consen  413 VRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP---------EAQFKAQGRIFGKIKEEN  483 (584)
T ss_pred             eeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh---------HHHHhhhhhhhhhhhhhc
Confidence            89999999999999999999999999999999998765 34689999999963         45555555555444332 


Q ss_pred             ----CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010746          342 ----SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL  417 (502)
Q Consensus       342 ----~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~  417 (502)
                          ......++.+.||...+|+||||||.+++||++.|+|.|.|+++ +.|-  ..+..+|.|+|..-+.+.|+..|.+
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 4453  4566789999999999999999999


Q ss_pred             HHHhchh
Q 010746          418 RLRANTF  424 (502)
Q Consensus       418 ~l~~~~~  424 (502)
                      +|.+...
T Consensus       561 iv~qvkq  567 (584)
T KOG2193|consen  561 IVNQVKQ  567 (584)
T ss_pred             HHHHHHH
Confidence            9988653

>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=5.8e-35  Score=266.56  Aligned_cols=343  Identities=21%  Similarity=0.340  Sum_probs=224.7

Q ss_pred             CCCCCCCCCCCCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCccc
Q 010746           23 GGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNL  102 (502)
Q Consensus        23 ~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~  102 (502)
                      +...+|..+|- +..-+....+.++||+.++.+|.||||+|++||+|+.+++|+|.|++.  +.+||+++|+.+.+.   
T Consensus        28 ~~~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~t---  101 (390)
T KOG2192|consen   28 GEFGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIET---  101 (390)
T ss_pred             ccccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHH---
Confidence            44445555553 333346677999999999999999999999999999999999999988  788999999987443   


Q ss_pred             ccCCccCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCC
Q 010746          103 FEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL  182 (502)
Q Consensus       103 ~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~  182 (502)
                                +-+-|.+|+..+. +      .......+.+||||+.+++|.|||++|++||+|++++.|+++|..+   
T Consensus       102 ----------i~~ilk~iip~le-e------~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~---  161 (390)
T KOG2192|consen  102 ----------IGEILKKIIPTLE-E------GFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE---  161 (390)
T ss_pred             ----------HHHHHHHHhhhhh-h------CCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc---
Confidence                      2334444444432 1      2245677999999999999999999999999999999999999876   


Q ss_pred             CcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccccc--CCCCccCCCCccccCCCcCCCCCCCcccCccccc
Q 010746          183 PLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLS--SSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAR  260 (502)
Q Consensus       183 p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~--~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~  260 (502)
                       .|.+++||+|.|.|.+.+|..+++.|.++|.+.+-+.....+.  .....|..||..|++.-.....+...++..... 
T Consensus       162 -c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp-  239 (390)
T KOG2192|consen  162 -CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP-  239 (390)
T ss_pred             -cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC-
Confidence             5678999999999999999999999999999987665332111  112223344444322110000000000000000 


Q ss_pred             cceEEEeccCCcccccc---ccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccc--
Q 010746          261 EFSLRLVCPAGNIGGVI---GKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCS--  335 (502)
Q Consensus       261 ~~~~~i~vp~~~~g~II---Gk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~--  335 (502)
                            .-|.......+   |+-|..       +.-.+.|......          ...++. ...-++++..-+..-  
T Consensus       240 ------p~~~~sdlmay~r~GrpG~r-------ydg~vdFs~detw----------~saidt-w~~SewqmaYePQgGs~  295 (390)
T KOG2192|consen  240 ------PPPRGSDLMAYDRRGRPGDR-------YDGMVDFSADETW----------PSAIDT-WSPSEWQMAYEPQGGSG  295 (390)
T ss_pred             ------CCCCccccceeccCCCCCcc-------ccccccccccccC----------CCcCCC-cCccccccccCCCCCCC
Confidence                  00000111111   122222       1111222221110          000000 001111111111000  


Q ss_pred             ------c--ccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHH
Q 010746          336 ------E--KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV  407 (502)
Q Consensus       336 ------~--~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~  407 (502)
                            .  ..-.+......|.++.||.++-|.||||+|++|++|++++||.|+|...    . .++.+|+++|+||.+|
T Consensus       296 ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep----l-eGsedrIitItGTqdQ  370 (390)
T KOG2192|consen  296 YDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP----L-EGSEDRIITITGTQDQ  370 (390)
T ss_pred             CCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc----C-CCCCceEEEEeccHHH
Confidence                  0  0011234567899999999999999999999999999999999999542    2 3688999999999999


Q ss_pred             HHHHHHHHHHHHHhc
Q 010746          408 ASSALSQVTLRLRAN  422 (502)
Q Consensus       408 v~~A~~~I~~~l~~~  422 (502)
                      ++.|++|++..++.+
T Consensus       371 IqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  371 IQNAQYLLQNSVKQY  385 (390)
T ss_pred             HhhHHHHHHHHHHhh
Confidence            999999999999864

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

Probab=99.96  E-value=3.2e-29  Score=254.01  Aligned_cols=229  Identities=28%  Similarity=0.374  Sum_probs=178.7

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC--CCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHH
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET--VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF  118 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~--~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~  118 (502)
                      ...++.+|+||..++|+||||+|+|||+|++.+||++.+-.+  ......+.+.|+|+++.|             +.|..
T Consensus       136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a~~  202 (600)
T KOG1676|consen  136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQAKQ  202 (600)
T ss_pred             ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHHHH
Confidence            567899999999999999999999999999999999987643  222367889999998874             45666


Q ss_pred             HHHHHHhhhcccCCC-----cCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010746          119 RVHDRIVAEDSLADD-----EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (502)
Q Consensus       119 ~i~~~i~~~~~~~~~-----~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v  193 (502)
                      ++++.+.++.-....     ........++++.||.+.||.||||+|++||+|+.+|||+|+|.++ +.|   .+.||.+
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            666655432111000     0122334489999999999999999999999999999999999998 445   3789999


Q ss_pred             EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCcc
Q 010746          194 QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNI  273 (502)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~  273 (502)
                      .|.|+.++|..|.++|.++|.+.....             .+++-.         +  .|     .....+.|.||+.+|
T Consensus       279 ~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------~~~~~~---------G--~P-----~~~~~fy~~VPa~Kc  329 (600)
T KOG1676|consen  279 QIIGTVDQIEHAAELINEIIAEAEAGA-------------GGGMGG---------G--AP-----GLVAQFYMKVPADKC  329 (600)
T ss_pred             eeecCHHHHHHHHHHHHHHHHHHhccC-------------CCCcCC---------C--Cc-----cceeeEEEecccccc
Confidence            999999999999999999998853210             000000         0  00     011178899999999


Q ss_pred             ccccccCcccccchhhhcCCeEEecCCC--CCCCCeEEEecCCC
Q 010746          274 GGVIGKGGGIIKQIRQESGASIKVDSSG--AEGDDCIIFISTKE  315 (502)
Q Consensus       274 g~IIGk~G~~Ik~i~~~sga~I~v~~~~--~~~~~~ii~i~g~~  315 (502)
                      |+|||++|++||.|..++||++.+.+..  ....+++++|.|.+
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  23578999999875

>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=5.6e-27  Score=220.66  Aligned_cols=237  Identities=28%  Similarity=0.393  Sum_probs=172.3

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEec---CCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF  118 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~---~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~  118 (502)
                      +.+.++||||+..+|.||||+|++|.+|+++|||+|+++   +.+|++.||+|.|.|+.|++             ...+.
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av~e  103 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAVHE  103 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHHHH
Confidence            449999999999999999999999999999999999997   45899999999999986542             22334


Q ss_pred             HHHHHHhhhcccCCC-cC-----CCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCce
Q 010746          119 RVHDRIVAEDSLADD-EF-----GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL  192 (502)
Q Consensus       119 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~  192 (502)
                      .|.++|.+....... .+     .....-.++|+||++..|.||||+|.+||.|+|+++|.|+|++-  .|.-....||+
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            445555433211111 00     11122358999999999999999999999999999999999943  13333467999


Q ss_pred             EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCc
Q 010746          193 LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGN  272 (502)
Q Consensus       193 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~  272 (502)
                      |++.|++++..+|+.+|.++|.+++.....+..+..   +-.|++.-..|...+|..- .   ..........+.++...
T Consensus       182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaNsnPtGspya~~-~---~~~~astas~~sva~~~  254 (402)
T KOG2191|consen  182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVANSNPTGSPYAYQ-A---HVLPASTASTISVAAGL  254 (402)
T ss_pred             EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccccCCCCCCCCCC-C---ccccccchhhccccccc
Confidence            999999999999999999999999887665542211   1112111122222222211 1   11222334456788889


Q ss_pred             cccccccCcccccchhhhcCCeEEecCC
Q 010746          273 IGGVIGKGGGIIKQIRQESGASIKVDSS  300 (502)
Q Consensus       273 ~g~IIGk~G~~Ik~i~~~sga~I~v~~~  300 (502)
                      .|..-|.++.++-.|-..+|..+.++..
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            9999999999999999999998877763

>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=6.3e-28  Score=233.20  Aligned_cols=242  Identities=25%  Similarity=0.411  Sum_probs=189.5

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS  218 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  218 (502)
                      ....+|+|||..+||.||||.|.+||+|...|.|+|.|...++    ++..|++|+|-++++...+|+++|.+++..+..
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            3568999999999999999999999999999999999998854    357899999999999999999999999988643


Q ss_pred             ccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEec
Q 010746          219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD  298 (502)
Q Consensus       219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~  298 (502)
                      ..                                    ....++.++++.-+.+||++|||.|.+||+|.++||++|.+.
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            32                                    234567888999999999999999999999999999999999


Q ss_pred             CCCCC---CCCeEEEecCC-CccCCCchhHHH-----------HHhhCCccccc--------------c-cc---C----
Q 010746          299 SSGAE---GDDCIIFISTK-EFFEDPSPTITA-----------ALRLQPRCSEK--------------T-ER---E----  341 (502)
Q Consensus       299 ~~~~~---~~~~ii~i~g~-~~~~~~~~~~~a-----------~~~~~~~~~~~--------------~-~~---~----  341 (502)
                      +-..-   ..||+|++.|. +.|..+...+.+           ++.++..+...              + .+   .    
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            74322   47999999883 111111111111           11122211000              0 00   0    


Q ss_pred             ---------CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHH
Q 010746          342 ---------SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSAL  412 (502)
Q Consensus       342 ---------~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~  412 (502)
                               .....-..+|.||...||.|||++|..||.|.+.+||.|+|.+.+ .|   +..+|+|+|+|++++.-+|+
T Consensus       397 ~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE-~p---dvseRMViItGppeaqfKAQ  472 (584)
T KOG2193|consen  397 FASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQ  472 (584)
T ss_pred             cCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC-CC---CcceeEEEecCChHHHHhhh
Confidence                     011233578999999999999999999999999999999997653 33   57899999999999999999


Q ss_pred             HHHHHHHHhchh
Q 010746          413 SQVTLRLRANTF  424 (502)
Q Consensus       413 ~~I~~~l~~~~~  424 (502)
                      -.|..+|++..+
T Consensus       473 grifgKikEenf  484 (584)
T KOG2193|consen  473 GRIFGKIKEENF  484 (584)
T ss_pred             hhhhhhhhhhcc
Confidence            999999998644

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

Probab=99.91  E-value=5.5e-23  Score=193.80  Aligned_cols=170  Identities=25%  Similarity=0.446  Sum_probs=138.0

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC-CCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE-HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (502)
                      ..+.+++|||+..+|.||||+|++|.+|+.+|||+|++++.. .+|.   .+||+|.|+|+.+++...+..|.++|++.+
T Consensus        37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG---TTeRvcli~Gt~eai~av~efI~dKire~p  113 (402)
T KOG2191|consen   37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG---TTERVCLIQGTVEALNAVHEFIADKIREKP  113 (402)
T ss_pred             CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC---ccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence            348999999999999999999999999999999999999863 4564   899999999999999999999999999853


Q ss_pred             CccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEe
Q 010746          218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV  297 (502)
Q Consensus       218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v  297 (502)
                      .....                                        ...++-|.                           
T Consensus       114 ~~~~k----------------------------------------~v~~~~pq---------------------------  126 (402)
T KOG2191|consen  114 QAVAK----------------------------------------PVDILQPQ---------------------------  126 (402)
T ss_pred             HhhcC----------------------------------------CccccCCC---------------------------
Confidence            21100                                        00000000                           


Q ss_pred             cCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhC
Q 010746          298 DSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATR  377 (502)
Q Consensus       298 ~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG  377 (502)
                         .   .+                                      ..-..++.||..-+|.||||+|.+||.|++++|
T Consensus       127 ---t---~~--------------------------------------r~kqikivvPNstag~iigkggAtiK~~~Eqsg  162 (402)
T KOG2191|consen  127 ---T---PD--------------------------------------RIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSG  162 (402)
T ss_pred             ---C---cc--------------------------------------ccceeEEeccCCcccceecCCcchHHHHHHhhC
Confidence               0   00                                      112367899999999999999999999999999


Q ss_pred             CeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhchh
Q 010746          378 ASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (502)
Q Consensus       378 a~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  424 (502)
                      |.|+|.+.  .|..-.-.+|+|++.|++|+..+|+.+|+++|.+++.
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  3433456789999999999999999999999999864

>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=6.8e-23  Score=187.70  Aligned_cols=172  Identities=27%  Similarity=0.384  Sum_probs=141.6

Q ss_pred             ccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccc
Q 010746          260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE  339 (502)
Q Consensus       260 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~  339 (502)
                      ..+++++++..+.+|+||||+|++||.|+.+++++|.|+++..  .+++.+|++..     ....+-+..+.+++.+.+.
T Consensus        46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~-----~ti~~ilk~iip~lee~f~  118 (390)
T KOG2192|consen   46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADI-----ETIGEILKKIIPTLEEGFQ  118 (390)
T ss_pred             cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccH-----HHHHHHHHHHhhhhhhCCC
Confidence            4578999999999999999999999999999999999998774  68999998743     2233333444444444332


Q ss_pred             cCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          340 RESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       340 ~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                         ....++++|+|+++++|.|||++|++||+||+++.|+++|.-. ++|   .+++|+|.|.|.+..|..++..|++.|
T Consensus       119 ---~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~i  191 (390)
T KOG2192|consen  119 ---LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDLI  191 (390)
T ss_pred             ---CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHHh
Confidence               2346899999999999999999999999999999999999865 566   589999999999999999999999999


Q ss_pred             HhchhcccCccCCCCCCCcCCCCCCCCCCCCCCCCC
Q 010746          420 RANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNR  455 (502)
Q Consensus       420 ~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~~~~~~~  455 (502)
                      .+.++        ++...||+|+.+++.+  .||+.
T Consensus       192 ~e~pi--------kgsa~py~p~fyd~t~--dyggf  217 (390)
T KOG2192|consen  192 SESPI--------KGSAQPYDPNFYDETY--DYGGF  217 (390)
T ss_pred             hcCCc--------CCcCCcCCccccCccc--ccCCc
Confidence            99765        6678899998887752  45554

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

Probab=99.83  E-value=7.1e-20  Score=189.45  Aligned_cols=160  Identities=36%  Similarity=0.570  Sum_probs=134.2

Q ss_pred             cceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccc-
Q 010746          261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-  339 (502)
Q Consensus       261 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-  339 (502)
                      ..++|++|+...+|.||||+|..|++||.++.++|++.....+..+|+++|++...-...+++.+|+.+.+..+...+. 
T Consensus        42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence            3458999999999999999999999999999999999998888899999999942111236677777777665544322 


Q ss_pred             ---------cCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHH
Q 010746          340 ---------RESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASS  410 (502)
Q Consensus       340 ---------~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~  410 (502)
                               .+.....++.+|+||..++|+||||+|++||+|++.|||+|+|..+ .+|.   .++|.|+|.|.+++|.+
T Consensus       122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~  197 (485)
T KOG2190|consen  122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK  197 (485)
T ss_pred             cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence                     1112235789999999999999999999999999999999999876 7885   68889999999999999


Q ss_pred             HHHHHHHHHHhchh
Q 010746          411 ALSQVTLRLRANTF  424 (502)
Q Consensus       411 A~~~I~~~l~~~~~  424 (502)
                      |+.+|..+|.+...
T Consensus       198 al~~Is~~L~~~~~  211 (485)
T KOG2190|consen  198 ALVQISSRLLENPP  211 (485)
T ss_pred             HHHHHHHHHHhcCC
Confidence            99999999999653

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.62  E-value=3.8e-15  Score=135.27  Aligned_cols=146  Identities=21%  Similarity=0.322  Sum_probs=105.4

Q ss_pred             EEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEE---ecCHHHHHHHHHHHHHHHhcCCCccc
Q 010746          145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQV---AGEPAVVRKALVQIASRLHENPSRSQ  221 (502)
Q Consensus       145 llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~  221 (502)
                      |.||.+.++.|||++|++|+.|+++|||+|.+..+          +..|.|   +++++++.+|..+|..+........ 
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~-   70 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK-   70 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-
Confidence            56899999999999999999999999999999765          246888   8899999999999998765411000 


Q ss_pred             cccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcC-CeEEecCC
Q 010746          222 HLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSS  300 (502)
Q Consensus       222 ~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sg-a~I~v~~~  300 (502)
                                                                         +-.++|          +.+. .-+.+.+-
T Consensus        71 ---------------------------------------------------A~~l~g----------d~y~~~Vi~I~~~   89 (172)
T TIGR03665        71 ---------------------------------------------------ALKLLD----------DDYMLEVIDLKEY   89 (172)
T ss_pred             ---------------------------------------------------HHHhcC----------CcceEEEEEhhhc
Confidence                                                               000000          0000 00011100


Q ss_pred             CCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeE
Q 010746          301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI  380 (502)
Q Consensus       301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  380 (502)
                                 +..       +  +                    .+       ...+|.|||++|++++.|++.|||+|
T Consensus        90 -----------~~~-------~--~--------------------~~-------~~~~griIG~~G~t~~~ie~~t~~~i  122 (172)
T TIGR03665        90 -----------GKS-------P--N--------------------AL-------RRIKGRIIGEGGKTRRIIEELTGVSI  122 (172)
T ss_pred             -----------cCC-------H--H--------------------HH-------HHHHhhhcCCCcHHHHHHHHHHCCeE
Confidence                       000       0  0                    00       23589999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       381 ~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      .|..            ..|.|+|++++++.|..+|.++++.
T Consensus       123 ~i~~------------~~v~i~G~~~~~~~A~~~i~~li~~  151 (172)
T TIGR03665       123 SVYG------------KTVGIIGDPEQVQIAREAIEMLIEG  151 (172)
T ss_pred             EEcC------------CEEEEECCHHHHHHHHHHHHHHHcC
Confidence            9952            3799999999999999999998855

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=99.60  E-value=3.1e-15  Score=135.81  Aligned_cols=137  Identities=21%  Similarity=0.216  Sum_probs=96.7

Q ss_pred             EEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEE---cCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746           48 YLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY---SSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (502)
Q Consensus        48 i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~---G~~e~~~~~~~~~~~~~~a~~al~~i~~~i  124 (502)
                      |.||.+.+|.|||++|++|++|+++|+|+|++.+.     +..|.|.   ++++.             +++|...|....
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            57899999999999999999999999999999864     4568883   33222             333433333311


Q ss_pred             hhhcccCCCc-CCCCccEEEE-EEeeC---------CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010746          125 VAEDSLADDE-FGELTLITVR-MLVPA---------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (502)
Q Consensus       125 ~~~~~~~~~~-~~~~~~~~~~-llVp~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v  193 (502)
                      ..  +..++. ......++++ +-|+.         ...|+|||++|++++.|++.|+|+|.|..            +.|
T Consensus        64 ~g--f~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v  129 (172)
T TIGR03665        64 RG--FSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTV  129 (172)
T ss_pred             cC--CCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEE
Confidence            11  000000 0001111222 23332         36899999999999999999999999853            469


Q ss_pred             EEecCHHHHHHHHHHHHHHHhcC
Q 010746          194 QVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      .|.|++++++.|..+|.+++...
T Consensus       130 ~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       130 GIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             EEECCHHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999654

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=99.59  E-value=2.9e-14  Score=130.33  Aligned_cols=65  Identities=23%  Similarity=0.340  Sum_probs=57.5

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe----cCHHHHHHHHHHHHHHHhc
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----GEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~----G~~~~V~~A~~~I~~~l~~  215 (502)
                      +...+.||.+.++.|||++|++|+.|+++|||+|.+..+          +..|.|.    ++++++.+|+.+|..++..
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          3568885    8999999999999997763

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.56  E-value=3.4e-14  Score=129.93  Aligned_cols=141  Identities=20%  Similarity=0.165  Sum_probs=99.6

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEE----cCCCCcccccCCccCCCHHHHHHHH
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY----SSSEGTNLFEDSGEFVSPAQDALFR  119 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~----G~~e~~~~~~~~~~~~~~a~~al~~  119 (502)
                      +...+.||.+.++.|||++|++|+.|+++|||+|++.+.     +..|.|.    ++++.             +.+|...
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             3334433


Q ss_pred             HHHHHhhhcccCCCc-CCCCccEEEEE-E----ee-----CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCC
Q 010746          120 VHDRIVAEDSLADDE-FGELTLITVRM-L----VP-----ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALS  188 (502)
Q Consensus       120 i~~~i~~~~~~~~~~-~~~~~~~~~~l-l----Vp-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~  188 (502)
                      +...+..  +..++. ......+..++ -    .+     ...+|+|||++|++++.|++.|||+|.|..+         
T Consensus        65 I~ai~~g--f~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~---------  133 (180)
T PRK13763         65 VKAIGRG--FSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK---------  133 (180)
T ss_pred             HHHHhcC--CCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC---------
Confidence            3332211  000000 00011112221 1    11     1368999999999999999999999999533         


Q ss_pred             CCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          189 FDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       189 ~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                         .|.|.|++++++.|...|..++...
T Consensus       134 ---~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        134 ---TVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             ---EEEEEeCHHHHHHHHHHHHHHHcCC
Confidence               4999999999999999999999654

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.39  E-value=9.7e-13  Score=99.76  Aligned_cols=64  Identities=39%  Similarity=0.605  Sum_probs=57.4

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT  416 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~  416 (502)
                      .+|.||.+.+|+|||++|++|++|+++|||+|++.+... +   ...+|.|+|.|++++|..|+.||.
T Consensus         2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhhC
Confidence            689999999999999999999999999999999976532 2   467899999999999999999873

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=99.35  E-value=2.1e-12  Score=97.86  Aligned_cols=64  Identities=47%  Similarity=0.783  Sum_probs=57.9

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  209 (502)
                      +++|+||.+.+++|||++|.+|++|+++|||+|.+.+... +   ...+|+|+|+|++++|.+|+.+|
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            3789999999999999999999999999999999987632 2   36789999999999999999887

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

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.27  E-value=6.9e-12  Score=94.24  Aligned_cols=61  Identities=20%  Similarity=0.335  Sum_probs=54.8

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT  416 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~  416 (502)
                      .+|.||.+++++|||++|++|++|+++|||+|.+++..       +.++.|+|+|++++|..|+.+|+
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            57899999999999999999999999999999997542       45679999999999999988873

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=99.24  E-value=1.8e-11  Score=134.36  Aligned_cols=307  Identities=22%  Similarity=0.271  Sum_probs=197.7

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      .-+..++.+-...+.++||++|.+++.++.++.+.|+|+...  .......|.+...++..+      ..-.++++.++-
T Consensus       199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~------~~~i~~~~~~le  270 (753)
T KOG2208|consen  199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSI------NVEIQEALTRLE  270 (753)
T ss_pred             eeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceeh------hhhhHHHHHHhc
Confidence            347788999999999999999999999999999999998652  222334444433332110      000111111110


Q ss_pred             H-----HHhhhccc-------------------------CC-------------Cc--------------CCCCccEEEE
Q 010746          122 D-----RIVAEDSL-------------------------AD-------------DE--------------FGELTLITVR  144 (502)
Q Consensus       122 ~-----~i~~~~~~-------------------------~~-------------~~--------------~~~~~~~~~~  144 (502)
                      .     .+....+.                         .+             +.              .-....+.+.
T Consensus       271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~  350 (753)
T KOG2208|consen  271 SEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIK  350 (753)
T ss_pred             ChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeE
Confidence            0     00000000                         00             00              0112235677


Q ss_pred             EEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccc
Q 010746          145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLL  224 (502)
Q Consensus       145 llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~  224 (502)
                      +-+-...+..++||+|.+|.+|++++.|.|.+...       .+.+..+.++|...++.+|...|...+.+...      
T Consensus       351 ~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------  417 (753)
T KOG2208|consen  351 REIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------  417 (753)
T ss_pred             EeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------
Confidence            88889999999999999999999999999999763       25677899999999999999999998877421      


Q ss_pred             ccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcC-CeEEecCCCCC
Q 010746          225 LSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSSGAE  303 (502)
Q Consensus       225 ~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sg-a~I~v~~~~~~  303 (502)
                                                         ......+.+|...+.++||.+|..|+.|..+++ +.|++......
T Consensus       418 -----------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~  462 (753)
T KOG2208|consen  418 -----------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNS  462 (753)
T ss_pred             -----------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcc
Confidence                                               023456889999999999999999999999999 88888875543


Q ss_pred             CCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEe
Q 010746          304 GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (502)
Q Consensus       304 ~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~  383 (502)
                      ...-.+...... ++.   .+..++.+....    .........+...+.|..+.+..+|+.|..+    +..+...-++
T Consensus       463 ~~~~~~~~~~~d-v~~---~~~~~~~~~~~a----~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~----d~~~~~~i~~  530 (753)
T KOG2208|consen  463 SDMVTIRGISKD-VEK---SVSLLKALKADA----KNLKFRDVVTKDKLLPVKYIGKEIGKNGTIR----DSLGDKSIFP  530 (753)
T ss_pred             cccceEeccccc-cch---hHHHHHhhhhhh----hcchhhhhhhccccchHHhhcccccCceeee----ccCCceeecc
Confidence            222222211111 111   111111111000    0001112345666777778777777766655    4555555554


Q ss_pred             cCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          384 TNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       384 ~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ...      ..++..++|.|..+.|..|.+.+..++...
T Consensus       531 ~~~------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~  563 (753)
T KOG2208|consen  531 PNE------DEDHEKITIEGKLELVLEAPAELKALIEAL  563 (753)
T ss_pred             ccc------ccccceeeecccccchhhhHHHHHhcchhh
Confidence            331      356678999999999999999888777663

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

Probab=99.23  E-value=3.7e-11  Score=89.57  Aligned_cols=58  Identities=26%  Similarity=0.354  Sum_probs=52.5

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQV  415 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I  415 (502)
                      ....+.||.+++|+|||++|++|++|+++|||+|.|..           ++.|.|+|+ +++++.|+.+|
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            45789999999999999999999999999999999953           347999998 99999999887

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.

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

Probab=99.23  E-value=3.4e-11  Score=121.91  Aligned_cols=231  Identities=26%  Similarity=0.385  Sum_probs=168.1

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ....+.+++.||...|.+++|+.|.+|+.|+..++++|.+..++ .     ..++..++.|.+.+|.+|...+..++.++
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~  137 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTEN  137 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence            44678899999999999999999999999999999999998773 2     34666777779999999999999999774


Q ss_pred             CCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEE
Q 010746          217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK  296 (502)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~  296 (502)
                      .                                           .+.....+|...++.|+|++|++++.++..++++|.
T Consensus       138 ~-------------------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~  174 (608)
T KOG2279|consen  138 T-------------------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKIT  174 (608)
T ss_pred             C-------------------------------------------cccccccchhhhcccccccchhhhcchhcccccccc
Confidence            2                                           345567789999999999999999999999999999


Q ss_pred             ecCCCCCCCCeEEEecCCCccCCC-c-------hhHHHHHhhCC-----cc---------cccc----------------
Q 010746          297 VDSSGAEGDDCIIFISTKEFFEDP-S-------PTITAALRLQP-----RC---------SEKT----------------  338 (502)
Q Consensus       297 v~~~~~~~~~~ii~i~g~~~~~~~-~-------~~~~a~~~~~~-----~~---------~~~~----------------  338 (502)
                      +..+......+++.|.+....... .       ..-+...+..+     +.         .+.+                
T Consensus       175 ~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~  254 (608)
T KOG2279|consen  175 CDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTS  254 (608)
T ss_pred             cccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccch
Confidence            998876666777777764422211 0       00000000000     00         0000                


Q ss_pred             -----c-----cCC-----------------------CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746          339 -----E-----RES-----------------------GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (502)
Q Consensus       339 -----~-----~~~-----------------------~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  385 (502)
                           +     .+.                       .....--.|.||..++|.+||+.|++|+.+...|++.+.|.. 
T Consensus       255 ~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  255 SSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT-  333 (608)
T ss_pred             hccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEe-
Confidence                 0     000                       111223578999999999999999999999999999988853 


Q ss_pred             CCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          386 ENVPKVAYE-DEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       386 ~~~P~~~~~-~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                        .|..... .-.++.+.|+..-+..|+.|+..+.
T Consensus       334 --~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~  366 (608)
T KOG2279|consen  334 --QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHV  366 (608)
T ss_pred             --ccccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence              2321000 1146789999999999999888433

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.22  E-value=1e-11  Score=92.60  Aligned_cols=60  Identities=33%  Similarity=0.530  Sum_probs=54.1

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV  415 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I  415 (502)
                      |.+|.||.+++|+|||++|++|++|+++|||+|+++++       + ....|+|+|++++|+.|+.+|
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 345999999999999999886

; 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 ....

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

Probab=99.19  E-value=6.1e-11  Score=120.08  Aligned_cols=234  Identities=23%  Similarity=0.309  Sum_probs=159.9

Q ss_pred             CCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHH
Q 010746           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFR  119 (502)
Q Consensus        40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~  119 (502)
                      ..+++..++.||...+..+|||.|++|+.|+..|+++|.+.... -.++++.++.|-+.          .+++|..++  
T Consensus        64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~----------~v~~a~a~~--  130 (608)
T KOG2279|consen   64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV----------QVCKAKAAI--  130 (608)
T ss_pred             chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC----------CCChHHHHH--
Confidence            34789999999999999999999999999999999999997652 23356666665433          345455444  


Q ss_pred             HHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010746          120 VHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP  199 (502)
Q Consensus       120 i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~  199 (502)
                       ++++.           .+..+...+-+|...++.|+|++|+++++|+..++|+|.+....   .|  ...++..|.+..
T Consensus       131 -~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~--g~~~~~~i~~qq  193 (608)
T KOG2279|consen  131 -HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL--GLSRLIKISGQQ  193 (608)
T ss_pred             -HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhccccccccccccc---cc--ccccceeccccc
Confidence             33332           33456778999999999999999999999999999999997651   12  557888999998


Q ss_pred             HHHHHHHHHHHHHHhcCCCc-------cc-cccccCCCCc-----cCCCCcc----------ccCCCcCC----------
Q 010746          200 AVVRKALVQIASRLHENPSR-------SQ-HLLLSSSSNI-----YQSSGVY----------LSAPLVGS----------  246 (502)
Q Consensus       200 ~~V~~A~~~I~~~l~~~~~~-------~~-~~~~~~~~~~-----~~~gg~~----------~~~p~~~~----------  246 (502)
                      .-++.|..++.+.+.++-+.       .+ ...+-.+.+.     +.+++..          +..|....          
T Consensus       194 k~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v  273 (608)
T KOG2279|consen  194 KEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAV  273 (608)
T ss_pred             chHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCccee
Confidence            88999999998888775221       11 0111111111     1111100          01111000          


Q ss_pred             ----CCCCCcccC---ccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCC
Q 010746          247 ----YGNYSARRD---EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAE  303 (502)
Q Consensus       247 ----~~~~~~~~~---~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~  303 (502)
                          -+.+..+.+   ..........|.+|...+|.+||..|+.++.+...+++.+.|......
T Consensus       274 ~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt  337 (608)
T KOG2279|consen  274 VVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYT  337 (608)
T ss_pred             EEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecccc
Confidence                001111111   122334456889999999999999999999999999999999875543

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

Probab=99.17  E-value=1.2e-10  Score=87.97  Aligned_cols=62  Identities=37%  Similarity=0.627  Sum_probs=55.5

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV  415 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I  415 (502)
                      .+|.||.+++++|||++|++|++|+++|||+|.|+....     .+.++.|+|.|+.+++..|+.+|
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            578999999999999999999999999999999975422     35678999999999999998876

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.15  E-value=3.3e-11  Score=89.86  Aligned_cols=60  Identities=37%  Similarity=0.573  Sum_probs=54.1

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  209 (502)
                      |.+|.||.+++++|||++|.+|++|+++|||+|.|+++        ..+..|+|+|++++|.+|+++|
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            67899999999999999999999999999999999655        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 ....

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.14  E-value=6.5e-11  Score=88.90  Aligned_cols=60  Identities=28%  Similarity=0.369  Sum_probs=54.7

Q ss_pred             EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (502)
Q Consensus       143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  209 (502)
                      .+|.||..++++|||++|++|++|+++|||+|.|++..       +.++.|+|+|+.++|..|+.+|
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            57899999999999999999999999999999997752       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.

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

Probab=99.10  E-value=3.4e-10  Score=84.33  Aligned_cols=58  Identities=34%  Similarity=0.437  Sum_probs=52.3

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHH
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQI  209 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I  209 (502)
                      ....|.||.+++++||||+|++|++|+++|||+|.+.+           ++.|.|.|+ +++|++|+.+|
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            35679999999999999999999999999999999854           357999998 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.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=99.05  E-value=4.1e-10  Score=123.70  Aligned_cols=290  Identities=17%  Similarity=0.200  Sum_probs=189.8

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      ......+-+-...+..|+||+|.+|.+|++++.|.|.++..  +..+..+++++...++.          +|.+.+..+.
T Consensus       345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~~----------ka~~~v~~~~  412 (753)
T KOG2208|consen  345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSANDE----------KAVEDVEKII  412 (753)
T ss_pred             cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccchh----------HHHHHHHHHH
Confidence            34667777888999999999999999999999999999985  56788899999988743          2455554444


Q ss_pred             HHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcC-ceEEEeecCCCCcccCCCCceEEEecCHH
Q 010746          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR-AQIRILKDEHLPLCALSFDELLQVAGEPA  200 (502)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~er~v~I~G~~~  200 (502)
                      ..+..            ..+...+++|...+.+|||.+|..|+.|.++++ +.|++....       +....+++.|...
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            44321            134566999999999999999999999999999 666654442       3344588888888


Q ss_pred             HHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccC
Q 010746          201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKG  280 (502)
Q Consensus       201 ~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~  280 (502)
                      .|..+..++..+........                                     ......-+...|..+.+..+|+.
T Consensus       474 dv~~~~~~~~~~~~~a~~~~-------------------------------------~~~~~~~d~~~~~~~~~~~~g~~  516 (753)
T KOG2208|consen  474 DVEKSVSLLKALKADAKNLK-------------------------------------FRDVVTKDKLLPVKYIGKEIGKN  516 (753)
T ss_pred             ccchhHHHHHhhhhhhhcch-------------------------------------hhhhhhccccchHHhhcccccCc
Confidence            88887766655544321110                                     01112234455666666667776


Q ss_pred             cccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCc-ee
Q 010746          281 GGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQ-IG  359 (502)
Q Consensus       281 G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~-vg  359 (502)
                      +..+..+.++..+.+..+.     +...+++-+......  .+..+...+.+.+         .......+.+|..+ .-
T Consensus       517 ~~i~d~~~~~~i~~~~~~~-----~~~~i~i~gk~~~v~--~a~~~L~~~~~~~---------~~~~~~~v~~~~~~~~~  580 (753)
T KOG2208|consen  517 GTIRDSLGDKSIFPPNEDE-----DHEKITIEGKLELVL--EAPAELKALIEAL---------IKATLLEVNNPPGQHRP  580 (753)
T ss_pred             eeeeccCCceeeccccccc-----ccceeeecccccchh--hhHHHHHhcchhh---------hhhhhhhccCcchheee
Confidence            6666555555544443333     556667766542111  1111111111111         11233445555444 46


Q ss_pred             eeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          360 CLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       360 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ++++++....+..+...|+.+..++..       .+.+.++|.|..+.++.|...+.+.++..
T Consensus       581 ~l~~~~~~~~~~~e~~~gv~~~fp~~~-------~~~~e~~i~g~~~~v~aa~~~~~~i~~~~  636 (753)
T KOG2208|consen  581 FLIGKGIENRTYVEVFGGVVVPFPRSP-------TSSDEVSIKGAKDEVKAAKGRLEEIVEYL  636 (753)
T ss_pred             eeeccccccccceeecCcccccCCCCC-------CchhhhccchhHHHHHHhhccchhhhhhc
Confidence            777777777777777777777775542       34447999999999999988888777653

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

Probab=99.04  E-value=7.1e-10  Score=83.70  Aligned_cols=62  Identities=40%  Similarity=0.629  Sum_probs=55.7

Q ss_pred             EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI  209 (502)
Q Consensus       143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I  209 (502)
                      .+|.||.+++++|||++|++|++|+++|+|+|.|.....     ...++.|.|.|+.+++..|+.+|
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            579999999999999999999999999999999987522     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=98.98  E-value=8.7e-10  Score=76.11  Aligned_cols=42  Identities=48%  Similarity=0.823  Sum_probs=38.9

Q ss_pred             ceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEc
Q 010746           54 KIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYS   95 (502)
Q Consensus        54 ~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G   95 (502)
                      ++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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=98.90  E-value=2.9e-09  Score=73.49  Aligned_cols=43  Identities=47%  Similarity=0.734  Sum_probs=37.4

Q ss_pred             ceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc
Q 010746          357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG  403 (502)
Q Consensus       357 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G  403 (502)
                      +||+|||++|++|++|+++|||+|+|++ +..|   .++++.|+|+|
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            5899999999999999999999999987 2333   57889999998

>smart00322 KH K homology RNA-binding domain

Probab=98.88  E-value=1.2e-08  Score=77.52  Aligned_cols=66  Identities=29%  Similarity=0.538  Sum_probs=58.7

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      .+.++.||.+.++++||++|++|++|++.||++|.+....       .....|+|.|+.+++..|+.+|.+.+
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            5788999999999999999999999999999999995431       24578999999999999999998876

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

Probab=98.83  E-value=7.4e-08  Score=86.78  Aligned_cols=147  Identities=22%  Similarity=0.266  Sum_probs=101.9

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      ......+.||.+..+.|||+.|++.+.|.+.++++|.++..     +..|.|........       .     -++++..
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~D-------p-----~~~~ka~   68 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTED-------P-----LALLKAR   68 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCC-------h-----HHHHHHH
Confidence            44567799999999999999999999999999999999755     68899988632110       0     1122222


Q ss_pred             HHHhh--hcccCCCcC-CCCccEEEEE-----Eee------CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          122 DRIVA--EDSLADDEF-GELTLITVRM-----LVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       122 ~~i~~--~~~~~~~~~-~~~~~~~~~l-----lVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+.+  ..|..+..- -....+.+.+     ++.      ....|+|||++|.+-+.|++-|+|.|.|...        
T Consensus        69 d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~--------  140 (194)
T COG1094          69 DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK--------  140 (194)
T ss_pred             HHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc--------
Confidence            22221  222221100 0000111111     111      1246999999999999999999999999644        


Q ss_pred             CCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746          188 SFDELLQVAGEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       188 ~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (502)
                          .|.|.|.+++|..|..+|..++...+
T Consensus       141 ----tVaiiG~~~~v~iAr~AVemli~G~~  166 (194)
T COG1094         141 ----TVAIIGGFEQVEIAREAVEMLINGAP  166 (194)
T ss_pred             ----EEEEecChhhhHHHHHHHHHHHcCCC
Confidence                69999999999999999999997643

>smart00322 KH K homology RNA-binding domain

Probab=98.76  E-value=4.6e-08  Score=74.30  Aligned_cols=66  Identities=39%  Similarity=0.664  Sum_probs=59.1

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      ++.++.||...+++|||++|.+|++|++.|+++|.+....       .....+.|.|+.+++..|..+|.+.+
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            5788999999999999999999999999999999996541       24678999999999999999998876

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

Probab=98.74  E-value=1.2e-07  Score=85.51  Aligned_cols=54  Identities=22%  Similarity=0.314  Sum_probs=48.4

Q ss_pred             CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          356 AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       356 ~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ...|+|||++|.+-+-|++.|+|.|.|...            +|.|.|.+++|+.|...|..++..
T Consensus       111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVaiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         111 RIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVAIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             HhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEEEecChhhhHHHHHHHHHHHcC
Confidence            346899999999999999999999999643            899999999999999999888855

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

Probab=98.40  E-value=7.4e-07  Score=84.73  Aligned_cols=136  Identities=22%  Similarity=0.334  Sum_probs=104.4

Q ss_pred             ccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCcccccc-
Q 010746          260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT-  338 (502)
Q Consensus       260 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~-  338 (502)
                      .+++..+.+|..+++.|+|++|..||.|+.+|...|+-+...   .+.++.++|..      +.++.+.+..+...+.+ 
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            677888999999999999999999999999999999988755   56888888864      34444444443322221 


Q ss_pred             ------------ccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010746          339 ------------ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD  406 (502)
Q Consensus       339 ------------~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~  406 (502)
                                  .........+..+.||...+|.|.|.+|.+|+.|++.+...|.-+-++        .+-++.++|.+.
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                        111123456788899999999999999999999999999998876543        334899999888


Q ss_pred             H-HHHHH
Q 010746          407 V-ASSAL  412 (502)
Q Consensus       407 ~-v~~A~  412 (502)
                      . +++|.
T Consensus       167 nC~kra~  173 (394)
T KOG2113|consen  167 NCVKRAR  173 (394)
T ss_pred             chhhhcc
Confidence            7 55554

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

Probab=98.32  E-value=2.4e-06  Score=72.55  Aligned_cols=67  Identities=21%  Similarity=0.328  Sum_probs=51.9

Q ss_pred             CCceeeeeCCCchhHHHHHHHhCCeEEEecCCCC-----------CC-CCCCCceEEEEEcC---HHHHHHHHHHHHHHH
Q 010746          355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PK-VAYEDEEMVQITGS---LDVASSALSQVTLRL  419 (502)
Q Consensus       355 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~-----------P~-~~~~~~r~v~I~G~---~~~v~~A~~~I~~~l  419 (502)
                      .+++|.|||++|++||+|+++|||+|.|..+...           |. ...++.-.|.|++.   .+++..|+.+|..+|
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   599999999999988


Q ss_pred             Hh
Q 010746          420 RA  421 (502)
Q Consensus       420 ~~  421 (502)
                      ..
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=98.28  E-value=3.3e-06  Score=71.65  Aligned_cols=68  Identities=24%  Similarity=0.351  Sum_probs=52.2

Q ss_pred             CCceeeeecCCChHHHHHHhhcCceEEEeecCCC-----------Cccc-CCCCceEEEecCH---HHHHHHHHHHHHHH
Q 010746          149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL-----------PLCA-LSFDELLQVAGEP---AVVRKALVQIASRL  213 (502)
Q Consensus       149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------p~~~-~~~er~v~I~G~~---~~V~~A~~~I~~~l  213 (502)
                      .+.+|.|||++|.+||.|+++|||+|.|..+...           |... ...+-.|.|++..   +++.+|+.+|..+|
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            4678999999999999999999999999865211           0000 1123468899964   99999999999999


Q ss_pred             hcC
Q 010746          214 HEN  216 (502)
Q Consensus       214 ~~~  216 (502)
                      ...
T Consensus        94 ~~~   96 (120)
T cd02395          94 KPA   96 (120)
T ss_pred             ccC
Confidence            764

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.

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=98.13  E-value=4.7e-06  Score=72.85  Aligned_cols=103  Identities=19%  Similarity=0.267  Sum_probs=70.1

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHH
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDR  123 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~  123 (502)
                      -.+.++|+...+|..||++|++|++|++..|-+|.|-+-           +-   +             .++-+..++..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~---d-------------~~~fI~n~l~P   84 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SD---D-------------PEEFIKNIFAP   84 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CC---C-------------HHHHHHHHcCC
Confidence            457788899999999999999999999999888876321           11   1             12222222111


Q ss_pred             HhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEE
Q 010746          124 IVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI  176 (502)
Q Consensus       124 i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i  176 (502)
                      ..-....-   ........+.+.|+....+.+|||+|++|+.++.-++-.+.|
T Consensus        85 a~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         85 AAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             CEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            11010000   011223466788999999999999999999999999988766

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

Probab=98.12  E-value=5.1e-06  Score=79.17  Aligned_cols=141  Identities=22%  Similarity=0.338  Sum_probs=104.2

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS  218 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  218 (502)
                      ..++..+-||..+++.|.|++|.+||.|+.+|.+.|+-+.....|        +..++|..+.|+.|++.|...-+.   
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eeP--------iF~vTg~~edv~~aRrei~saaeH---   92 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEP--------IFPVTGRHEDVRRARREIPSAAEH---   92 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCC--------cceeccCchhHHHHhhcCccccce---
Confidence            678888999999999999999999999999999999987664434        688999999999999877542211   


Q ss_pred             ccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEec
Q 010746          219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD  298 (502)
Q Consensus       219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~  298 (502)
                          +.+.-....+           .+...++.      ...+....+.+|...++.+.|..|.+|+.+++.++..|.-+
T Consensus        93 ----~~l~~~s~s~-----------Sgg~~~~s------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~  151 (394)
T KOG2113|consen   93 ----FGLIRASRSF-----------SGGTNGAS------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATP  151 (394)
T ss_pred             ----eeeeeecccc-----------cCCCcccc------ccCCCceeeeccceeeeeccccccCccchheecccceEeee
Confidence                1110000000           00001111      23445667888999999999999999999999999999888


Q ss_pred             CCCCCCCCeEEEecCC
Q 010746          299 SSGAEGDDCIIFISTK  314 (502)
Q Consensus       299 ~~~~~~~~~ii~i~g~  314 (502)
                      -..   .+.++.++|.
T Consensus       152 v~~---~~~Vf~Vtg~  164 (394)
T KOG2113|consen  152 VRC---GEPVFCVTGA  164 (394)
T ss_pred             ccC---CCceEEEecC
Confidence            665   5677777773

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.98  E-value=2.2e-05  Score=85.14  Aligned_cols=97  Identities=25%  Similarity=0.347  Sum_probs=78.0

Q ss_pred             ccCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCccc
Q 010746          107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA  186 (502)
Q Consensus       107 ~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~  186 (502)
                      .+.+..|.++..+|++.+....... .+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..+       
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            3556678888888888766554444 33344556778899999999999999999999999999999999643       


Q ss_pred             CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          187 LSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       187 ~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                          ..|.|.+ +.+.+++|+.+|..++..
T Consensus       617 ----G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       617 ----GTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             ----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence                4688888 688899999999988874

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=97.75  E-value=7.4e-05  Score=65.35  Aligned_cols=103  Identities=19%  Similarity=0.319  Sum_probs=70.7

Q ss_pred             ceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC
Q 010746          262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE  341 (502)
Q Consensus       262 ~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~  341 (502)
                      -.+.+.|+...+|..||++|++|+.|++..|-+|.+-.-+.+                +..-+..++...  -.....-.
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----------------PEEFIKNIFAPA--AVRSVTIK   93 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC----------------HHHHHHHHcCCC--EEEEEEEE
Confidence            356778888999999999999999999999888877653311                111222222111  00100000


Q ss_pred             CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEE
Q 010746          342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI  382 (502)
Q Consensus       342 ~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i  382 (502)
                      .........+.|+.+..|..|||+|.+|+.++..++-.+.|
T Consensus        94 ~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di  134 (140)
T PRK08406         94 KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI  134 (140)
T ss_pred             ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence            01123456678999999999999999999999999988877

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.61  E-value=0.00011  Score=64.06  Aligned_cols=103  Identities=21%  Similarity=0.253  Sum_probs=68.5

Q ss_pred             EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (502)
Q Consensus        45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i  124 (502)
                      .+-++|....+|..||++|++|++|++..|=+|.|-+-           +.+++                +-+   .+.+
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~----------------~fI---~N~l   83 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE----------------EFV---ANKL   83 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH----------------HHH---HHcC
Confidence            77788999999999999999999998888888876321           11111                000   0000


Q ss_pred             hhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEe
Q 010746          125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL  177 (502)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~  177 (502)
                      .......-..........+.+.||.+..+..|||+|++|+...+-++-++.|.
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            00000000000112234677889999999999999999999999998877663

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.59  E-value=0.00013  Score=80.45  Aligned_cols=97  Identities=24%  Similarity=0.299  Sum_probs=72.3

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++..+|++.+.........+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..+        
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            445556777777777665443332222334456678899999999999999999999999999999999654        


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          188 SFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                         -.|.|.+ ..+.+.+|..+|..+..+
T Consensus       590 ---G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       590 ---GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             ---eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence               3577766 577889999998887643

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).

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.59  E-value=0.00016  Score=78.62  Aligned_cols=67  Identities=22%  Similarity=0.275  Sum_probs=59.3

Q ss_pred             CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ..+....+.||.+.++.|||.||.+||+|+++|||+|.|..           +..|.|.+ +.+++++|+.+|...+..
T Consensus       575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence            34567899999999999999999999999999999999953           35788888 788999999999998874

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.

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

Probab=97.52  E-value=0.0006  Score=69.33  Aligned_cols=78  Identities=18%  Similarity=0.265  Sum_probs=58.3

Q ss_pred             CccEEEEEEee------CCceeeeecCCChHHHHHHhhcCceEEEeecCC----------CCc-ccCCCCceEEEec-CH
Q 010746          138 LTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH----------LPL-CALSFDELLQVAG-EP  199 (502)
Q Consensus       138 ~~~~~~~llVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~-~~~~~er~v~I~G-~~  199 (502)
                      ...++-+|.||      .+.||+|||..|.|.|+|+++|||+|.|.-+..          +.. -....+--|.|+. +-
T Consensus       135 p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~  214 (554)
T KOG0119|consen  135 PAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ  214 (554)
T ss_pred             ccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH
Confidence            33678889998      457899999999999999999999999975210          110 0112233467887 56


Q ss_pred             HHHHHHHHHHHHHHhc
Q 010746          200 AVVRKALVQIASRLHE  215 (502)
Q Consensus       200 ~~V~~A~~~I~~~l~~  215 (502)
                      |.|++|++.|..+|.+
T Consensus       215 eki~~Ai~vienli~~  230 (554)
T KOG0119|consen  215 EKIKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            7799999999999986

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

Probab=97.44  E-value=0.00098  Score=67.87  Aligned_cols=75  Identities=17%  Similarity=0.321  Sum_probs=58.0

Q ss_pred             eeEEEEEecC------CceeeeeCCCchhHHHHHHHhCCeEEEecCCC-------------CCCCCCCCceEEEEEc-CH
Q 010746          346 VITTRILVPS------AQIGCLIGRGGAIISEMRSATRASIRILTNEN-------------VPKVAYEDEEMVQITG-SL  405 (502)
Q Consensus       346 ~~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~-------------~P~~~~~~~r~v~I~G-~~  405 (502)
                      .++.+|.||.      ++||.|||..|.|.|.|+++|||+|.|-.+..             .+.  ..++--+.|+. |.
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            4566777774      58999999999999999999999999976221             111  12333477887 77


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010746          406 DVASSALSQVTLRLRAN  422 (502)
Q Consensus       406 ~~v~~A~~~I~~~l~~~  422 (502)
                      |.|++|+++|..+|.+.
T Consensus       215 eki~~Ai~vienli~~a  231 (554)
T KOG0119|consen  215 EKIKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            89999999999999874

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.41  E-value=0.00028  Score=61.49  Aligned_cols=103  Identities=21%  Similarity=0.307  Sum_probs=70.4

Q ss_pred             eEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCC
Q 010746          263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES  342 (502)
Q Consensus       263 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  342 (502)
                      .+-+.|....+|..||++|++|+.|++..|-+|.+-.-+.+                +..-+..+  +.+.-...+....
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----------------LEEFVANK--LAPAEVKNVTVSE   95 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------HHHHHHHc--CCCceEEEEEEEc
Confidence            56678888999999999999999999888888877653211                11111111  1111111110000


Q ss_pred             CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEe
Q 010746          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (502)
Q Consensus       343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~  383 (502)
                      .+......+.||.+..+..|||+|.+|+-..+.++-++.|.
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            11235677889999999999999999999999999888773

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.30  E-value=0.00029  Score=78.27  Aligned_cols=97  Identities=16%  Similarity=0.242  Sum_probs=76.3

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCce-EEEeecCCCCccc
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLCA  186 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~  186 (502)
                      +.+..|.++...|++.+.+.......+.....+....|.||.+.++.|||.+|.+||.|.++||+. |.+..+       
T Consensus       652 eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd-------  724 (891)
T PLN00207        652 RALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD-------  724 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC-------
Confidence            455667778888887776554444333344556788899999999999999999999999999999 877443       


Q ss_pred             CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          187 LSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       187 ~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                          -.|.|.+ +.+.+.+|+.+|..++.+
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                4688888 688899999999988864

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

Probab=97.30  E-value=0.00025  Score=70.70  Aligned_cols=63  Identities=22%  Similarity=0.408  Sum_probs=53.8

Q ss_pred             CCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010746           33 ETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (502)
Q Consensus        33 ~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (502)
                      +++..-...+++++.+.|-++++|.|||++|++|+.|+..|+++|+|-..   ..+-.|+|.|..+
T Consensus        36 ~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~   98 (629)
T KOG0336|consen   36 SRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH   98 (629)
T ss_pred             CCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence            44555577889999999999999999999999999999999999999754   3467799999754

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.08  E-value=0.00079  Score=74.33  Aligned_cols=66  Identities=24%  Similarity=0.302  Sum_probs=56.3

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      .....++.||.+.++.|||++|++||+|+++|||+|.|..           +..|.|.+ ..+.+++|..+|......
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            4567889999999999999999999999999999999953           24677776 678899999998887654

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).

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=97.01  E-value=0.0017  Score=59.49  Aligned_cols=104  Identities=25%  Similarity=0.265  Sum_probs=67.6

Q ss_pred             EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI  124 (502)
Q Consensus        45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i  124 (502)
                      .+-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+-.           -+++.            -+.+|+.    -.
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-----------~d~~~------------fI~nal~----Pa  129 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-----------EDPAE------------FIKNALA----PA  129 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-----------CCHHH------------HHHHhcC----cc
Confidence            344444567789999999999999999998666653221           00000            0111111    00


Q ss_pred             hhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      .-....-.   ..... .+.+.||.++.+.+|||+|.+++.+.+-||-++.|...
T Consensus       130 ~v~~V~~~---~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         130 EVLSVNIK---EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             eEeEEEEE---eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence            00000000   00111 67889999999999999999999999999999999765

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

Probab=97.01  E-value=0.0013  Score=70.07  Aligned_cols=97  Identities=24%  Similarity=0.270  Sum_probs=73.8

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.+|-.+|+..+.........+...-.+-...+.|+...+.-+||++|.+|++|.++|||+|.+..         
T Consensus       519 ~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------  589 (692)
T COG1185         519 KALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------  589 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------
Confidence            34455777777777766554433332333344556778999999999999999999999999999999973         


Q ss_pred             CCCceEEEecCH-HHHHHHHHHHHHHHhc
Q 010746          188 SFDELLQVAGEP-AVVRKALVQIASRLHE  215 (502)
Q Consensus       188 ~~er~v~I~G~~-~~V~~A~~~I~~~l~~  215 (502)
                        +-.|.|.+.. +.+.+|+..|..+..+
T Consensus       590 --dGtv~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         590 --DGTVKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             --CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence              3468898865 7789999999998866

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

Probab=96.80  E-value=0.0012  Score=62.44  Aligned_cols=41  Identities=29%  Similarity=0.476  Sum_probs=35.9

Q ss_pred             CCCceEEEEEecCC------ceeeeecCChhHHHHHHHhhCCeEEec
Q 010746           40 GSEDTVYRYLCPLR------KIGSIIGKGGEIVKQLRSETKSNIRIS   80 (502)
Q Consensus        40 ~~~~~~~~i~vp~~------~~g~iIGk~G~~I~~I~~~tga~I~i~   80 (502)
                      ..-.++.+|+||.+      +||.|+|++|.++|+|+++|+|+|.|-
T Consensus        88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            34466789999986      799999999999999999999998874

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

Probab=96.79  E-value=0.0014  Score=65.62  Aligned_cols=72  Identities=22%  Similarity=0.365  Sum_probs=59.6

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .....+.+.|-|-+++||.+||++|++|+.||..|+++|+|.+.        ..+-.|+|-|...--.+|+..|...+..
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            34456678889999999999999999999999999999999877        3456799999888777887777655544

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

Probab=96.74  E-value=0.001  Score=64.74  Aligned_cols=69  Identities=29%  Similarity=0.328  Sum_probs=54.2

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHH
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~  122 (502)
                      +....+++++...+.|||++|.|.++|++||+++|.+|.+  +.....|+|.|-..++            +..|+.+|..
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            5667899999999999999999999999999999999976  4445567777765442            5566666655


Q ss_pred             HHh
Q 010746          123 RIV  125 (502)
Q Consensus       123 ~i~  125 (502)
                      .|.
T Consensus       122 ~id  124 (345)
T KOG2814|consen  122 LID  124 (345)
T ss_pred             HHH
Confidence            553

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.71  E-value=0.0038  Score=57.30  Aligned_cols=102  Identities=27%  Similarity=0.370  Sum_probs=68.2

Q ss_pred             EEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCC
Q 010746          264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESG  343 (502)
Q Consensus       264 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  343 (502)
                      +...+-.+.+|..||++|.+|+.|.++.|-+|.+-.-+.+                +..-+..++.  +.-...+.-...
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d----------------~~~fI~nal~--Pa~v~~V~~~~~  139 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED----------------PAEFIKNALA--PAEVLSVNIKED  139 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC----------------HHHHHHHhcC--cceEeEEEEEeC
Confidence            3445556778999999999999999999977776643211                1111111111  111111100000


Q ss_pred             CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEec
Q 010746          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (502)
Q Consensus       344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  384 (502)
                      +.. ...+.||.+..+.+|||+|.+++-+.+-||-++.|..
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            112 6788899999999999999999999999999999954

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

Probab=96.71  E-value=0.0017  Score=63.18  Aligned_cols=72  Identities=24%  Similarity=0.333  Sum_probs=59.2

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      .....-++|++...++|||++|.+-++|+++|+|+|.++...      ...+.++.+.+..++|.+|...|..+|.+.
T Consensus        55 ~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   55 KDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             ccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            345667999999999999999999999999999999997662      133444555558899999999999988775

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

Probab=96.70  E-value=0.0027  Score=47.12  Aligned_cols=37  Identities=30%  Similarity=0.433  Sum_probs=34.5

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEe
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI   79 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i   79 (502)
                      .....+.||.+..|..|||+|.+|+.+++.++-+|.|
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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.67  E-value=0.0017  Score=72.02  Aligned_cols=97  Identities=25%  Similarity=0.330  Sum_probs=72.0

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++..+|++.+.........+.....+....+.||.+.++.+||++|.+||.|.++||++|.+..         
T Consensus       521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------  591 (693)
T PRK11824        521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------  591 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------
Confidence            45556778888888877654433322223334445667789999999999999999999999999888733         


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          188 SFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                        +-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus       592 --~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        592 --DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             --CceEEEEcccHHHHHHHHHHHHHhccc
Confidence              34588888 678889999999887753

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

Probab=96.59  E-value=0.0056  Score=58.08  Aligned_cols=44  Identities=27%  Similarity=0.516  Sum_probs=38.3

Q ss_pred             CCCccEEEEEEeeC------CceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          136 GELTLITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       136 ~~~~~~~~~llVp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      .....++.+++||-      +.||+|+|.+|.++|.|+++|+|+|.|--.
T Consensus        87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr  136 (259)
T KOG1588|consen   87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR  136 (259)
T ss_pred             CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence            44556788999994      489999999999999999999999999765

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.46  E-value=0.0032  Score=70.21  Aligned_cols=67  Identities=18%  Similarity=0.252  Sum_probs=58.0

Q ss_pred             CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      .......+.||.+.++.|||.||.+||+|.++||+. |.+.           ++-.|.|.+ +.+.++.|+.+|..++.+
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            356678999999999999999999999999999999 8873           235788888 788999999999988764

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

Probab=96.37  E-value=0.0046  Score=66.14  Aligned_cols=69  Identities=23%  Similarity=0.274  Sum_probs=58.9

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHhch
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL-DVASSALSQVTLRLRANT  423 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~~  423 (502)
                      .....++.|+.+.+..|||++|.+|++|.++|||+|.|. +          +-.|.|.++. +.+..|+..|...+++..
T Consensus       550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-d----------dGtv~i~~s~~~~~~~ak~~I~~i~~e~e  618 (692)
T COG1185         550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-D----------DGTVKIAASDGESAKKAKERIEAITREVE  618 (692)
T ss_pred             CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-C----------CCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence            445678999999999999999999999999999999995 2          2368888855 789999999999998754


Q ss_pred             h
Q 010746          424 F  424 (502)
Q Consensus       424 ~  424 (502)
                      .
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=96.20  E-value=0.009  Score=44.32  Aligned_cols=36  Identities=31%  Similarity=0.516  Sum_probs=33.4

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEE
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI  382 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i  382 (502)
                      ....+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            567899999999999999999999999999988876

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=96.06  E-value=0.023  Score=57.34  Aligned_cols=96  Identities=19%  Similarity=0.115  Sum_probs=63.3

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|+.|+.|.++. |=+|+|-.-.++           +                .   ..+...+.......
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D-----------~----------------~---~fI~Nal~Pa~V~~  300 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV-----------P----------------E---IFIARALAPAIISS  300 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC-----------H----------------H---HHHHHhCCCceeeE
Confidence            458999999999999999998 777776321100           0                0   00000000000000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (502)
                      -.  -....-.+.+.||..+.+..|||+|++++-...-||.+|.|..-+
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  001123678899999999999999999999999999999998753

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.05  E-value=0.013  Score=56.14  Aligned_cols=64  Identities=17%  Similarity=0.260  Sum_probs=52.9

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHHhc
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRAN  422 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~  422 (502)
                      -..+.||.++++.+||++|.+|+.|.+.|+++|.|-.           +-.|.|.++ .+.+..|+.+|...-++.
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            3678899999999999999999999999999999932           347889985 558888888887666554

>PRK00468 hypothetical protein; Provisional

Probab=96.03  E-value=0.0067  Score=46.86  Aligned_cols=34  Identities=26%  Similarity=0.546  Sum_probs=30.2

Q ss_pred             CCCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (502)
Q Consensus        40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t   73 (502)
                      .++.+.+++.|..+..|.||||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            3456889999999999999999999999998764

>TIGR01953 NusA transcription termination factor NusA

Probab=95.96  E-value=0.02  Score=57.71  Aligned_cols=96  Identities=24%  Similarity=0.375  Sum_probs=63.0

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|+.|+.|.++. |=+|.|-.-.           -+++.            -+..||.-  ..+..-... 
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~~~------------fi~nal~P--a~v~~v~i~-  296 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-----------DDPAE------------FIANALSP--AKVISVEVL-  296 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-----------CCHHH------------HHHHhcCC--ceEEEEEEE-
Confidence            468999999999999999998 7777763211           00000            00011100  000000000 


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      +   .  ..-.+.+.||..+.+..|||+|++++....-||.+|.|...
T Consensus       297 ~---~--~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       297 D---E--DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             c---C--CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            0   0  11368899999999999999999999999999999999765

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=95.94  E-value=0.017  Score=58.17  Aligned_cols=96  Identities=25%  Similarity=0.374  Sum_probs=64.0

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  349 (502)
                      +-+|+.||.+|++|+.|.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+..... .....
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d----------------~~~fi~na--l~Pa~v~~v~i~~~-~~~~~  303 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD----------------PAEFIANA--LSPAKVISVEVLDE-DKHSA  303 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--cCCceEEEEEEEcC-CCcEE
Confidence            357999999999999999888 677776543321                00011111  11111111100001 12467


Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  385 (502)
                      .+.||.++.+..|||+|.+++-..+.||.+|.|...
T Consensus       304 ~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       304 EVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             EEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence            899999999999999999999999999999999653

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=95.92  E-value=0.021  Score=57.72  Aligned_cols=97  Identities=23%  Similarity=0.226  Sum_probs=65.3

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  349 (502)
                      +-+|..||.+|.+|+.|.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+...  ......
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D----------------~~~fI~Na--l~Pa~V~~V~i~--~~~~~~  310 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV----------------PEIFIARA--LAPAIISSVKIE--EEEKKA  310 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--CCCceeeEEEEc--CCCcEE
Confidence            457999999999999999888 677776543311                00111111  111111111111  112467


Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCC
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN  387 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~  387 (502)
                      .+.||.++.+..|||+|.+++-..+.||.+|.|..-+.
T Consensus       311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence            88999999999999999999999999999999977543

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.83  E-value=0.013  Score=59.47  Aligned_cols=96  Identities=23%  Similarity=0.285  Sum_probs=63.4

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|+.|+.|.++. |=+|.|-.-            ..  +             ..+   .+...+.......
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~------------s~--d-------------~~~---fi~nal~Pa~v~~  294 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW------------SE--D-------------PAE---FVANALSPAKVVS  294 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEc------------CC--C-------------HHH---HHHHhCCCceEEE
Confidence            468999999999999999998 777776321            10  0             000   0000000000000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      -. ......-.+.+.||..+.+..|||+|.+++-...-||.+|.|...
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 000112367899999999999999999999999999999999776

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.73  E-value=0.17  Score=47.57  Aligned_cols=131  Identities=14%  Similarity=0.135  Sum_probs=87.4

Q ss_pred             EEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHh
Q 010746           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV  125 (502)
Q Consensus        46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~  125 (502)
                      +.+.++....-+|...+|..++.|-...||+|.+...     +..|.|+|+...++.          +...|..++..+.
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            4455568889999999999999998888999999765     678999998665322          3334444444432


Q ss_pred             hhcccCCCcCCCCccEEEEEEeeCCceeeee----cCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----
Q 010746          126 AEDSLADDEFGELTLITVRMLVPADQIGCVI----GKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA-----  196 (502)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~llVp~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~-----  196 (502)
                                      +..+-++.-..-.-.    -.....++.|++.|++.|....+          +..+.|.     
T Consensus        93 ----------------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~  146 (210)
T PF14611_consen   93 ----------------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASP  146 (210)
T ss_pred             ----------------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeec
Confidence                            333333322111111    12467889999999999998665          2234444     


Q ss_pred             cCHHHHHHHHHHHHHHHhcCC
Q 010746          197 GEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       197 G~~~~V~~A~~~I~~~l~~~~  217 (502)
                      -....+..|+..+...+..++
T Consensus       147 ~~~~~~~~a~RlL~~a~~~~~  167 (210)
T PF14611_consen  147 ENEKRADRAKRLLLWALDYNP  167 (210)
T ss_pred             cccchHHHHHHHHHHhccCCc
Confidence            456778889888888775443

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=95.72  E-value=0.023  Score=60.77  Aligned_cols=67  Identities=19%  Similarity=0.243  Sum_probs=52.1

Q ss_pred             ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ...+..|.+|. ++-|.||||.|.+|+-+...||++|.|.   +       +...|+|++ .|---+.|..-|..+|.+
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            45667788996 6779999999999999999999999994   2       334788999 776666676666555544

>PRK00106 hypothetical protein; Provisional

Probab=95.72  E-value=0.025  Score=60.27  Aligned_cols=67  Identities=22%  Similarity=0.264  Sum_probs=52.6

Q ss_pred             ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ......|.+|. ++-|.||||-|.+|+-+...||++|.|.   +       +...|+|++ .|---+.|..-|..++.+
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d-------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D-------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            45667888996 6779999999999999999999999994   2       334788999 777666676666555544

>PRK02821 hypothetical protein; Provisional

Probab=95.72  E-value=0.01  Score=46.05  Aligned_cols=35  Identities=20%  Similarity=0.400  Sum_probs=30.8

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhhCC
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS   75 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga   75 (502)
                      ++.+.+.+.|..+.+|.||||+|.+|+.||.--.+
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            45578999999999999999999999999987644

>PRK12704 phosphodiesterase; Provisional

Probab=95.61  E-value=0.025  Score=60.51  Aligned_cols=66  Identities=20%  Similarity=0.235  Sum_probs=50.3

Q ss_pred             ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHH
Q 010746          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR  420 (502)
Q Consensus       345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~  420 (502)
                      ...+..|.+|. ++-|.||||-|.+|+-+...||++|.|.   +       +...|.|+| .|-.-+.|..-+...+.
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~  275 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQ  275 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence            35567788996 6779999999999999999999999994   2       334888999 66555566555554443

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

Probab=95.61  E-value=0.031  Score=50.80  Aligned_cols=44  Identities=20%  Similarity=0.399  Sum_probs=37.2

Q ss_pred             CCCccEEEEEEee------CCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          136 GELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       136 ~~~~~~~~~llVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      .....++-++.||      .+.||.|||..|.+.|+|++.|+|+|-|-..
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            3445567778888      5689999999999999999999999999765

>PRK02821 hypothetical protein; Provisional

Probab=95.53  E-value=0.025  Score=43.82  Aligned_cols=35  Identities=31%  Similarity=0.462  Sum_probs=29.6

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR  171 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg  171 (502)
                      ....+.++|.+.+.-+|.||||+|.+|+.||.--.
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~   61 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA   61 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence            34457899999999999999999999999996533

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.48  E-value=0.035  Score=57.07  Aligned_cols=96  Identities=20%  Similarity=0.226  Sum_probs=62.2

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|+.|+.|.++. |=+|.|-.-.           -++                .+   .|...+.......
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-----------~Dp----------------~~---fI~NaLsPA~V~~  326 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-----------PDP----------------AT---YIANALSPARVDE  326 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-----------CCH----------------HH---HHHHhcCCceeeE
Confidence            468999999999999999998 7777763210           000                00   0000000000000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      -.- .....-.+.+.||..+.+..|||+|++++-...-||.+|.|...
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 00111356899999999999999999999999999999998654

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=95.43  E-value=0.32  Score=45.71  Aligned_cols=87  Identities=13%  Similarity=0.237  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEE
Q 010746          115 DALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ  194 (502)
Q Consensus       115 ~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~  194 (502)
                      ..+.+|+..+..-...+..+  ...  .+.+.++....-.|...+|..++.|-...||+|.+..+          +..|.
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--ELG--DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIR   69 (210)
T ss_pred             HHHHHHHHHhcCCcccceee--ccc--eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEE
Confidence            34556666665443322211  112  33455568889999999999999999999999999766          45799


Q ss_pred             EecCHHHHHHHHHHHHHHHhc
Q 010746          195 VAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       195 I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      |+|+...+..+...|.+++..
T Consensus        70 I~g~k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   70 ITGTKSTAEYIEASINEILSN   90 (210)
T ss_pred             EEccHHHHHHHHHHHHHHHhh
Confidence            999999999999999988866

>PRK00468 hypothetical protein; Provisional

Probab=95.42  E-value=0.025  Score=43.69  Aligned_cols=34  Identities=29%  Similarity=0.490  Sum_probs=29.6

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~  169 (502)
                      .....+.++|.+..+-+|.||||+|.+|+.||.-
T Consensus        25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             eCCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            3445688999999999999999999999999964

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

Probab=95.40  E-value=0.016  Score=44.68  Aligned_cols=34  Identities=21%  Similarity=0.444  Sum_probs=30.3

Q ss_pred             CCCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (502)
Q Consensus        40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t   73 (502)
                      .+..+.+++.+..+..|.||||+|.+|+.||.-.
T Consensus        26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            3567789999999999999999999999998754

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.32  E-value=0.035  Score=56.41  Aligned_cols=96  Identities=23%  Similarity=0.330  Sum_probs=64.2

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  349 (502)
                      +-+|..||.+|.+|+.|.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+... .......
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d----------------~~~fi~na--l~Pa~v~~v~i~-~~~~~~~  305 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED----------------PAEFVANA--LSPAKVVSVEVD-DEEEKAA  305 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--CCCceEEEEEEE-cCCCcEE
Confidence            357999999999999999888 677776543321                00011111  111110111000 0112467


Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  385 (502)
                      .+.||.++.+..|||+|.+++--.+.||.+|.|...
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

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.26  E-value=0.044  Score=57.70  Aligned_cols=95  Identities=20%  Similarity=0.264  Sum_probs=62.9

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|+.|+.|.++. |=+|.|-.-            ..  +.             .   ..+...+.......
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~------------s~--d~-------------~---~fi~nal~pa~v~~  294 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILW------------SD--DP-------------A---QFIINALSPAEVSS  294 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEc------------CC--CH-------------H---HHHHHhCCCCEEEE
Confidence            458999999999999999998 777776321            10  00             0   00011110000000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      --  -....-.+.+.||..+.+..|||+|++|+...+-||.+|.|...
T Consensus       295 v~--~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        295 VV--VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EE--EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            00  00011277899999999999999999999999999999999875

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

Probab=95.25  E-value=0.024  Score=51.45  Aligned_cols=43  Identities=23%  Similarity=0.400  Sum_probs=36.2

Q ss_pred             CCCceEEEEEecC------CceeeeecCChhHHHHHHHhhCCeEEecCC
Q 010746           40 GSEDTVYRYLCPL------RKIGSIIGKGGEIVKQLRSETKSNIRISET   82 (502)
Q Consensus        40 ~~~~~~~~i~vp~------~~~g~iIGk~G~~I~~I~~~tga~I~i~~~   82 (502)
                      .+..+.-++.||.      .++|+|||+.|.|+|+|+..|+|+|-|-..
T Consensus       144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            3445667888885      579999999999999999999999999643

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

Probab=95.24  E-value=0.035  Score=42.76  Aligned_cols=34  Identities=38%  Similarity=0.561  Sum_probs=30.2

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~  169 (502)
                      .....+.++|.+...-+|.||||+|.+|+.|+.-
T Consensus        25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            3467788999999999999999999999999953

>PRK01064 hypothetical protein; Provisional

Probab=95.21  E-value=0.023  Score=44.23  Aligned_cols=33  Identities=30%  Similarity=0.548  Sum_probs=29.9

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET   73 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t   73 (502)
                      +..+.+++.|..+..|.+|||+|.+|++||.-.
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            566889999999999999999999999998854

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.09  E-value=0.035  Score=57.03  Aligned_cols=95  Identities=25%  Similarity=0.341  Sum_probs=63.0

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  349 (502)
                      +-+|..||.+|.+|+.|.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+... .......
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D----------------p~~fI~Na--LsPA~V~~V~i~-~~~~k~a  337 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD----------------PATYIANA--LSPARVDEVRLV-DPEGRHA  337 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--cCCceeeEEEEE-cCCCcEE
Confidence            457999999999999999888 667766543311                00111111  111111111000 0112356


Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEec
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILT  384 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~  384 (502)
                      .+.||.++.+..|||+|.+|+--.+.||.+|.|..
T Consensus       338 ~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        338 HVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             EEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            89999999999999999999999999999999954

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.05  E-value=0.044  Score=52.51  Aligned_cols=62  Identities=21%  Similarity=0.242  Sum_probs=51.1

Q ss_pred             EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746          143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (502)
Q Consensus       143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~  215 (502)
                      +.+.||.+.++.|||++|.+|+.|.++++++|.+-..           -.|.|.++ .+++.+|+.+|..+-++
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            4578999999999999999999999999999988432           46888886 55788888888765554

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=94.82  E-value=0.05  Score=57.30  Aligned_cols=94  Identities=22%  Similarity=0.321  Sum_probs=63.4

Q ss_pred             ccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEE
Q 010746          272 NIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTR  350 (502)
Q Consensus       272 ~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  350 (502)
                      -+|+.||.+|++|+.|.++. |-+|.+-.-+.+                  +..-..-.+.+.-...+..+..  .-...
T Consensus       246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~pa~v~~v~~~~~--~~~~~  305 (470)
T PRK09202        246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD------------------PAQFIINALSPAEVSSVVVDED--EHSAD  305 (470)
T ss_pred             hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCCEEEEEEEeCC--CCEEE
Confidence            47999999999999999888 667766543211                  1111111111111011100111  23678


Q ss_pred             EEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746          351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (502)
Q Consensus       351 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  385 (502)
                      +.||.++.+..|||+|.+|+-..+.||.+|.|...
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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=94.80  E-value=0.023  Score=63.06  Aligned_cols=66  Identities=27%  Similarity=0.338  Sum_probs=55.4

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ......+.||.+.++.+||.||.+||+|.++||+.|.+.           ++-.|.|.+ ..+.+++|+.+|......
T Consensus       552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             CchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence            345677888999999999999999999999999988773           234688888 788999999999887764

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

Probab=94.78  E-value=0.06  Score=56.12  Aligned_cols=97  Identities=18%  Similarity=0.221  Sum_probs=73.0

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+.+|.+|-..|++.+...............++...|.|+++....+||.+|...|+|+.+||+.-.+.          
T Consensus       564 eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------  633 (760)
T KOG1067|consen  564 EALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------  633 (760)
T ss_pred             HHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------
Confidence            4455566777777777665554444445566778889999999999999999999999999999544442          


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010746          188 SFDELLQVAG-EPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~~  216 (502)
                        +..+.|-- ++.+.++|+..|..++..+
T Consensus       634 --e~t~~i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  634 --EGTFSIFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             --CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence              23466655 5778899999998888764

>PRK01064 hypothetical protein; Provisional

Probab=94.62  E-value=0.071  Score=41.49  Aligned_cols=34  Identities=35%  Similarity=0.477  Sum_probs=29.8

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE  169 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~  169 (502)
                      .....+.+++.|...-.|.+|||+|.+|+.|+.-
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            3356688999999999999999999999999864

>PRK12704 phosphodiesterase; Provisional

Probab=94.50  E-value=0.13  Score=55.06  Aligned_cols=63  Identities=22%  Similarity=0.388  Sum_probs=47.4

Q ss_pred             EEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          143 VRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       143 ~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                      -.+.+|+ ++.|+|||+.|.+|+.++.-||+.|.|...   |       ..|.|+| .+-.-+.|...+..++.+
T Consensus       212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC---C-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence            3466776 678999999999999999999999999533   3       4688999 444445666666665554

>PRK00106 hypothetical protein; Provisional

Probab=94.41  E-value=0.16  Score=54.32  Aligned_cols=64  Identities=22%  Similarity=0.423  Sum_probs=50.3

Q ss_pred             EEEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       142 ~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                      .-.+.+|+ ++-|+|||+.|.+|+.++.-|||.+.|...   |       ..|+|++ +|-.-+-|...+..++.+
T Consensus       226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT---P-------EVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC---C-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            34467777 678999999999999999999999999533   3       4688999 566666777777776665

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.38  E-value=0.14  Score=54.79  Aligned_cols=64  Identities=22%  Similarity=0.391  Sum_probs=49.7

Q ss_pred             EEEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746          142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE  215 (502)
Q Consensus       142 ~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~  215 (502)
                      .-.+.+|+ ++-|+|||+.|.+|+.++.-|||.|.|...   |       ..|+|++ +|---+-|...+..++.+
T Consensus       205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC---C-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence            34467777 678999999999999999999999999533   3       3688888 566566677777666655

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=93.45  E-value=0.044  Score=42.19  Aligned_cols=36  Identities=17%  Similarity=0.217  Sum_probs=30.7

Q ss_pred             CCCceEEEEEecCCceeeeecCChhHHHHHHHhhCC
Q 010746           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS   75 (502)
Q Consensus        40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga   75 (502)
                      ..+...+.+.|..+..|.||||+|.++++||.-++.
T Consensus        25 ~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   25 EEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             ETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             cCCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            356678888899999999999999999999876543

>PRK12705 hypothetical protein; Provisional

Probab=92.95  E-value=0.11  Score=55.11  Aligned_cols=64  Identities=25%  Similarity=0.266  Sum_probs=45.3

Q ss_pred             ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Q 010746          345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLR  418 (502)
Q Consensus       345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~  418 (502)
                      ......+.+|. ++-|.||||-|.+|+-+...||+.|.|.   +.|       +.|+|.+ .|..-+.|...+..+
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp-------~~V~ls~fdp~rreia~~~l~~L  261 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTP-------EAVVISSFNPIRREIARLTLEKL  261 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCc-------cchhhcccCccchHHHHHHHHHH
Confidence            45667788886 5669999999999999999999999994   233       3566666 444444444444333

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

Probab=91.75  E-value=0.37  Score=43.78  Aligned_cols=57  Identities=26%  Similarity=0.392  Sum_probs=50.3

Q ss_pred             CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746          149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (502)
                      +..+|+|+||+|.+--.|++.|.++|.+...            .|.|-|..+++.-|...|+.+|.-.+
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~------------kIHiLG~~~niriAR~avcsLIlGsp  233 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS------------KIHILGAFQNIRIARDAVCSLILGSP  233 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecCc------------eEEEeecchhhHHHHHhhHhhhccCC
Confidence            4568999999999999999999999988533            59999999999999999999997643

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=91.09  E-value=0.77  Score=47.69  Aligned_cols=204  Identities=15%  Similarity=0.144  Sum_probs=124.3

Q ss_pred             eeecCChhHHHHHHHhhCCeEEec--CCCCCCCccEEEE-EcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCCC
Q 010746           57 SIIGKGGEIVKQLRSETKSNIRIS--ETVPGCDERIVTI-YSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADD  133 (502)
Q Consensus        57 ~iIGk~G~~I~~I~~~tga~I~i~--~~~~~~~ervv~I-~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~  133 (502)
                      +|=||+--.+.+|++...|.+.+.  +.. |  .++.++ .|..-                 +..+.+..+         
T Consensus       393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~-g--s~~~~~~~g~~~-----------------~F~k~~~~~---------  443 (657)
T COG5166         393 FLRGKKNGKATRIMKGVSCSELSSIVSST-G--SIVETNGIGEKM-----------------SFSKKLSIP---------  443 (657)
T ss_pred             HhccccCcchhhhhhhcccceeeEEEecC-C--cEEEEeccCcch-----------------hhHHHhcCC---------
Confidence            677777666999999998885543  321 2  243333 22110                 111112211         


Q ss_pred             cCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          134 EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       134 ~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                        ..+-.-.+.+.||.+.|..|||.||..|++++...++.|++...-++|.   +                +       -
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----------------Q-------W  495 (657)
T ss_pred             --cccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---h----------------h-------h
Confidence              1122235679999999999999999999999999999998866533332   0                0       1


Q ss_pred             hcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhc--
Q 010746          214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQES--  291 (502)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~s--  291 (502)
                      ++                                               .+-+.+|.+..+.|+|++......+++..  
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            11                                               13466888888999998887777776544  


Q ss_pred             --CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeC---CCc
Q 010746          292 --GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIG---RGG  366 (502)
Q Consensus       292 --ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIG---k~G  366 (502)
                        ...|.|.+.    ..+++++-+-.      ..++.+.+-- .+       .........+.+|.+.++.-+|   -.|
T Consensus       529 ~~Kgdirf~~~----~~sI~~v~~~~------~~I~rv~kne-~v-------~~~~p~~~~~y~~se~h~~g~gena~R~  590 (657)
T COG5166         529 NLKGDIRFCPQ----STSIFTVDIYS------DEIERVIKNE-TV-------LLEFPAEMHFYVPSEIHKKGIGENAFRG  590 (657)
T ss_pred             ccccceEEcCC----ceEEEEEcccc------cHHHHHhhcc-ce-------EEecccccccccchhhhhccCCcccccc
Confidence              234455442    34577766532      2344333311 11       0112355677899999999999   677


Q ss_pred             hhHHHHHHHhCCeEEE
Q 010746          367 AIISEMRSATRASIRI  382 (502)
Q Consensus       367 ~~Ik~I~~~tGa~I~i  382 (502)
                      ++|..+.....-.|..
T Consensus       591 ~ni~~~t~~y~~~ie~  606 (657)
T COG5166         591 ENIQRVTKLYNSYIEF  606 (657)
T ss_pred             cchhhhhhhhhcccee
Confidence            7777666655444444

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

Probab=90.98  E-value=0.083  Score=59.31  Aligned_cols=69  Identities=22%  Similarity=0.183  Sum_probs=57.6

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ..+.+|.....+|||++|++|+.++..|||.|.|..-  -|.  ...+|.+.+.|+++.++.|...|.-.+.+
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            4677888889999999999999999999999999651  121  35789999999999999998887766654

>PRK12705 hypothetical protein; Provisional

Probab=90.84  E-value=0.43  Score=50.71  Aligned_cols=62  Identities=21%  Similarity=0.315  Sum_probs=43.2

Q ss_pred             EEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746          144 RMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (502)
Q Consensus       144 ~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~  215 (502)
                      .+.+|+ ++-|+|||+.|.+|+.++..||+.+.|...   |       +.|+|++. +..-+.|...+..+|.+
T Consensus       201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT---P-------EAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeecCChHhhccccCccchhHHHHHHhhCCceEecCC---c-------cchhhcccCccchHHHHHHHHHHHhc
Confidence            355665 578999999999999999999999999543   3       24556653 33344555555555544

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

Probab=90.77  E-value=0.36  Score=35.94  Aligned_cols=35  Identities=17%  Similarity=0.245  Sum_probs=28.5

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeE
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI   77 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I   77 (502)
                      .....+.+.....|.+|||+|.+|++|+..++-.+
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.

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

Probab=90.60  E-value=0.82  Score=50.81  Aligned_cols=21  Identities=14%  Similarity=0.366  Sum_probs=12.4

Q ss_pred             EEEEEecCCceeeeeCCCchh
Q 010746          348 TTRILVPSAQIGCLIGRGGAI  368 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~  368 (502)
                      .+.|.|-.+.+.||+|-.-+.
T Consensus      1085 WIklqIshEaAAcItgLr~Am 1105 (1282)
T KOG0921|consen 1085 WIKLQISHEAAACITGLRPAM 1105 (1282)
T ss_pred             eeeEeccHHHHHHHhhhHHHH
Confidence            455666666666666654443

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

Probab=89.45  E-value=2.2  Score=37.18  Aligned_cols=91  Identities=23%  Similarity=0.345  Sum_probs=59.1

Q ss_pred             CChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhc-ccCCCcCCCCc
Q 010746           61 KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAED-SLADDEFGELT  139 (502)
Q Consensus        61 k~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~-~~~~~~~~~~~  139 (502)
                      .++..|++|-++..-+|.|-.              ++..          +.+-.+|...|.+.+-++. ..+-..+.   
T Consensus        23 ~~~dli~~lAk~lrKRIvvR~--------------dps~----------l~~~e~A~~~I~~ivP~ea~i~di~Fd~---   75 (145)
T cd02410          23 EDGDLVKDLAKDLRKRIVIRP--------------DPSV----------LKPPEEAIKIILEIVPEEAGITDIYFDD---   75 (145)
T ss_pred             cccHHHHHHHHHHhceEEEcC--------------Chhh----------cCCHHHHHHHHHHhCCCccCceeeEecC---
Confidence            467889999988876666632              2211          1123456666665443221 10000011   


Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                       .+-++.|-...-|.+||++|.++++|..+||-+-.+.+.
T Consensus        76 -~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          76 -DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             -CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence             134567778888999999999999999999999999877

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.

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=88.89  E-value=0.18  Score=38.69  Aligned_cols=33  Identities=18%  Similarity=0.300  Sum_probs=27.7

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETR  171 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg  171 (502)
                      ....+.+.+..+..|.||||.|.+++.||--.+
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            344777888999999999999999999996544

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

Probab=88.73  E-value=0.21  Score=45.32  Aligned_cols=55  Identities=24%  Similarity=0.335  Sum_probs=48.3

Q ss_pred             CCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       355 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      +..+|.|+||+|.+---|.+.|.++|.+..            ..|.|-|..++++.|...|+.+|-.
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            457899999999998899999999999853            2799999999999999999988733

>COG5166 Uncharacterized conserved protein [Function unknown]

Probab=88.50  E-value=1.1  Score=46.59  Aligned_cols=157  Identities=13%  Similarity=0.100  Sum_probs=104.7

Q ss_pred             eeeecCCChHHHHHHhhcCceEEEe--ecCCCCcccCCCCce-EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCC
Q 010746          153 GCVIGKGGQVIQNIRTETRAQIRIL--KDEHLPLCALSFDEL-LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSS  229 (502)
Q Consensus       153 g~IIGk~G~~Ik~I~~~tga~I~i~--~~~~~p~~~~~~er~-v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~  229 (502)
                      -+|-||+--++.+|++...|-+.+.  .++        ..++ -.+.|..-+..+++..+.+   +              
T Consensus       392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~--------gs~~~~~~~g~~~~F~k~~~~~~~---E--------------  446 (657)
T COG5166         392 DFLRGKKNGKATRIMKGVSCSELSSIVSST--------GSIVETNGIGEKMSFSKKLSIPPT---E--------------  446 (657)
T ss_pred             HHhccccCcchhhhhhhcccceeeEEEecC--------CcEEEEeccCcchhhHHHhcCCcc---c--------------
Confidence            3677887777999999988885443  331        1122 2356666666666543321   1              


Q ss_pred             CccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEE
Q 010746          230 NIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII  309 (502)
Q Consensus       230 ~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii  309 (502)
                        |+                            ..+.+.||...|..|||.||..|++...+.++.|.+.....-      
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                            145678999999999999999999999999998888752210      


Q ss_pred             EecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHh----CCeEEEecC
Q 010746          310 FISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT----RASIRILTN  385 (502)
Q Consensus       310 ~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t----Ga~I~i~~~  385 (502)
                                .    +.++                 .-..-+..|..-.+.|+|++-.....++++.    ...|++.+ 
T Consensus       491 ----------~----qs~~-----------------~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-  538 (657)
T COG5166         491 ----------G----QSQW-----------------HDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-  538 (657)
T ss_pred             ----------c----hhhh-----------------hcceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-
Confidence                      0    0000                 1224577899999999999999988888665    55677732 


Q ss_pred             CCCCCCCCCCceEEEEEcCHHHHHH
Q 010746          386 ENVPKVAYEDEEMVQITGSLDVASS  410 (502)
Q Consensus       386 ~~~P~~~~~~~r~v~I~G~~~~v~~  410 (502)
                              ...+.+++-|-.+-+.+
T Consensus       539 --------~~~sI~~v~~~~~~I~r  555 (657)
T COG5166         539 --------QSTSIFTVDIYSDEIER  555 (657)
T ss_pred             --------CceEEEEEcccccHHHH
Confidence                    23458888876655544

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

Probab=87.86  E-value=0.81  Score=33.94  Aligned_cols=35  Identities=31%  Similarity=0.440  Sum_probs=28.3

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI  174 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I  174 (502)
                      ...+.+.+.....+.+||++|++++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35566677766789999999999999999888544

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.

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=87.61  E-value=1.2  Score=42.23  Aligned_cols=47  Identities=21%  Similarity=0.352  Sum_probs=40.1

Q ss_pred             EEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCC
Q 010746           47 RYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG   99 (502)
Q Consensus        47 ~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~   99 (502)
                      -+.||..++-.+|||+|+.++.|.++|+|.|-|...      -.|-|.|..+.
T Consensus       149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~~  195 (239)
T COG1097         149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENES  195 (239)
T ss_pred             EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCcc
Confidence            467899999999999999999999999999999654      24788887664

>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.56  E-value=1.7  Score=42.34  Aligned_cols=22  Identities=41%  Similarity=0.943  Sum_probs=11.6

Q ss_pred             CCCCCCCCC-CCCCCCCCCCCCC
Q 010746          477 YGSYGGSLS-GGGNAYGAYGDHS  498 (502)
Q Consensus       477 yg~yg~~~~-~~~~~yg~~~~~~  498 (502)
                      ||+||++.+ +-|+||+.+++|+
T Consensus        78 yg~YGgGygg~fGgGyN~~~~~g  100 (362)
T KOG3875|consen   78 YGPYGGGYGGGFGGGYNRFGPYG  100 (362)
T ss_pred             CCCcCCCcCcccCcccccccccc
Confidence            345554433 2356666666665

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=87.44  E-value=0.53  Score=36.57  Aligned_cols=34  Identities=21%  Similarity=0.244  Sum_probs=27.1

Q ss_pred             EEEEEecCCceeeeecCChhHHHHHHHhhCCeEE
Q 010746           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR   78 (502)
Q Consensus        45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~   78 (502)
                      .+.+.+..+..|.+|||+|+++.+|+--+..-+.
T Consensus        25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~   58 (77)
T cd02414          25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN   58 (77)
T ss_pred             EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence            3556666788999999999999999987765444

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.

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

Probab=87.29  E-value=1.1  Score=46.36  Aligned_cols=39  Identities=33%  Similarity=0.436  Sum_probs=35.9

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (502)
                      .+.+.||.+.++.+|||+|.+|++|++..|-+|.|...+
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            567899999999999999999999999999999998763

>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.22  E-value=1  Score=43.85  Aligned_cols=14  Identities=36%  Similarity=0.781  Sum_probs=6.0

Q ss_pred             CCCCCCCCCCCCCC
Q 010746          479 SYGGSLSGGGNAYG  492 (502)
Q Consensus       479 ~yg~~~~~~~~~yg  492 (502)
                      +||++.+++|+|||
T Consensus        73 ~~G~Gyg~YGgGyg   86 (362)
T KOG3875|consen   73 NYGSGYGPYGGGYG   86 (362)
T ss_pred             ccCCCCCCcCCCcC
Confidence            34444333444444

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=87.06  E-value=1.1  Score=42.95  Aligned_cols=51  Identities=12%  Similarity=0.193  Sum_probs=45.9

Q ss_pred             eeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      -+|||.+|.+++.|+--|.|-|-|...            .|.+.|....+..+...|.+.+.+
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            569999999999999999999998544            699999999999999999988876

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

Probab=87.01  E-value=2.4  Score=44.36  Aligned_cols=95  Identities=24%  Similarity=0.393  Sum_probs=65.2

Q ss_pred             eecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCCCcCCC
Q 010746           58 IIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGE  137 (502)
Q Consensus        58 iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~  137 (502)
                      ++=+.|..|++|-++..-+|.|-.+              +..          +++..+|...|++.+-++.--.+-   .
T Consensus        43 ~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv----------l~~~e~A~~~I~eivP~ea~i~~i---~   95 (637)
T COG1782          43 LFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV----------LKPPEEARKIILEIVPEEAGITDI---Y   95 (637)
T ss_pred             HhccchhHHHHHHHHHhhceEeccC--------------chh----------cCCHHHHHHHHHHhCccccCceeE---E
Confidence            4557889999999998777776433              111          223567777777655332211110   0


Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      -...+-+++|-.+.-|.+|||+|++.++|..+||-.-+|.+.
T Consensus        96 Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~  137 (637)
T COG1782          96 FDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT  137 (637)
T ss_pred             ecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence            011245678888999999999999999999999998888876

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

Probab=86.76  E-value=0.28  Score=55.35  Aligned_cols=60  Identities=20%  Similarity=0.155  Sum_probs=51.5

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCc
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGT  100 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~  100 (502)
                      .+....++-+|......|||++|.+|+.++.-|||.|.|.. ...+..||.+++.|.++.+
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            34555778889999999999999999999999999999986 4445789999999998764

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=86.56  E-value=0.75  Score=35.74  Aligned_cols=33  Identities=27%  Similarity=0.509  Sum_probs=26.7

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI  174 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I  174 (502)
                      .+.+.+..+..|.||||.|+++..||--.+.-+
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            456777888999999999999999996655433

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.

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

Probab=86.52  E-value=0.95  Score=47.61  Aligned_cols=68  Identities=18%  Similarity=0.237  Sum_probs=57.4

Q ss_pred             CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ....+...+.|+.+....+||.+|-..|.|..+||+.-.+            ++..|+|.- ++.+.+.|+.+|...+..
T Consensus       593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence            4567888999999999999999999999999999965555            234788877 788999999999988877


Q ss_pred             c
Q 010746          422 N  422 (502)
Q Consensus       422 ~  422 (502)
                      .
T Consensus       661 ~  661 (760)
T KOG1067|consen  661 D  661 (760)
T ss_pred             c
Confidence            3

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=85.98  E-value=0.52  Score=35.82  Aligned_cols=37  Identities=27%  Similarity=0.491  Sum_probs=29.7

Q ss_pred             EEEEeeCCc-----eeeeecCCChHHHHHHhhc-CceEEEeec
Q 010746          143 VRMLVPADQ-----IGCVIGKGGQVIQNIRTET-RAQIRILKD  179 (502)
Q Consensus       143 ~~llVp~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~  179 (502)
                      +.+.|-+..     +|..||++|..|+.|+++. |-+|.|...
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~   47 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY   47 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence            456666766     8999999999999999999 999999765

>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A

Probab=85.90  E-value=0.61  Score=35.42  Aligned_cols=36  Identities=25%  Similarity=0.488  Sum_probs=27.8

Q ss_pred             EEEEecCCc-----eeeeeCCCchhHHHHHHHh-CCeEEEec
Q 010746          349 TRILVPSAQ-----IGCLIGRGGAIISEMRSAT-RASIRILT  384 (502)
Q Consensus       349 ~~i~VP~~~-----vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~  384 (502)
                      ..+.|-...     +|..||++|++|+.|.++. |-+|+|-.
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 88898854

>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]

Probab=84.19  E-value=2.1  Score=41.06  Aligned_cols=51  Identities=20%  Similarity=0.221  Sum_probs=43.6

Q ss_pred             eeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          359 GCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       359 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      -++||.+|++++.|+-.|.|.|-|+..            +|.+.|....++.+...+.+.+..
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            367999999999999999999999643            799999999888887777776654

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=83.64  E-value=3.2  Score=39.30  Aligned_cols=47  Identities=17%  Similarity=0.403  Sum_probs=39.6

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD  406 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~  406 (502)
                      .-+.||+..|-.+||++|+.++-|.+.|+|+|-|-.+           -.|-|.+..+
T Consensus       148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~  194 (239)
T COG1097         148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENE  194 (239)
T ss_pred             EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCc
Confidence            5688999999999999999999999999999998543           2566777655

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.24  E-value=0.55  Score=36.48  Aligned_cols=35  Identities=23%  Similarity=0.397  Sum_probs=29.4

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEE
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR   78 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~   78 (502)
                      ....+.+.....+.|||++|++|++|.++..-.+.
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 ....

>PRK13764 ATPase; Provisional

Probab=83.17  E-value=1.3  Score=48.21  Aligned_cols=43  Identities=23%  Similarity=0.405  Sum_probs=38.7

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCC
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVP  389 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P  389 (502)
                      ....+.||.+.++.+|||+|.+|++|.+..|.+|.|...++.|
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            4677899999999999999999999999999999998776654

>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3

Probab=82.58  E-value=0.76  Score=36.14  Aligned_cols=37  Identities=14%  Similarity=0.292  Sum_probs=31.3

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEec
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS   80 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~   80 (502)
                      ..+++.|-...-|.|||++|+.|++|+++..-...+.
T Consensus        30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~   66 (81)
T cd02413          30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP   66 (81)
T ss_pred             CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence            3478888889999999999999999999887666654

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.

>PRK13764 ATPase; Provisional

Probab=82.54  E-value=3.1  Score=45.42  Aligned_cols=43  Identities=30%  Similarity=0.440  Sum_probs=38.2

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCC
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLP  183 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p  183 (502)
                      -.+.+.||.+.++.+|||+|.+|++|.++.|..|.|...+..|
T Consensus       481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~  523 (602)
T PRK13764        481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP  523 (602)
T ss_pred             CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence            3677899999999999999999999999999999998775443

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

Probab=82.34  E-value=0.83  Score=47.17  Aligned_cols=38  Identities=24%  Similarity=0.368  Sum_probs=34.4

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~   81 (502)
                      -...+.||.+.++.+|||+|.+|++|++..|-+|.|-.
T Consensus       486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~  523 (604)
T COG1855         486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP  523 (604)
T ss_pred             CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence            34668899999999999999999999999999999964

>PRK06418 transcription elongation factor NusA-like protein; Validated

Probab=81.20  E-value=1.9  Score=38.68  Aligned_cols=36  Identities=31%  Similarity=0.422  Sum_probs=30.0

Q ss_pred             EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (502)
Q Consensus        45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~   81 (502)
                      .+-++|-... |.-|||+|++|++|++..|-+|.+-+
T Consensus        62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE   97 (166)
T PRK06418         62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE   97 (166)
T ss_pred             EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence            3456666666 99999999999999999998888743

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=80.89  E-value=0.73  Score=35.78  Aligned_cols=33  Identities=39%  Similarity=0.634  Sum_probs=28.4

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI  174 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I  174 (502)
                      .+.+.+...+.+.|||++|++|++|++...-.+
T Consensus        26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l   58 (78)
T PF07650_consen   26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL   58 (78)
T ss_dssp             EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence            567889999999999999999999997766554

; 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	502
2jzx_A	160	Pcbp2 Kh1-Kh2 Domains Length = 160		4e-07
2ann_A	178	Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDE		5e-04
2anr_A	178	Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TAND		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 = 52.8 bits (125), 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|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 = 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---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|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH 25NT 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---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|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	502
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-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	4e-24
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-09
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	4e-40
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-30
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-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	2e-39
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	4e-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	3e-10
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	8e-10
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-37
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	6e-32
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-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	4e-35
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-26
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	6e-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	3e-17
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	5e-15
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	8e-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	8e-12
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	5e-10
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	8e-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	6e-12
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	8e-10
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-08
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	2e-13
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	3e-12
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	7e-11
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	5e-14
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-13
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	3e-12
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-11
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	2e-13
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	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,	6e-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	4e-13
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	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	8e-12
1we8_A	104	Tudor and KH domain containing protein; structural	2e-08
1we8_A	104	Tudor and KH domain containing protein; structural	6e-08
1we8_A	104	Tudor and KH domain containing protein; structural	8e-08
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	9e-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	2e-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	9e-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	5e-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,	7e-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,	8e-08
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-08
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	6e-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
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	6e-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	4e-04
1tua_A	191	Hypothetical protein APE0754; structural genomics,	7e-07
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-07
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
2cxc_A	144	NUSA; transcription termination, RNA binding prote	1e-05
2cxc_A	144	NUSA; transcription termination, RNA binding prote	6e-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	8e-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 =  147 bits (373), Expect = 3e-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 =  118 bits (298), 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 = 98.0 bits (244), Expect = 4e-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 = 4e-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 =  141 bits (357), Expect = 4e-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 =  115 bits (290), Expect = 1e-30
 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 = 90.2 bits (224), Expect = 2e-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 = 50.1 bits (120), 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 =  139 bits (352), Expect = 2e-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 (308), Expect = 4e-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 = 95.6 bits (238), 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 = 57.9 bits (140), Expect = 3e-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 = 8e-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 =  133 bits (337), 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 (300), Expect = 6e-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 (260), Expect = 3e-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 =  127 bits (322), Expect = 4e-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 =  104 bits (262), Expect = 1e-26
 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 = 6e-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 = 57.5 bits (139), 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 = 12/65 (18%), Positives = 25/65 (38%)

Query: 29  NPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDE 88
             G                   P   +G +IG+ GE++K+++++    I+  +      E
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 135

Query: 89  RIVTI 93
           +I  I
Sbjct: 136 KIAHI 140

>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 = 75.4 bits (186), Expect = 3e-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 = 68.8 bits (169), Expect = 5e-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 = 65.4 bits (160), Expect = 8e-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 = 70.0 bits (172), 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 = 8e-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 = 5e-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 = 8e-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 = 60.4 bits (147), Expect = 6e-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 = 8e-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 = 1e-08
 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 = 2e-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 = 61.1 bits (149), 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 = 57.3 bits (139), Expect = 7e-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 = 66.6 bits (163), Expect = 5e-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 = 1e-13
 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 = 57.7 bits (140), Expect = 6e-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 = 65.0 bits (159), Expect = 2e-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 = 58.1 bits (141), Expect = 4e-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 = 56.1 bits (136), 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 = 53.6 bits (129), 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 = 6e-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 = 63.5 bits (155), Expect = 4e-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 = 59.6 bits (145), Expect = 1e-11
 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 = 55.4 bits (134), 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 = 60.6 bits (147), Expect = 8e-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 = 49.8 bits (119), Expect = 6e-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 = 49.4 bits (118), Expect = 8e-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 = 60.7 bits (147), Expect = 9e-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 = 59.5 bits (144), 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 = 2e-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 = 57.3 bits (138), 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 = 53.1 bits (127), Expect = 9e-09
 Identities = 29/171 (16%), Positives = 52/171 (30%), Gaps = 37/171 (21%)

Query: 47  RYLCPLRKIGSIIGKGGEIVKQLRSETK-SNIRISETVPGCDERIVTIYSSSEGTNLFED 105
           +++     +G  IG  G  ++Q R     + I + E     D     IY   +       
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE-----DTCTFHIYGEDQ------- 54

Query: 106 SGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQN 165
                                           L      + VP + +G VIGK G++IQ 
Sbjct: 55  -----------------------DAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQE 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 = 55.9 bits (135), 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 = 5e-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 = 52.8 bits (127), 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 = 7e-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 = 49.0 bits (117), Expect = 8e-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 = 1e-08
 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 = 45.9 bits (109), 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 = 50.5 bits (120), 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 = 48.9 bits (116), 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 = 46.2 bits (109), 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 = 47.1 bits (112), 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 = 6e-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

>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 = 51.8 bits (123), Expect = 5e-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

>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 = 6e-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 = 41.3 bits (97), 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 = 4e-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 = 7e-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

>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

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Length = 144

 Score = 44.2 bits (105), 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 = 39.2 bits (92), Expect = 6e-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

>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 = 8e-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 = 42.5 bits (101), 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 = 42.1 bits (100), 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 = 41.8 bits (99), 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	502
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.93
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	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
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	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	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.9
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.88
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.84
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.75
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.74
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.65
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.64
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.55
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.54
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.53
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.53
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.51
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.51
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.5
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.5
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.5
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.49
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.48
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.47
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.46
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.45
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.45
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.45
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.44
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.44
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.44
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.43
1we8_A	104	Tudor and KH domain containing protein; structural	99.41
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.4
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.39
1we8_A	104	Tudor and KH domain containing protein; structural	99.38
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.38
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.38
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
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.36
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.35
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.35
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.34
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.33
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.31
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.27
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
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.14
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.13
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.09
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.06
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.05
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.84
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	98.47
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.38
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.13
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	98.05
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	98.03
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.83
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.62
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.52
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.5
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.31
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.23
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.85
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.62
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.57
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.55
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.31
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.23
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	94.94
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.72
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.48
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.13
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	90.11

>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=4.1e-26  Score=205.75  Aligned_cols=155  Identities=25%  Similarity=0.381  Sum_probs=130.4

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC-CCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET-VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~-~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      .-+++|+||.+++|.||||+|++|++|+++|||+|+|++. .+++.+|+|+|+|++++             +.+|..+++
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            4589999999999999999999999999999999999875 57889999999998765             567777777


Q ss_pred             HHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHH
Q 010746          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAV  201 (502)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~  201 (502)
                      +.+.+.....   ......++++|+||.+++|+||||+|++|++|+++|||+|.|.++ ..|.  ...++.|+|+|++++
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            7765542211   122345788999999999999999999999999999999999765 4454  134458999999999


Q ss_pred             HHHHHHHHHHHHhcC
Q 010746          202 VRKALVQIASRLHEN  216 (502)
Q Consensus       202 V~~A~~~I~~~l~~~  216 (502)
                      |.+|+.+|.++|.+.
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

>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=1.8e-26  Score=211.19  Aligned_cols=161  Identities=27%  Similarity=0.438  Sum_probs=129.0

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC---CCCCCccEEEEEcCCCCcccccCCccCCCHHHHHH
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET---VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL  117 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~---~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al  117 (502)
                      .+.++++|+||.+++|.||||+|++|++|+++|||+|+|++.   .+++.+|+|+|+|+.++             +.+|+
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            467999999999999999999999999999999999999854   46889999999998665             45565


Q ss_pred             HHHHHHHhhhcccCC-----------CcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCccc
Q 010746          118 FRVHDRIVAEDSLAD-----------DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA  186 (502)
Q Consensus       118 ~~i~~~i~~~~~~~~-----------~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~  186 (502)
                      .++.+.+........           .........+++|+||.+++|+||||+|++|++|+++|||+|+|.++..   +.
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            555555432211000           0011223578999999999999999999999999999999999987633   33


Q ss_pred             CCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746          187 LSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       187 ~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (502)
                      .+.++.|+|+|++++|.+|+.+|.++|.++|
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            4678999999999999999999999999865

>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=6.2e-26  Score=203.94  Aligned_cols=155  Identities=35%  Similarity=0.515  Sum_probs=129.5

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      ..++++|+||.+++|.||||+|++|++|+++|||+|+|++.  ++++|+|+|+|+.++             +.+|..++.
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             456766676


Q ss_pred             HHHhhhcccCCC--cCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010746          122 DRIVAEDSLADD--EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP  199 (502)
Q Consensus       122 ~~i~~~~~~~~~--~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~  199 (502)
                      +.+.+.......  .......++++|+||.+++|+||||+|.+|++|+++|||+|.|.++ .+|.   +.++.|+|+|++
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  0122346899999999999999999999999999999999999765 4454   678999999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 010746          200 AVVRKALVQIASRLHE  215 (502)
Q Consensus       200 ~~V~~A~~~I~~~l~~  215 (502)
                      ++|.+|+.+|.+++.+
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=4.9e-25  Score=201.59  Aligned_cols=174  Identities=22%  Similarity=0.398  Sum_probs=134.3

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC-CCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE-HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ...++++|+||.+++|.||||+|++|++|+++|||+|+|.++. ..|.   +.+|+|+|+|++++|.+|+.+|.+++.+.
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            3568999999999999999999999999999999999998653 2443   67899999999999999999999999774


Q ss_pred             CCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEE
Q 010746          217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK  296 (502)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~  296 (502)
                      +....                                    ...        +                         +.
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 010746          297 VDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT  376 (502)
Q Consensus       297 v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  376 (502)
                      +....           .         .                 .......+.+|.||.+++|+||||+|++|++|+++|
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 010746          377 RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       377 Ga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ||+|+|.+....|   .++++.|+|+|++++|+.|+.+|.++|++++
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   4678999999999999999999999998754

>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=4.8e-25  Score=200.84  Aligned_cols=156  Identities=23%  Similarity=0.355  Sum_probs=123.0

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHH
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~  122 (502)
                      ..+++|+||.+++|.||||+|++|++|+++|+|+|+|.+..+++++|+|+|+|+.++             +.+|+.+|.+
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            467999999999999999999999999999999999987666888999999998766             3445555544


Q ss_pred             HHhhhcccC---C-----------Cc---CCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcc
Q 010746          123 RIVAEDSLA---D-----------DE---FGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLC  185 (502)
Q Consensus       123 ~i~~~~~~~---~-----------~~---~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  185 (502)
                      .+.......   .           .+   ......++++|+||.+++|+||||+|++|++|+++|||+|+|.++.  +.+
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            443221000   0           00   0012346889999999999999999999999999999999998752  334


Q ss_pred             cCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          186 ALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       186 ~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      ..+.++.|+|+|++++|.+|+.+|.++|
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            5577899999999999999999998864

>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=3e-25  Score=200.36  Aligned_cols=154  Identities=25%  Similarity=0.377  Sum_probs=124.0

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC--CCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET--VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~--~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      ++++|+||.+++|.||||+|++|++|+++|||+|+|.+.  .++..+|+|+|+|++++             +..|+..|.
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  35677999999998665             456666666


Q ss_pred             HHHhhhcc---cCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC
Q 010746          122 DRIVAEDS---LADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE  198 (502)
Q Consensus       122 ~~i~~~~~---~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~  198 (502)
                      +.+.+...   ....+......++++|+||.+++|+||||+|.+|++|+++|||+|.|.+.+  +   .+.++.|+|+|+
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            65543221   000111111135688999999999999999999999999999999998762  2   256899999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010746          199 PAVVRKALVQIASRLHE  215 (502)
Q Consensus       199 ~~~V~~A~~~I~~~l~~  215 (502)
                      +++|.+|+.+|.++|.+
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

>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=2.1e-24  Score=194.58  Aligned_cols=155  Identities=27%  Similarity=0.439  Sum_probs=129.8

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcc
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRS  220 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  220 (502)
                      .+++|+||.+.+|.||||+|++|++|+++|||+|+|.++ ..|   .+.+|+|+|+|+++++.+|+.+|.+++.+...  
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   37899999999999999999999998876310  


Q ss_pred             ccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCC
Q 010746          221 QHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS  300 (502)
Q Consensus       221 ~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~  300 (502)
                                 +                                   -|                             . 
T Consensus        77 -----------~-----------------------------------~~-----------------------------~-   80 (163)
T 3krm_A           77 -----------F-----------------------------------GP-----------------------------K-   80 (163)
T ss_dssp             -----------S-----------------------------------CS-----------------------------S-
T ss_pred             -----------c-----------------------------------cc-----------------------------c-
Confidence                       0                                   00                             0 


Q ss_pred             CCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeE
Q 010746          301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI  380 (502)
Q Consensus       301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  380 (502)
                                                                .....+.+|.||.+++|+|||++|++|++|++.|||+|
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 010746          381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       381 ~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      +|++. ..|.  ..+++.|+|+|++++|+.|+.+|.++|++.
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            99654 3443  344558999999999999999999999874

>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=7.1e-24  Score=191.33  Aligned_cols=160  Identities=23%  Similarity=0.390  Sum_probs=128.5

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcc
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRS  220 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~  220 (502)
                      ++.+|+||.+++|+||||+|++|++|+++|||+|+|.++...+   ...+|.|+|+|++++|.+|+.+|.+++.+.... 
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 010746          221 QHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSS  300 (502)
Q Consensus       221 ~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~  300 (502)
                                .|.                                   |..                  .++        
T Consensus        78 ----------~~~-----------------------------------~~~------------------~~~--------   86 (164)
T 2jvz_A           78 ----------GFG-----------------------------------DRN------------------EYG--------   86 (164)
T ss_dssp             ----------CCS-----------------------------------SCS------------------SCT--------
T ss_pred             ----------CCC-----------------------------------Ccc------------------ccC--------
Confidence                      000                                   000                  000        


Q ss_pred             CCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeE
Q 010746          301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI  380 (502)
Q Consensus       301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I  380 (502)
                                   .                             ....+.+|.||.+++|+||||+|++|++|+++|||+|
T Consensus        87 -------------~-----------------------------~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I  124 (164)
T 2jvz_A           87 -------------S-----------------------------RIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRI  124 (164)
T ss_dssp             -------------T-----------------------------SCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEE
T ss_pred             -------------C-----------------------------CCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeE
Confidence                         0                             0012356889999999999999999999999999999


Q ss_pred             EEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       381 ~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      +|.+.+  +   .+.++.|+|+|++++|+.|+.+|.++|++.
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            997642  2   356799999999999999999999999763

>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=191.26  Aligned_cols=157  Identities=27%  Similarity=0.520  Sum_probs=130.4

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS  218 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~  218 (502)
                      .+++++|+||.+.+|.||||+|++|++|+++|||+|+|....       ..+|.|+|+|++++|.+|+.+|.+++.+...
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            467999999999999999999999999999999999998651       4589999999999999999999998876210


Q ss_pred             ccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEec
Q 010746          219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD  298 (502)
Q Consensus       219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~  298 (502)
                      .                                         .      .+.           +                
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 010746          299 SSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA  378 (502)
Q Consensus       299 ~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa  378 (502)
                        .           .                            ......+.+|.||.+++|+|||++|++|++|+++|||
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 010746          379 SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       379 ~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      +|+|.+. .+|   .++++.|+|+|++++|+.|+.+|.+.|.+
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   46789999999999999999999999876

>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=1.5e-23  Score=191.05  Aligned_cols=173  Identities=20%  Similarity=0.334  Sum_probs=128.0

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCc
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSR  219 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~  219 (502)
                      ..+++|+||.+++|.||||+|++|++|+++|||+|+|.+.+  +   ...+|+|+|+|++++|.+|+.+|.+++.+....
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            35789999999999999999999999999999999997642  2   256899999999999999999999999873210


Q ss_pred             cccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecC
Q 010746          220 SQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDS  299 (502)
Q Consensus       220 ~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~  299 (502)
                                 .+.+                  +              -|..   .-.++       ..           
T Consensus        77 -----------~~~~------------------~--------------~p~~---~~~~~-------~~-----------   92 (174)
T 1j4w_A           77 -----------NPGG------------------P--------------GPGG---RGRGR-------GQ-----------   92 (174)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             -----------CCCC------------------C--------------CCCC---CCCCC-------CC-----------
Confidence                       0000                  0              0000   00000       00           


Q ss_pred             CCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCe
Q 010746          300 SGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS  379 (502)
Q Consensus       300 ~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~  379 (502)
                                     ..+..                     .......+.+|.||.+++|+||||+|++|++|+++|||+
T Consensus        93 ---------------~~~~~---------------------~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~  136 (174)
T 1j4w_A           93 ---------------GNWNM---------------------GPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGAR  136 (174)
T ss_dssp             -----------------------------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCE
T ss_pred             ---------------Ccccc---------------------CCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCE
Confidence                           00000                     000123578999999999999999999999999999999


Q ss_pred             EEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          380 IRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       380 I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      |+|.+.  .+++.+++++.|+|+|++++|+.|+.+|.++|
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

>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA binding, cell cycle; 2.79A {Caenorhabditis elegans}

Probab=99.88  E-value=6.5e-23  Score=203.78  Aligned_cols=231  Identities=13%  Similarity=0.120  Sum_probs=155.4

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCC--hHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGG--QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G--~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      .....+|+++-||..+|++||||+|  ++|++|+++|+|+|+|+..+.-..........|+|+|.+++|++|+.+|.+++
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  99999999999999997652000011134567999999999999999887733


Q ss_pred             hcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCC
Q 010746          214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGA  293 (502)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga  293 (502)
                      .                                               +++.+.+|...+..  ......|.+ ++.+++
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                                               13344444432221  011223433 567999


Q ss_pred             eEEecCCCCC--CCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCc--hhH
Q 010746          294 SIKVDSSGAE--GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGG--AII  369 (502)
Q Consensus       294 ~I~v~~~~~~--~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G--~~I  369 (502)
                      +|.|+.....  .....|+|.|.+.  +...+.+|+..+...+.+.  .......++..|.|+..+|..|||++|  ..|
T Consensus       135 ~I~Fp~~~~~~~~~sd~V~IrG~~~--nv~~akeA~~~Ll~~l~~~--e~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~I  210 (376)
T 3n89_A          135 EMSFVDAPEKNGIVTTYLRITAREK--NQHELIEAAKRLNEILFRE--SPAPENNFTLHFTLSTYYVDQVLGSSSTAQLM  210 (376)
T ss_dssp             EEEEEEEC-----CEEEEEEEEEGG--GHHHHHHHHHHHHHHHCC----CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHH
T ss_pred             EEEeCCcccccCCCCCEEEEEcChh--hHHHHHHHHHHHHHHHHhh--hcccccceEEEEEeCHHHHHHhhcCCCcchHH
Confidence            9999764321  1256788888641  0112334433333222221  111234689999999999999999999  667


Q ss_pred             HHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          370 SEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       370 k~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ++|+++|||+|.++..++ +.........|+|+|++++|..|+.+|+++|=-
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 110112456899999999999999999988744

>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=4.9e-21  Score=190.32  Aligned_cols=286  Identities=11%  Similarity=0.060  Sum_probs=177.9

Q ss_pred             CCCCceEEEEEecCCceeeeecCCh--hHHHHHHHhhCCeEEecCCC-----CCCCccEEEEEcCCCCcccccCCccCCC
Q 010746           39 IGSEDTVYRYLCPLRKIGSIIGKGG--EIVKQLRSETKSNIRISETV-----PGCDERIVTIYSSSEGTNLFEDSGEFVS  111 (502)
Q Consensus        39 ~~~~~~~~~i~vp~~~~g~iIGk~G--~~I~~I~~~tga~I~i~~~~-----~~~~ervv~I~G~~e~~~~~~~~~~~~~  111 (502)
                      .....+++++.||..+|++||||+|  ++|++|+++|+|+|+|++..     +......|+|+|.+++|           
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            3467899999999999999999999  99999999999999999764     11345789999998885           


Q ss_pred             HHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCc
Q 010746          112 PAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDE  191 (502)
Q Consensus       112 ~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er  191 (502)
                        ++|..++.+.               ..+++.+-+|...+..  ..-...|.. ++.++++|.|.......   .....
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              3344444331               1335555556543222  111234544 67899999997652211   11245


Q ss_pred             eEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCC
Q 010746          192 LLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAG  271 (502)
Q Consensus       192 ~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~  271 (502)
                      .|+|+|...+|.+|++++..++..-....                                   ......+++.|.|+..
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            79999999777766655555443311100                                   0123457889999999


Q ss_pred             ccccccccCccc--ccchhhhcCCeEEecCCCCC----CCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCc
Q 010746          272 NIGGVIGKGGGI--IKQIRQESGASIKVDSSGAE----GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDP  345 (502)
Q Consensus       272 ~~g~IIGk~G~~--Ik~i~~~sga~I~v~~~~~~----~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  345 (502)
                      ++..|||++|.+  |++|+++|||+|.||+..+.    .....|+|+|..      ..+++|.+....+          -
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            999999999955  59999999999999975432    235688999874      3444444433222          2


Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCC---ceEEEEEcCHHHHH
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYED---EEMVQITGSLDVAS  409 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~---~r~v~I~G~~~~v~  409 (502)
                      .+...+.++.+..-.-.-.--..|..+.++.++-|.|.++.-.|..--++   -..|.|..-.-++.
T Consensus       260 Pv~l~Fd~~~~d~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~s~e~n~~  326 (376)
T 3n89_A          260 PISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVPLNCASLRSKEFNIK  326 (376)
T ss_dssp             EEEEEEEEEGGGBC--------CBEEEECTTSCEEEEEEEEECCSSSSCCCEEEEEEEEEEEGGGHH
T ss_pred             CEEEEEecCCcccccccccchhHHHHHHHhcCeEEEEeecCCCchhhcccccccceEEEEEEeccHH
Confidence            46677776654332223333333445668889999997764323100111   13577777444443

>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=99.75  E-value=3.2e-18  Score=149.92  Aligned_cols=139  Identities=19%  Similarity=0.242  Sum_probs=101.2

Q ss_pred             cceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCcccccccc
Q 010746          261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTER  340 (502)
Q Consensus       261 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~  340 (502)
                      .++.++.||.+.+|++||++|++|++|++++|+.+..+...   .+.++......      ..+..+..+..        
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            46789999999999999999999999999999544333322   33343333321      23333322211        


Q ss_pred             CCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCC-eEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          341 ESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRA-SIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       341 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa-~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                           ..+.++.||.+++|++|||+|.+|+.|++.||| +|+|.+.++......+..+.|+|+|++++|+.|+.+|.++|
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 99998754321101112246899999999999999999998


Q ss_pred             Hh
Q 010746          420 RA  421 (502)
Q Consensus       420 ~~  421 (502)
                      ..
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=99.74  E-value=6.8e-18  Score=147.85  Aligned_cols=136  Identities=18%  Similarity=0.256  Sum_probs=100.3

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEc-CCCCcccccCCccCCCHHHHHHHHHH
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYS-SSEGTNLFEDSGEFVSPAQDALFRVH  121 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G-~~e~~~~~~~~~~~~~~a~~al~~i~  121 (502)
                      .++.+|+||.+.+|++||++|++|++|++++|  |++.... ..+++ +++.+ +++.                 +.++.
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~-~i~~~~~p~~-----------------v~~~~   61 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCT-FHIYGEDQDA-----------------VKKAR   61 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTE-EEEEESSHHH-----------------HHHHH
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchh-eeeccCCHHH-----------------HHHHH
Confidence            56889999999999999999999999999999  5443221 12344 44544 3332                 22221


Q ss_pred             HHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCc-eEEEeecCCCCcccCCCCc--eEEEecC
Q 010746          122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRA-QIRILKDEHLPLCALSFDE--LLQVAGE  198 (502)
Q Consensus       122 ~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga-~I~i~~~~~~p~~~~~~er--~v~I~G~  198 (502)
                      ..+ .  +           .++++.||.+++|++|||+|++|+.|++.||| +|+|..+++...  ...++  .|+|+|+
T Consensus        62 ~~l-~--~-----------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~  125 (144)
T 2qnd_A           62 SFL-E--F-----------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGT  125 (144)
T ss_dssp             HHH-C--E-----------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEE
T ss_pred             Hhh-h--c-----------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeC
Confidence            111 0  0           13789999999999999999999999999997 999998643211  12344  4899999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 010746          199 PAVVRKALVQIASRLHE  215 (502)
Q Consensus       199 ~~~V~~A~~~I~~~l~~  215 (502)
                      +++|.+|+.+|.++|.+
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=4e-16  Score=145.21  Aligned_cols=155  Identities=20%  Similarity=0.206  Sum_probs=109.5

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-----HHHHHHHHHHHHHHH
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-----PAVVRKALVQIASRL  213 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-----~~~V~~A~~~I~~~l  213 (502)
                      .+...++.||.+.++.|||++|.+|+.|+++|||+|.|..+          ++.|+|.++     ++++.+|+.+|.++.
T Consensus        32 aP~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~----------~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           32 FKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE----------TGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             -CCEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT----------TCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC----------CCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            34467899999999999999999999999999999999643          456888875     699999999999987


Q ss_pred             hcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCC
Q 010746          214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGA  293 (502)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga  293 (502)
                      .......                                                     +.++         +.++..+
T Consensus       102 rg~~~e~-----------------------------------------------------g~~l---------l~dd~~~  119 (219)
T 2e3u_A          102 RGFSPER-----------------------------------------------------AFRL---------LNEGEYL  119 (219)
T ss_dssp             TTCCHHH-----------------------------------------------------HGGG---------GSTTCEE
T ss_pred             ccCCccc-----------------------------------------------------ccee---------ccCCccc
Confidence            5311000                                                     0000         0000000


Q ss_pred             eEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHH
Q 010746          294 SIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMR  373 (502)
Q Consensus       294 ~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~  373 (502)
                      .             ++.+..-                               .+...-..+...+|+||||+|++|+.|+
T Consensus       120 e-------------~i~i~~~-------------------------------~v~~~~~~~~r~~GriIGk~G~tik~ie  155 (219)
T 2e3u_A          120 E-------------IINLTDI-------------------------------IIGNEKNALPRVRGRIIGRKGRTRQIIE  155 (219)
T ss_dssp             E-------------EEEGGGC-------------------------------C------CHHHHHHHHHCGGGHHHHHHH
T ss_pred             e-------------eEEcccc-------------------------------cccCCchhhhhhhheeECCCchHHHHHH
Confidence            0             0000000                               0000001123468999999999999999


Q ss_pred             HHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          374 SATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       374 ~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      +.|||+|.|..            +.|+|.|++++|+.|..+|+++|..
T Consensus       156 ~~Tg~~I~v~~------------~~v~i~G~~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          156 EMSGASVSVYG------------KTVAIIGNPIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHCCEEEEET------------TEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             HHhCceEEECC------------eEEEEEeCHHHHHHHHHHHHHHHcC
Confidence            99999999952            3799999999999999999999965

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=99.64  E-value=2.6e-16  Score=146.50  Aligned_cols=144  Identities=22%  Similarity=0.195  Sum_probs=104.0

Q ss_pred             ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHH
Q 010746           43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD  122 (502)
Q Consensus        43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~  122 (502)
                      .-..++.||.+.++.|||++|++|+.|+++|||+|+|+..     ++.|+|+++...-        ....+++|...|..
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     5789999864210        01124555555544


Q ss_pred             HHhh------hcccCCCcCCCCccEEEEEEe-----eC------CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcc
Q 010746          123 RIVA------EDSLADDEFGELTLITVRMLV-----PA------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLC  185 (502)
Q Consensus       123 ~i~~------~~~~~~~~~~~~~~~~~~llV-----p~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~  185 (502)
                      .+..      ..+..+   +   ...-.+-+     +.      ..+|+||||+|.+|+.|++.|||+|.|..       
T Consensus       100 i~rg~~~e~g~~ll~d---d---~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~-------  166 (219)
T 2e3u_A          100 IGRGFSPERAFRLLNE---G---EYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG-------  166 (219)
T ss_dssp             HHTTCCHHHHGGGGST---T---CEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET-------
T ss_pred             HhccCCccccceeccC---C---ccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC-------
Confidence            3310      111111   0   11111222     21      26899999999999999999999999952       


Q ss_pred             cCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746          186 ALSFDELLQVAGEPAVVRKALVQIASRLHENP  217 (502)
Q Consensus       186 ~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~  217 (502)
                           +.|+|.|+.++|+.|..+|.++|...+
T Consensus       167 -----~~v~i~G~~~~i~~A~~~i~~li~g~~  193 (219)
T 2e3u_A          167 -----KTVAIIGNPIQIEIAKTAIEKLARGSP  193 (219)
T ss_dssp             -----TEEEEEECHHHHHHHHHHHHHHHTTCC
T ss_pred             -----eEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence                 469999999999999999999996643

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=6.4e-15  Score=122.04  Aligned_cols=73  Identities=21%  Similarity=0.311  Sum_probs=64.2

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      +.+|.||.+++|+||||+|++|++|+++|||+|+|.+.. .| ..+.++++|+|+|++++|+.|+.+|.++|++.
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            789999999999999999999999999999999997642 22 23457899999999999999999999998663

>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=99.54  E-value=5.3e-15  Score=113.73  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=64.4

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ..++.+|+||.+++|+|||++|++|++|+++|||+|+|.+.       +..+|.|+|.|++++|..|+.+|.++|++
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            45789999999999999999999999999999999999754       24689999999999999999999999976

>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=1.2e-14  Score=113.02  Aligned_cols=73  Identities=25%  Similarity=0.357  Sum_probs=64.0

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+..  .++.++.|+|+|++++|+.|+.+|.++|.+
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            5789999999999999999999999999999999998653322  246789999999999999999999998754

>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=99.53  E-value=2.2e-14  Score=113.05  Aligned_cols=73  Identities=29%  Similarity=0.514  Sum_probs=65.9

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+++++.
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            46889999999999999999999999999999999999642  22   467899999999999999999999999874

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=99.51  E-value=1.3e-14  Score=112.73  Aligned_cols=73  Identities=34%  Similarity=0.528  Sum_probs=65.6

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+.|++.
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            35789999999999999999999999999999999999752  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=99.51  E-value=1.9e-14  Score=113.46  Aligned_cols=73  Identities=36%  Similarity=0.498  Sum_probs=64.7

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+++.+.
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--VE---GSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CT---TCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--CC---CCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            45789999999999999999999999999999999999753  22   568999999999999999999999999775

>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=99.50  E-value=1.4e-14  Score=111.30  Aligned_cols=70  Identities=29%  Similarity=0.553  Sum_probs=64.9

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.++       ...+|+|+|.|++++|.+|+.+|.++|.+
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            45799999999999999999999999999999999999865       14689999999999999999999999986

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=2.7e-14  Score=117.67  Aligned_cols=72  Identities=21%  Similarity=0.345  Sum_probs=64.0

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      .+.+|.||.+++++||||+|++||+|+++|||+|+|.+++  +   .+.+|.|+|+|++++|++|+.+|.+++++..
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~--~---~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--G---TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSC--S---SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCC--C---CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            4689999999999999999999999999999999997542  1   3568999999999999999999999998753

>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=99.50  E-value=7.6e-14  Score=126.54  Aligned_cols=151  Identities=19%  Similarity=0.219  Sum_probs=110.2

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----cCHHHHHHHHHHHHHHHhcC
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA-----GEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~-----G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ..+++||...+|.|||++|++++.|++.++++|++...          ++.|+|.     |++.++.+|..+|..+.+..
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            36899999999999999999999999999999999643          5678888     99999999999998888753


Q ss_pred             CCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEE
Q 010746          217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK  296 (502)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~  296 (502)
                      +......+                                 ..+.+.+.                               
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 010746          297 VDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT  376 (502)
Q Consensus       297 v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t  376 (502)
                                 ++.+.             .....            .       -..+...+|+|||++|.+|+.|+..|
T Consensus        91 -----------~i~i~-------------~~~~~------------~-------~~~~~r~~GrIIGk~G~tik~iE~~T  127 (191)
T 1tua_A           91 -----------VVDLK-------------QVVGD------------S-------QNHLKRIKGRIIGEGGRARRTIEEMT  127 (191)
T ss_dssp             -----------EEETH-------------HHHTT------------C-------HHHHHHHHHHHHCGGGHHHHHHHHHH
T ss_pred             -----------EEEcc-------------ccccc------------C-------chhHHHHhhheeCCCccHHHHHHHHH
Confidence                       00000             00000            0       00124578999999999999999999


Q ss_pred             CCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          377 RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       377 Ga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ||+|.|..            ..|.|.|++++++.|...|..+|..
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            2799999999999999999999864

>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=99.49  E-value=2.3e-14  Score=114.28  Aligned_cols=77  Identities=25%  Similarity=0.318  Sum_probs=67.2

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhchhc
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTFE  425 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~  425 (502)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+..  .++.++.|+|+|++++|+.|+.+|.++|.+....
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            5789999999999999999999999999999999997653321  2467899999999999999999999999886543

>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=99.48  E-value=3e-14  Score=114.06  Aligned_cols=75  Identities=29%  Similarity=0.530  Sum_probs=67.2

Q ss_pred             CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ....++.+|.||.+++|+||||+|++|++|+++|||+|+|.+.  .|   +++++.|+|+|++++|+.|+.+|.+++++.
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            4467899999999999999999999999999999999999642  22   467899999999999999999999999874

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.47  E-value=1.4e-13  Score=109.25  Aligned_cols=74  Identities=19%  Similarity=0.333  Sum_probs=64.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|.|.++...+   .+.+|.|+|+|++++++.|+.+|.+++++
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            356789999999999999999999999999999999997643222   46789999999999999999999998853

>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=99.46  E-value=7.6e-14  Score=112.36  Aligned_cols=73  Identities=26%  Similarity=0.388  Sum_probs=65.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..  +   +..++.|+|+|++++|+.|+.+|.++|++.
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            457899999999999999999999999999999999997542  2   457899999999999999999999999874

>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=99.45  E-value=6.7e-14  Score=126.89  Aligned_cols=144  Identities=16%  Similarity=0.140  Sum_probs=101.9

Q ss_pred             EEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHh
Q 010746           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV  125 (502)
Q Consensus        46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~  125 (502)
                      ++++||...+|.|||++|++++.|+++++|+|.++..     ++.|+|..+.+.-.        ...+++|...|.....
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        1113444433332211


Q ss_pred             hhcccCCCc-CCCCccEEEE-EEee----------CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010746          126 AEDSLADDE-FGELTLITVR-MLVP----------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL  193 (502)
Q Consensus       126 ~~~~~~~~~-~~~~~~~~~~-llVp----------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v  193 (502)
                        .+..++. .-..+.+.+. +-++          ....|+||||+|.+|+.|++.|||+|.|..            +.|
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              1110000 0001122333 2233          235899999999999999999999999942            379


Q ss_pred             EEecCHHHHHHHHHHHHHHHhcC
Q 010746          194 QVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       194 ~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      .|.|+.++++.|...|++++...
T Consensus       139 ~i~G~~~~i~~Ar~~i~~li~g~  161 (191)
T 1tua_A          139 AIIGDYERAMAAKQAIEMLAEGR  161 (191)
T ss_dssp             EEEEEHHHHHHHHHHHHHHHTTC
T ss_pred             EEEeChHHHHHHHHHHHHHHcCC
Confidence            99999999999999999999653

>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=99.45  E-value=4.2e-14  Score=111.01  Aligned_cols=69  Identities=20%  Similarity=0.315  Sum_probs=61.9

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|+|++.        ++++.|+|+|++++|+.|+.+|.+++..
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            45789999999999999999999999999999999999753        2357899999999999999999997654

>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=8.6e-14  Score=109.64  Aligned_cols=74  Identities=30%  Similarity=0.446  Sum_probs=65.4

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ...++++|+||.+++|+||||+|++|++|+++|||+|+|.+.     +..+.++.|+|+|++++|.+|+.+|.+++.++
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            356789999999999999999999999999999999999764     12367999999999999999999999999875

>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=99.44  E-value=1.1e-13  Score=107.44  Aligned_cols=72  Identities=31%  Similarity=0.499  Sum_probs=64.0

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .+++|+||.+.+|+||||+|++|++|+++|||+|.|.++.+ .|   .+.++.|+|+|++++|.+|+.+|.+++.+
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

>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=99.44  E-value=1.6e-13  Score=108.04  Aligned_cols=72  Identities=32%  Similarity=0.542  Sum_probs=65.3

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|.+.  .|   .+.+|.|+|+|++++|.+|+.+|.+++.+
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~--~~---~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   76 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LE---GSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TS---CSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCC--CC---CCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            46799999999999999999999999999999999999754  23   36789999999999999999999999976

>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=8.2e-14  Score=108.13  Aligned_cols=73  Identities=32%  Similarity=0.495  Sum_probs=65.8

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|.|.+.  .|   .+.++.|+|+|++++|.+|+.+|.+++.++
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            45789999999999999999999999999999999999763  22   467999999999999999999999998763

>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=99.43  E-value=1.1e-13  Score=111.79  Aligned_cols=75  Identities=19%  Similarity=0.339  Sum_probs=66.0

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+||||+|++|++|+++|||+|+|.+....+   ..++|.|+|+|++++|+.|+.+|.++|++.
T Consensus        13 ~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~---~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           13 GNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN---TGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCS---SCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCC---CCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            468899999999999999999999999999999999997643211   347899999999999999999999999763

>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=99.41  E-value=4.2e-13  Score=110.60  Aligned_cols=77  Identities=19%  Similarity=0.322  Sum_probs=66.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhchh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  424 (502)
                      ...+.+|.||.+++|+||||+|++|++|+++|||+|+|.+... +  ..++++.|+|+|++++|+.|+.+|.++|++...
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            5678999999999999999999999999999999999976432 1  124689999999999999999999999977543

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=99.40  E-value=5.4e-13  Score=105.74  Aligned_cols=75  Identities=25%  Similarity=0.476  Sum_probs=65.8

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ....+.+|+||.+.+|+||||+|++|++|+++|||+|.|.++...+   .+.+|.|+|+|++++|.+|+.+|.+++.+
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            3457889999999999999999999999999999999998763222   36789999999999999999999998854

>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=2.4e-13  Score=108.71  Aligned_cols=74  Identities=31%  Similarity=0.504  Sum_probs=66.6

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ....++++|+||.+.++.||||+|++|++|+++|||+|+|.+.  .|   .+.++.|+|+|++++|.+|+.+|.+++.+
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            3457899999999999999999999999999999999999753  23   36789999999999999999999999987

>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=99.38  E-value=4.2e-13  Score=110.56  Aligned_cols=87  Identities=25%  Similarity=0.382  Sum_probs=72.7

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ...+++++|+||.+.+|+||||+|++|++|+++|||+|.|.+...  .+ ...++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus        11 ~~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~--~~-~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE--GT-LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSC--CS-SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCC--CC-CCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            446688999999999999999999999999999999999987522  11 246899999999999999999999999887


Q ss_pred             CCcccccccc
Q 010746          217 PSRSQHLLLS  226 (502)
Q Consensus       217 ~~~~~~~~~~  226 (502)
                      +...+++..+
T Consensus        88 ~~~~~~~~~~   97 (104)
T 1we8_A           88 EELRKRIAHS   97 (104)
T ss_dssp             HHHHHHHHCC
T ss_pred             hHHHHHhccC
Confidence            6655554443

>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=99.38  E-value=4.5e-13  Score=107.79  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=66.7

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ...++++|+||.+++|+||||+|++|++|+++|||+|+|.++.  +   ...+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        12 ~~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~--~---g~~~r~v~I~G~~e~v~~A~~~I~~~i~~~   85 (92)
T 1x4n_A           12 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS--G---GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCC--C---CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3568999999999999999999999999999999999998752  2   256899999999999999999999999874

>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=2.8e-13  Score=107.92  Aligned_cols=73  Identities=29%  Similarity=0.488  Sum_probs=65.6

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCC-CCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH-LPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ++++|+||.+.+|+||||+|++|++|+++|||+|.|.++.+ .|   .+.++.|+|+|++++|.+|+.+|.+++.+.
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   367899999999999999999999999774

>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=3.3e-13  Score=109.06  Aligned_cols=77  Identities=22%  Similarity=0.436  Sum_probs=67.7

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ....++++|+||.+++++||||+|++|++|+++|||+|.|.++....   ...+|.|+|+|++++|.+|+.+|.+++.+.
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            34668999999999999999999999999999999999998763211   247899999999999999999999999773

>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=1.8e-13  Score=107.35  Aligned_cols=70  Identities=24%  Similarity=0.341  Sum_probs=63.5

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ...++++|.||.+++|+||||+|++||+|+++|||+|+|.+.        ..+++|+|+|++++|++|+.+|.+++..
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            456789999999999999999999999999999999999765        2368999999999999999999998765

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.36  E-value=7.1e-13  Score=109.68  Aligned_cols=73  Identities=23%  Similarity=0.401  Sum_probs=64.7

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      +++|+||.+++++||||+|++|++|+++|||+|+|.++. .| +....++.|+|+|++++|.+|+.+|.+++.+.
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

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=8.5e-13  Score=108.68  Aligned_cols=71  Identities=23%  Similarity=0.426  Sum_probs=63.7

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      .+++|+||.+++++||||+|++|++|+++|+|+|+|.+++  +   .+.+|.|+|+|++++|.+|+.+|.+++.+.
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  1   256899999999999999999999999873

>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=99.35  E-value=1.4e-12  Score=105.37  Aligned_cols=74  Identities=15%  Similarity=0.196  Sum_probs=65.3

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhchh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF  424 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~  424 (502)
                      ..++.+|.||.++++.|||++|++|++|+++|||+|+|+++.      ..+++.|+|+|++++|+.|+.+|.+++++...
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            468899999999999999999999999999999999996542      13467899999999999999999999887653

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.34  E-value=8.3e-13  Score=100.78  Aligned_cols=67  Identities=21%  Similarity=0.287  Sum_probs=59.7

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|+|+++.       +.++.|+|+|++++|+.|+.+|.+.+
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            46789999999999999999999999999999999996532       35679999999999999999998753

>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=99.33  E-value=1.3e-12  Score=105.45  Aligned_cols=72  Identities=18%  Similarity=0.320  Sum_probs=64.0

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ..++.+|.||.+++|.|||++|++|++|+++|||+|+|++.+       +.++.|+|+|++++|+.|+.+|.+++++..
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            468999999999999999999999999999999999996532       234689999999999999999999997743

>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=99.31  E-value=3.3e-12  Score=103.57  Aligned_cols=72  Identities=18%  Similarity=0.271  Sum_probs=63.8

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      .++..|.||.++++.|||++|++|++|+++|||+|+|++... |   ...++.|+|+|++++|..|+.+|..++++
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            478999999999999999999999999999999999976432 2   23678999999999999999999998876

>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=99.27  E-value=3.3e-12  Score=103.61  Aligned_cols=73  Identities=19%  Similarity=0.219  Sum_probs=64.5

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..+++.|.||.++++.||||+|++|++|+++|||+|.|.++.. |.   ..++.|+|+|..++|.+|+.+|..++.+
T Consensus        15 ~~~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~etg~~I~i~~~g~-~~---~~~~~V~I~G~~e~v~~A~~~I~~iv~e   87 (97)
T 2ctl_A           15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-GN---QPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-CS---SCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-CC---CCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999999999999999987631 21   3678999999999999999999998866

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=99.27  E-value=3e-12  Score=97.69  Aligned_cols=67  Identities=22%  Similarity=0.359  Sum_probs=60.0

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      ..+..|.||.++++.|||++|++|++|+++|||+|.|+++.       ..++.|+|+|+.++|.+|+.+|.+++
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            45789999999999999999999999999999999997652       35689999999999999999998753

>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=4.9e-12  Score=102.08  Aligned_cols=73  Identities=21%  Similarity=0.326  Sum_probs=64.9

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ....++.+|.||.+.++.|||++|.+|++|+++|||+|.|.+.+       ..++.|+|+|++++|.+|+.+|.+++.+.
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       23578999999999999999999998773

>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=6e-12  Score=101.57  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=65.0

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ....++..|.||..+++.|||++|++|++|+++|||+|+|..+..      ..++.|+|+|.+++|.+|+.+|..++.+
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            456789999999999999999999999999999999999976521      2467899999999999999999998876

>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=99.25  E-value=6.2e-12  Score=103.25  Aligned_cols=71  Identities=21%  Similarity=0.263  Sum_probs=63.1

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ..+.+|.||.+++|.|||++|++|++|+++|||+|+|++..       +..+.|+|+|++++|+.|+.+|.+++++..
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            57899999999999999999999999999999999997542       234589999999999999999999988744

>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=99.14  E-value=3.6e-11  Score=98.65  Aligned_cols=70  Identities=24%  Similarity=0.369  Sum_probs=62.6

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .+++..|.||.+.++.|||++|++|++|+++|||+|.|.++.       ...+.|+|+|+.++|.+|+.+|..++.+
T Consensus        15 ap~~~~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           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            357899999999999999999999999999999999997652       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=99.13  E-value=5.5e-11  Score=95.71  Aligned_cols=71  Identities=17%  Similarity=0.223  Sum_probs=63.3

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHh-CCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSAT-RASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++..|.||.++++.|||++|.+|++|+++| ||+|.|+..       ++..+.|+|.|+.++|+.|+.+|.+++++.
T Consensus        15 ~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~-------g~~~~~V~I~G~~~~v~~A~~~I~~iv~e~   86 (95)
T 2ctj_A           15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             SSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            46789999999999999999999999999999 999999653       234568999999999999999999998763

>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=99.09  E-value=1.8e-10  Score=93.97  Aligned_cols=68  Identities=16%  Similarity=0.271  Sum_probs=60.5

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~-tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      .++.+|.||+.+|++|||++|++|++|+++ ++++|++++          .++.|+|+|+++.|.+|..+|...+++..
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el~   94 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDLI   94 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999997 589999864          23589999999999999999999997743

>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=99.06  E-value=1.1e-10  Score=93.90  Aligned_cols=73  Identities=23%  Similarity=0.301  Sum_probs=64.8

Q ss_pred             CCCccEEEEEEeeCCceeeeecCCChHHHHHHhhc-CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHh
Q 010746          136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTET-RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLH  214 (502)
Q Consensus       136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~  214 (502)
                      +..+.++..|.||.++++.|||++|.+|++|+++| ||+|.|+.+.       +..+.|+|.|+..+|.+|+.+|.+++.
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       345689999999999999999999987


Q ss_pred             c
Q 010746          215 E  215 (502)
Q Consensus       215 ~  215 (502)
                      +
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=99.05  E-value=2.4e-10  Score=93.29  Aligned_cols=65  Identities=20%  Similarity=0.309  Sum_probs=59.4

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhh-cCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTE-TRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ++.+|.||..+|++|||++|++|++|+++ ++++|.|+..          ++.|+|+|+++.|.+|+.+|..++.+
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 5999998642          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=98.84  E-value=1.6e-09  Score=85.46  Aligned_cols=67  Identities=21%  Similarity=0.266  Sum_probs=57.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ..+...|.||.+++|.|||++|++|++|+++|||+ |.|..          ++..|+|.| +.+++++|+.+|...-+.
T Consensus        13 ~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e----------ddG~V~I~g~~~ea~~~A~~~I~~ie~~   81 (91)
T 2cpq_A           13 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             CceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            45788999999999999999999999999999998 99952          236899999 899999998887654433

>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=9.2e-09  Score=81.11  Aligned_cols=65  Identities=23%  Similarity=0.288  Sum_probs=57.1

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCce-EEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHH
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIAS  211 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~  211 (502)
                      ....+...|.||.+.++.|||++|.+|++|+++|||+ |.|..+          +..|+|.| +.+++.+|+.+|..
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            4456789999999999999999999999999999998 999533          46899999 89999999987754

>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=1.1e-07  Score=80.83  Aligned_cols=76  Identities=18%  Similarity=0.332  Sum_probs=61.7

Q ss_pred             eeEEEEEecCC------ceeeeeCCCchhHHHHHHHhCCeEEEecCCCC-----------CCCCCCCceEEEEEc-CHHH
Q 010746          346 VITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PKVAYEDEEMVQITG-SLDV  407 (502)
Q Consensus       346 ~~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~-----------P~~~~~~~r~v~I~G-~~~~  407 (502)
                      .++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+...           +.....++-.|.|++ +.+.
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            47889999988      88999999999999999999999999764210           111123456788999 7899


Q ss_pred             HHHHHHHHHHHHHh
Q 010746          408 ASSALSQVTLRLRA  421 (502)
Q Consensus       408 v~~A~~~I~~~l~~  421 (502)
                      ++.|+.+|..+|..
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=77.96  Aligned_cols=76  Identities=11%  Similarity=0.074  Sum_probs=58.2

Q ss_pred             eeEEEEEecCC-------ceeeeeCCCchhHHHHHHHhCCeEEEecCCC-----CCCCCCCCceEEEEEc-CHHHHHHHH
Q 010746          346 VITTRILVPSA-------QIGCLIGRGGAIISEMRSATRASIRILTNEN-----VPKVAYEDEEMVQITG-SLDVASSAL  412 (502)
Q Consensus       346 ~~~~~i~VP~~-------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~-----~P~~~~~~~r~v~I~G-~~~~v~~A~  412 (502)
                      ..+.+|.||.+       ++|.|||++|.+||+|+++|||+|.|..+..     .......++-.|.|.+ +++++++|+
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       7899999999999999999999999964421     0001112344677776 799999999


Q ss_pred             HHHHHHHHh
Q 010746          413 SQVTLRLRA  421 (502)
Q Consensus       413 ~~I~~~l~~  421 (502)
                      .+|.++|..
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999876

>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=98.47  E-value=2.9e-07  Score=78.33  Aligned_cols=77  Identities=27%  Similarity=0.352  Sum_probs=61.2

Q ss_pred             ccEEEEEEeeCC------ceeeeecCCChHHHHHHhhcCceEEEeecCCCC-----------cccCCCCceEEEec-CHH
Q 010746          139 TLITVRMLVPAD------QIGCVIGKGGQVIQNIRTETRAQIRILKDEHLP-----------LCALSFDELLQVAG-EPA  200 (502)
Q Consensus       139 ~~~~~~llVp~~------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~er~v~I~G-~~~  200 (502)
                      ..++.+|.||.+      .+|.|||++|.+||+|+++|||+|.|.......           ......+-.|.|++ +.+
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      788999999999999999999999997642100           00012355688899 688


Q ss_pred             HHHHHHHHHHHHHhc
Q 010746          201 VVRKALVQIASRLHE  215 (502)
Q Consensus       201 ~V~~A~~~I~~~l~~  215 (502)
                      ++.+|+.+|..+|.+
T Consensus        85 ~~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999976

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.38  E-value=4.9e-07  Score=75.33  Aligned_cols=77  Identities=17%  Similarity=0.129  Sum_probs=58.1

Q ss_pred             ccEEEEEEeeCC-------ceeeeecCCChHHHHHHhhcCceEEEeecCCC---C--cccCCCCceEEEec-CHHHHHHH
Q 010746          139 TLITVRMLVPAD-------QIGCVIGKGGQVIQNIRTETRAQIRILKDEHL---P--LCALSFDELLQVAG-EPAVVRKA  205 (502)
Q Consensus       139 ~~~~~~llVp~~-------~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~---p--~~~~~~er~v~I~G-~~~~V~~A  205 (502)
                      ..++.+|.||-+       .++.|||++|.+||+|+++|||+|.|..+...   +  ......+-.|.|.+ +.+++.+|
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            457888998865       67999999999999999999999999743110   0  00011233577775 69999999


Q ss_pred             HHHHHHHHhc
Q 010746          206 LVQIASRLHE  215 (502)
Q Consensus       206 ~~~I~~~l~~  215 (502)
                      +.+|.++|.+
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=98.13  E-value=1.9e-06  Score=73.57  Aligned_cols=76  Identities=18%  Similarity=0.352  Sum_probs=56.5

Q ss_pred             EEEEEEeeCCc------eeeeecCCChHHHHHHhhcCceEEEeecCCC------------Cccc-CCCCceEEEecC-HH
Q 010746          141 ITVRMLVPADQ------IGCVIGKGGQVIQNIRTETRAQIRILKDEHL------------PLCA-LSFDELLQVAGE-PA  200 (502)
Q Consensus       141 ~~~~llVp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~er~v~I~G~-~~  200 (502)
                      ++.+|.||.+.      +|.|||++|.++|+|+++|||+|.|..+...            |... ...+--|.|++. ++
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      8999999999999999999999999865211            1100 112235778884 32


Q ss_pred             -----HHHHHHHHHHHHHhcC
Q 010746          201 -----VVRKALVQIASRLHEN  216 (502)
Q Consensus       201 -----~V~~A~~~I~~~l~~~  216 (502)
                           .+.+|+.+|..+|...
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                 7899999999988753

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=98.05  E-value=4.1e-06  Score=71.54  Aligned_cols=74  Identities=19%  Similarity=0.303  Sum_probs=54.3

Q ss_pred             eEEEEEecCC------ceeeeeCCCchhHHHHHHHhCCeEEEecCCCC------------CC-CCCCCceEEEEEcC-HH
Q 010746          347 ITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNENV------------PK-VAYEDEEMVQITGS-LD  406 (502)
Q Consensus       347 ~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~------------P~-~~~~~~r~v~I~G~-~~  406 (502)
                      ++.+|.||.+      ++|.|||++|.++|+|+++|||+|.|-.+...            |. ...+++--|.|++. ++
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            4667888854      49999999999999999999999999765311            00 00122236778883 43


Q ss_pred             -----HHHHHHHHHHHHHH
Q 010746          407 -----VASSALSQVTLRLR  420 (502)
Q Consensus       407 -----~v~~A~~~I~~~l~  420 (502)
                           .++.|+.+|..+|.
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                 78899999988885

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=98.03  E-value=3.2e-06  Score=90.32  Aligned_cols=95  Identities=19%  Similarity=0.185  Sum_probs=72.1

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++...+++.+.+.......+.....+....|.||.+.++.|||++|.+||.|+++|||+|.|..         
T Consensus       534 ~aL~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d---------  604 (630)
T 3u1k_A          534 EAIQQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD---------  604 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC---------
Confidence            34556777788887766554433333333445668889999999999999999999999999999999953         


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHH
Q 010746          188 SFDELLQVAGE-PAVVRKALVQIASRL  213 (502)
Q Consensus       188 ~~er~v~I~G~-~~~V~~A~~~I~~~l  213 (502)
                        +-.|.|.+. .+++.+|+.+|..++
T Consensus       605 --~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          605 --EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             --SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             --CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence              347999996 688999998887654

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.83  E-value=3.7e-05  Score=64.19  Aligned_cols=69  Identities=16%  Similarity=0.137  Sum_probs=59.9

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ...+.|...+++.|||++|+.|++|+..|++.|+|..-+      .+....|+|.|++..-..|+.+|.....-+
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            367889999999999999999999999999999997542      245678999999999999999998777554

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=97.62  E-value=2.3e-05  Score=83.75  Aligned_cols=65  Identities=17%  Similarity=0.250  Sum_probs=54.9

Q ss_pred             CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHH
Q 010746          344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRL  419 (502)
Q Consensus       344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l  419 (502)
                      .......|.||.+.++.|||+||++||+|+++|||+|.|..           +..|.|.++ .+++++|+.+|.+.+
T Consensus       564 ~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-----------~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          564 NGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-----------EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             TCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-----------SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             cCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-----------CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            34567899999999999999999999999999999999942           348999995 788999999887654

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.52  E-value=1.1e-05  Score=69.45  Aligned_cols=109  Identities=24%  Similarity=0.310  Sum_probs=74.1

Q ss_pred             CCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHH
Q 010746           40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFR  119 (502)
Q Consensus        40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~  119 (502)
                      +++.-.+.++|+...+|..||++|+.|+.|++++|-+|.|-+-.           .++                .+   .
T Consensus        32 d~~~dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s-----------~d~----------------~~---f   81 (144)
T 2cxc_A           32 DEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYS-----------SDL----------------ER---I   81 (144)
T ss_dssp             EGGGTEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECC-----------SSH----------------HH---H
T ss_pred             eCCCCEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcC-----------CCH----------------HH---H
Confidence            34446788999999999999999999999999999999874321           000                00   0


Q ss_pred             HHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEee
Q 010746          120 VHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILK  178 (502)
Q Consensus       120 i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~  178 (502)
                      +.+.+.......-.-...+....+.+.||..+.+..|||+|++++-..+-||.+|.|..
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            11111000000000000023457889999999999999999999999999999887743

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.50  E-value=4.7e-05  Score=82.22  Aligned_cols=97  Identities=24%  Similarity=0.354  Sum_probs=29.6

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++...|++.+.........+-....+....|.||.+.++.|||++|.+||+|+++|||+|.|..+        
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            345667778888887765443332222233345567899999999999999999999999999999998533        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746          188 SFDELLQVAGE-PAVVRKALVQIASRLHE  215 (502)
Q Consensus       188 ~~er~v~I~G~-~~~V~~A~~~I~~~l~~  215 (502)
                         ..|.|.+. .+++.+|+..|..++.+
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               35777775 88899999999887754

>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A

Probab=97.31  E-value=6.6e-05  Score=64.48  Aligned_cols=104  Identities=22%  Similarity=0.322  Sum_probs=74.0

Q ss_pred             ceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC
Q 010746          262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE  341 (502)
Q Consensus       262 ~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~  341 (502)
                      -.+.+.|+...+|..||++|++|+.|.++.|-+|.+-.-+.+                +..-+..++  .|.-...+...
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d----------------~~~fI~naL--sPA~V~~V~i~   97 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSD----------------LERIVKNLF--PGVKIESINVR   97 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSS----------------HHHHHHHHS--TTSCEEEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCC----------------HHHHHHHhc--CCceEEEEEEe
Confidence            467788999999999999999999999999999888764321                111122222  11111111110


Q ss_pred             CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEe
Q 010746          342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL  383 (502)
Q Consensus       342 ~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~  383 (502)
                      ..+......+.||.++.+..|||+|.+++-..+.||.+|.|.
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            002345678899999999999999999999999999988774

>3v69_A Protein filia; RNA-binding, embryogenesis, KH domain, RNA binding, P binding; 2.20A {Mus musculus}

Probab=97.23  E-value=0.00053  Score=57.27  Aligned_cols=68  Identities=16%  Similarity=0.187  Sum_probs=59.2

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .+.|.|.+..++.|+|++|+.|+.|+..|++.|++..-+.      +..--|+|.|.+..-.+|+.+|..+...
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            5678999999999999999999999999999999986521      2355699999999999999999887754

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=96.85  E-value=0.00034  Score=75.56  Aligned_cols=68  Identities=21%  Similarity=0.311  Sum_probs=12.7

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhch
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ......+.||.+.++.|||+||.+||+|+++||++|.|..           +..|.|.+ +.++++.|+.+|...+.+..
T Consensus       568 ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d-----------dG~v~I~~~~~~~~~~A~~~i~~i~~~~~  636 (726)
T 4aid_A          568 APKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-----------DGVVKVSASDGAKIKAAIDWIKSITDEAE  636 (726)
T ss_dssp             CCC------------------------------------------------------CCSCHHHHHHHHHC---------
T ss_pred             CCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-----------CceEEEEeCCHHHHHHHHHHHHHHhhhhc
Confidence            3456789999999999999999999999999999999842           34677877 58899999999988876643

>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=95.62  E-value=0.0093  Score=55.67  Aligned_cols=97  Identities=23%  Similarity=0.227  Sum_probs=63.4

Q ss_pred             CceeeeecCChhHHHHH-HHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQL-RSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I-~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|++|+.| ++-.|=+|.|-.-.              ++             ..   ..+...+.......
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s--------------~d-------------p~---~fi~nalsPA~V~~  175 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD--------------DD-------------PA---RFVANALSPAKVVS  175 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC--------------SS-------------HH---HHHHHHTTTSCCSE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEec--------------CC-------------HH---HHHHhccCCcceEE
Confidence            46899999999999999 55567788763221              00             00   11111111100000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (502)
                      -.- .....-.+.+.||..+.+..|||+|++++.-..-||.+|.|....
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 000113688999999999999999999999999999999998763

>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=95.57  E-value=0.0094  Score=55.65  Aligned_cols=97  Identities=22%  Similarity=0.306  Sum_probs=65.8

Q ss_pred             CccccccccCcccccch-hhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccc-cCCCCceeE
Q 010746          271 GNIGGVIGKGGGIIKQI-RQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE-RESGDPVIT  348 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i-~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~  348 (502)
                      +-+|..||++|++|+.| ++-.|-+|.+-.-+.+                +..-+..+  +.+.-...+. .+.  ....
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d----------------p~~fi~na--lsPA~V~~V~i~~~--~~~~  185 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD----------------PARFVANA--LSPAKVVSVSVIDQ--TARA  185 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS----------------HHHHHHHH--TTTSCCSEEEEEET--TTTE
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC----------------HHHHHHhc--cCCcceEEEEEEcC--CCcE
Confidence            45799999999999999 6666777777653321                11112222  2121111111 011  1246


Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCC
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN  387 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~  387 (502)
                      ..+.||.++.+.-|||+|.+|+--.+.||.+|.|....+
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=95.55  E-value=0.0048  Score=60.95  Aligned_cols=97  Identities=25%  Similarity=0.241  Sum_probs=65.1

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||++|++|+.|.++. |=+|.|-+-.              ++             ..   ..+...+.......
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s--------------~d-------------p~---~fi~nalsPA~V~~  298 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYD--------------DD-------------PA---RFVANALSPAKVVS  298 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECC--------------SS-------------HH---HHHHHHTTTSCCSE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcC--------------CC-------------HH---HHHHHhcCCcceeE
Confidence            568999999999999999999 8788764321              00             00   11111111100000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE  180 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~  180 (502)
                      -.. .....-.+.+.||..+.+..|||+|++++-...-||.+|.|..+.
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 001123688999999999999999999999999999999998773

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.31  E-value=0.0041  Score=67.51  Aligned_cols=96  Identities=22%  Similarity=0.287  Sum_probs=13.2

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++...+++.+.........+-....+....+.||.+.++.+||++|.+|+.|.++||+.|.|..+        
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            345557777777777665433222222223345567789999999999999999999999999999988533        


Q ss_pred             CCCceEEEecC-HHHHHHHHHHHHHHHh
Q 010746          188 SFDELLQVAGE-PAVVRKALVQIASRLH  214 (502)
Q Consensus       188 ~~er~v~I~G~-~~~V~~A~~~I~~~l~  214 (502)
                         ..|.|.+. .+.+.+|...|..++.
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               35666664 5667778777766553

>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=95.23  E-value=0.012  Score=58.03  Aligned_cols=96  Identities=22%  Similarity=0.302  Sum_probs=66.4

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCcccccc-ccCCCCceeE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT-ERESGDPVIT  348 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~  348 (502)
                      +-+|..||++|.+|+.|.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+ ..+.  ....
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d----------------p~~fi~na--lsPA~V~~V~~~~~--~~~~  308 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD----------------PARFVANA--LSPAKVVSVSVIDQ--TARA  308 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS----------------HHHHHHHH--TTTSCCSEEEEEET--TTTE
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--cCCcceeEEEEEcC--CCcE
Confidence            457999999999999999998 777777653311                11112222  212111111 0011  1346


Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCC
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNE  386 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~  386 (502)
                      ..+.||.++.+..|||+|.+++-..+.||.+|.|....
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            78999999999999999999999999999999997654

>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=94.94  E-value=0.0022  Score=69.82  Aligned_cols=94  Identities=24%  Similarity=0.335  Sum_probs=37.1

Q ss_pred             cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746          108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL  187 (502)
Q Consensus       108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~  187 (502)
                      +.+..|.++...|++.+....... .+.....+....|.||.+.++.+||++|.+|+.|+++||+.|.|..+        
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            445667777777777665433222 22222334445688999999999999999999999999999988533        


Q ss_pred             CCCceEEEec-CHHHHHHHHHHHHHHH
Q 010746          188 SFDELLQVAG-EPAVVRKALVQIASRL  213 (502)
Q Consensus       188 ~~er~v~I~G-~~~~V~~A~~~I~~~l  213 (502)
                         ..|.|+. +.+...+|...|..+.
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               3466665 3566667766665543

>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=93.72  E-value=0.04  Score=54.14  Aligned_cols=96  Identities=23%  Similarity=0.315  Sum_probs=63.5

Q ss_pred             CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746           53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA  131 (502)
Q Consensus        53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~  131 (502)
                      +-+|..||.+|+.|+.|.++. |-+|.|-.-            .  ++             ..   ..+...+.......
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~------------s--~d-------------~~---~fi~nal~Pa~v~~  294 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKW------------S--DD-------------PK---QLIANALAPATVIE  294 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEEC------------C--SS-------------HH---HHHHHHTCSSCCSE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEec------------C--CC-------------HH---HHHHHhcCccEEEE
Confidence            468999999999999999998 667765321            1  00             00   11111110000000


Q ss_pred             CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      -. -..+..-.+.+.||..+.+..|||+|++++.-..-||.+|.|..+
T Consensus       295 v~-~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          295 VE-ILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EE-EEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EE-EEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            00 000112368899999999999999999999999999999999765

>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=93.48  E-value=0.078  Score=52.11  Aligned_cols=96  Identities=30%  Similarity=0.389  Sum_probs=64.5

Q ss_pred             CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746          271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT  349 (502)
Q Consensus       271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  349 (502)
                      +-+|+.||.+|.+|+.+.++. |-+|.+-.-+.+                +..-+..+  +.+.-...+... .......
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~d----------------~~~fi~na--l~Pa~v~~v~~~-d~~~~~~  305 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDD----------------PKQLIANA--LAPATVIEVEIL-DKENKAA  305 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSS----------------HHHHHHHH--TCSSCCSEEEEE-ETTTTEE
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCCC----------------HHHHHHHh--cCccEEEEEEEE-cCCCCEE
Confidence            357999999999999999888 566666542211                11112222  212111111110 0113467


Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN  385 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  385 (502)
                      .+.||.++.+.-|||+|.+++--.+.||.+|.|...
T Consensus       306 ~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          306 RVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             EEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             EEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence            899999999999999999999999999999999653

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=93.13  E-value=0.016  Score=62.77  Aligned_cols=66  Identities=21%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~  421 (502)
                      ......+.||.+.++.|||++|.+|+.|.++||+.|.|..           +..|.|.+ ..+.++.|..+|...+.+
T Consensus       558 ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~-----------dg~v~I~~~~~~~~~~a~~~i~~i~~~  624 (723)
T 3cdi_A          558 APRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED-----------DGTVKIAATDGEKAKHAIRRIEEITAE  624 (723)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             CceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC-----------CccEEEecCCHHHHHHHHHHHHHHhhh
Confidence            3456788999999999999999999999999999998842           34666766 456777787777666544

>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=90.11  E-value=0.016  Score=63.19  Aligned_cols=63  Identities=21%  Similarity=0.252  Sum_probs=21.9

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHH
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRL  419 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l  419 (502)
                      .....|.||.+.++.|||++|.+||+|++.||+.|.|..           +..|.|.. ..+..+.|+.+|....
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            445678899999999999999999999999999999842           34677777 4566677766665544

---

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	502
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	7e-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	8e-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	9e-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,	9e-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,	2e-09
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	4e-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	3e-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	6e-13
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	4e-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	6e-12
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-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,	7e-06
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	2e-10
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	6e-07
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	8e-07
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	3e-10
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	6e-08
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	1e-07
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	6e-10
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-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	6e-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/	1e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	1e-07
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	2e-06
d2ctja1	82	d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [T	3e-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	4e-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	4e-06
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-04
d1tuaa1	84	d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Ae	5e-04
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	3e-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	9e-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	3e-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
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 = 68.6 bits (168), 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 = 61.3 bits (149), Expect = 7e-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 = 52.1 bits (125), 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 = 65.4 bits (159), Expect = 8e-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 = 9e-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 = 42.7 bits (100), 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 = 64.1 bits (156), Expect = 9e-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 = 2e-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 = 45.2 bits (107), Expect = 4e-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 = 57.1 bits (138), Expect = 3e-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 = 51.7 bits (124), 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 = 6e-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 = 56.4 bits (136), Expect = 4e-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 = 48.7 bits (116), 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 = 6e-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 = 2e-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 = 7e-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 = 2e-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 = 4e-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 = 45.2 bits (107), Expect = 6e-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 = 8e-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 = 54.3 bits (131), Expect = 3e-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 = 6e-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 = 47.0 bits (112), Expect = 1e-07
 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 = 53.7 bits (129), Expect = 6e-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 = 49.5 bits (118), Expect = 2e-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 = 47.5 bits (113), 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 = 52.9 bits (127), 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 = 47.6 bits (113), Expect = 6e-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 = 48.1 bits (115), 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 = 46.2 bits (110), Expect = 1e-07
 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 = 46.2 bits (110), Expect = 1e-07
 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 = 42.7 bits (101), Expect = 2e-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 = 48.7 bits (116), Expect = 3e-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 = 41.4 bits (97), 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 = 43.6 bits (103), 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 = 4e-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 = 42.9 bits (101), 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 = 4e-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 = 5e-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 = 36.7 bits (85), Expect = 5e-04
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 5/49 (10%)

Query: 51 PLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99
             ++G++IG  GE+  ++   T + I +       +  +V +   +EG
Sbjct: 10 KPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEG 53

>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 = 3e-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 = 39.0 bits (91), Expect = 8e-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 = 39.0 bits (91), Expect = 9e-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 = 3e-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 = 35.2 bits (81), 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 = 34.9 bits (80), 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

>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	502
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.59
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.58
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.58
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.58
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.57
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.55
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.55
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.55
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.52
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.51
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.51
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.5
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.5
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.47
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.43
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.42
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.41
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.39
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.24
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.23
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.22
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.16
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.1
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.09
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.81
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.8
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.76
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.7
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.69
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.61
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.61
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.56
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.47
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.39
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	98.12
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.92
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.55
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.53
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.92
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.66
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.49
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.26
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	82.82
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	80.87

>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=99.59  E-value=1.2e-15  Score=116.38  Aligned_cols=72  Identities=28%  Similarity=0.467  Sum_probs=65.4

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      .+|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..     ..+++++|+|+|++++|+.|+.+|.++|+++
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            57889999999999999999999999999999999996432     2467899999999999999999999999875

>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=99.58  E-value=7e-16  Score=116.17  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=63.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ..++.+|+||.+++|+|||++|++|++|++.|||+|++++.       ...+|+|+|+|++++|..|+.+|.++|++
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            35789999999999999999999999999999999999653       24579999999999999999999999975

>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=99.58  E-value=1.3e-15  Score=114.79  Aligned_cols=70  Identities=23%  Similarity=0.414  Sum_probs=61.6

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      +.+|.||.+++|+||||+|++|++|++.|||+|+|++... + ...+++|.|+|+|++++|+.|+.+|.++|
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            4689999999999999999999999999999999976532 2 23567899999999999999999999874

>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=99.58  E-value=1e-15  Score=114.87  Aligned_cols=68  Identities=37%  Similarity=0.507  Sum_probs=61.7

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      .|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..     .+.++|.|+|+|++++|+.|+.+|.++|
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            5789999999999999999999999999999999996532     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=1.7e-15  Score=115.02  Aligned_cols=70  Identities=26%  Similarity=0.396  Sum_probs=62.4

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL  419 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l  419 (502)
                      +.+|.||.+++|+|||++|++|++|+++|||+|+|.+.++..  ..+++|.|+|+|++++|+.|+.+|.++|
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 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999999997754432  2467899999999999999999999875

>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=1.6e-15  Score=117.28  Aligned_cols=74  Identities=19%  Similarity=0.341  Sum_probs=66.6

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      ..++.+|.||.+++|+|||++|++|++|+++|||+|+|.+.+..+   .+.+|.|+|+|++++|..|+.+|.++|++
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            468999999999999999999999999999999999997654333   46789999999999999999999999865

>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=99.55  E-value=2e-15  Score=114.76  Aligned_cols=70  Identities=27%  Similarity=0.435  Sum_probs=63.8

Q ss_pred             eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      .+.+|.||.+++|+|||++|++|++|+++|||+|+|.+.+.     ...++.|+|+|++++|+.|+.+|.++|++
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            57899999999999999999999999999999999976532     45789999999999999999999999976

>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=99.55  E-value=1.6e-15  Score=114.12  Aligned_cols=70  Identities=29%  Similarity=0.553  Sum_probs=64.1

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|++.       ...+|+|+|+|++++|.+|+.+|.++|+|
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            35799999999999999999999999999999999999765       14589999999999999999999999875

>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=99.52  E-value=3.8e-15  Score=115.21  Aligned_cols=75  Identities=23%  Similarity=0.448  Sum_probs=67.9

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ...++.+|+||.+++++||||+|++|++|+++|||+|.|.+++..+   .+.+|+|+|+|++++|.+|+.+|.++|.+
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=99.51  E-value=9.9e-15  Score=110.73  Aligned_cols=70  Identities=29%  Similarity=0.473  Sum_probs=62.5

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      +++|+||.+++|+||||+|++|++|+++|||+|+|.++++...  .+.+|+|+|+|++++|.+|+.+|.++|
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            6899999999999999999999999999999999988643222  367899999999999999999998875

>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=8.3e-15  Score=110.21  Aligned_cols=70  Identities=27%  Similarity=0.513  Sum_probs=61.6

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      +++|+||.+.+|+||||+|++|++|+++|||+|+|.++.. + +..+.+|+|+|+|++++|.+|+.+|.++|
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

>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=99.51  E-value=1.1e-14  Score=111.97  Aligned_cols=73  Identities=26%  Similarity=0.397  Sum_probs=66.1

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|.|++.+     .+++++.|+|+|++++|+.|+.+|.+.|++.
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     2467899999999999999999999999874

>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=99.50  E-value=7.9e-15  Score=109.92  Aligned_cols=68  Identities=32%  Similarity=0.491  Sum_probs=61.6

Q ss_pred             EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746          141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL  213 (502)
Q Consensus       141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l  213 (502)
                      .|.+|+||.+++|+||||+|.+|++|+++|||+|.|.+..  +   .+.+|+|+|+|++++|.+|+.+|.++|
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--E---GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC--T---TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCC--C---CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            5889999999999999999999999999999999997652  2   356899999999999999999998876

>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=99.50  E-value=2.2e-14  Score=116.33  Aligned_cols=78  Identities=19%  Similarity=0.331  Sum_probs=68.1

Q ss_pred             CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ....++.+|.||..++|+|||++|.+|++|+++|||+|.|++.....   ...+|.|+|+|++++|..|+.+|.++|++.
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 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT---LLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCS---SSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCC---CCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            34568899999999999999999999999999999999997653322   356899999999999999999999999774


Q ss_pred             h
Q 010746          423 T  423 (502)
Q Consensus       423 ~  423 (502)
                      .
T Consensus        88 ~   88 (104)
T d1we8a_          88 E   88 (104)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=1.9e-14  Score=109.54  Aligned_cols=71  Identities=31%  Similarity=0.518  Sum_probs=64.6

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .+|.+|+||.+++|+||||+|++|++|+++|||+|+|....  +   .+.+|+|+|+|++++|.+|+.+|.++|++
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

>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=109.43  Aligned_cols=71  Identities=23%  Similarity=0.426  Sum_probs=64.2

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..+++|+||.+++|+||||+|++|++|+++|||+|+|...+.     .+.+|+|+|+|++++|.+|..+|.++|.+
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=99.47  E-value=3.7e-14  Score=109.48  Aligned_cols=73  Identities=15%  Similarity=0.218  Sum_probs=64.5

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ..++..+.||..++++|||++|++|++|+++|||+|++++.++      .+.+.|+|+|++++|+.|+.+|+++++++.
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 QMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999999999999976432      234689999999999999999999998764

>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=99.44  E-value=6.2e-14  Score=107.76  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=66.7

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ...++.+|+||.+++|+|||++|.+|++|+++|||+|.|.+.+  +   .+.+++|+|+|++++|.+|+.+|.++|.++
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            4568999999999999999999999999999999999997652  2   356899999999999999999999999874

>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=9e-14  Score=112.68  Aligned_cols=78  Identities=27%  Similarity=0.422  Sum_probs=68.4

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      ....++.+|+||..++++||||+|.+|++|+++|||+|.|.+.+..   ....+|+|+|+|++++|.+|+.+|.++|.+.
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            4557889999999999999999999999999999999999776322   2356899999999999999999999999875


Q ss_pred             C
Q 010746          217 P  217 (502)
Q Consensus       217 ~  217 (502)
                      .
T Consensus        88 ~   88 (104)
T d1we8a_          88 E   88 (104)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.42  E-value=8.7e-14  Score=107.31  Aligned_cols=71  Identities=18%  Similarity=0.299  Sum_probs=64.1

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||..++|+|||++|++|++|+++|||+|.+++.       ++.++.|+|+|++++|+.|+.+|++++++.
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            45789999999999999999999999999999999999654       345678999999999999999999998874

>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=99.41  E-value=1.8e-13  Score=106.38  Aligned_cols=73  Identities=18%  Similarity=0.253  Sum_probs=64.7

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      .++.+|.||..++++|||++|++|++|+++|||+|++++... +   ...++.|+|+|++++|..|+.+|.+.+++.
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~~~-~---~~~~~~i~I~G~~e~v~~A~~~I~~~i~e~   81 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD-G---NQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC-C---CCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999999999999999975432 2   456789999999999999999999998773

>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=99.39  E-value=1.9e-13  Score=102.53  Aligned_cols=66  Identities=21%  Similarity=0.286  Sum_probs=59.5

Q ss_pred             eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 010746          346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLR  418 (502)
Q Consensus       346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~  418 (502)
                      ..+.+|.||.+++++|||++|++|++|+++|||+|++++.       .++++.|+|+|++++|+.|+.+|+++
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            4678899999999999999999999999999999999653       34567999999999999999999875

>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=99.37  E-value=2e-13  Score=106.17  Aligned_cols=73  Identities=19%  Similarity=0.219  Sum_probs=64.9

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..++++|.||..++++|||++|++|++|+++|||+|+|++.+. +   ...++.|+|+|+.++|.+|..+|.+++.+
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            3468899999999999999999999999999999999976522 2   36688999999999999999999999876

>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=99.37  E-value=2.7e-13  Score=104.88  Aligned_cols=71  Identities=17%  Similarity=0.221  Sum_probs=62.7

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~-tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++.+|.||..+||+|||++|++|++|+++ ++|+|++++.       ++.++.|+|+|++++|+.|+.+|++++++.
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            4578999999999999999999999999987 5899988643       345679999999999999999999999874

>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=4.5e-13  Score=103.25  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=64.3

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ....++..+.||..++++|||++|++|++|+++|||+|+|++.+.      ..++.|+|+|++++|.+|+.+|.+++++
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            345678899999999999999999999999999999999976521      2356899999999999999999999876

>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=99.33  E-value=5.3e-13  Score=102.82  Aligned_cols=72  Identities=21%  Similarity=0.327  Sum_probs=64.9

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ....++.+|.||..++++|||++|.+|++|+++|||+|.|++.+       +.++.|+|+|++++|.+|..+|.+++.+
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=99.33  E-value=6e-13  Score=104.97  Aligned_cols=71  Identities=20%  Similarity=0.225  Sum_probs=63.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++..|.||.++|++|||++|++|++|+++|||+|.+++.       ++.+..|+|+|++++|+.|+.+|.+++++.
T Consensus         8 ~~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~V~~A~~~I~~~v~e~   78 (91)
T d2ctka1           8 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP-------ELQSDIIAITGLAANLDRAKAGLLERVKEL   78 (91)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT-------TTTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECCC-------CCCcceEEEECCHHHHHHHHHHHHHHHHHH
Confidence            35899999999999999999999999999999999999654       345568999999999999999999998763

>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=99.29  E-value=1.3e-12  Score=97.92  Aligned_cols=66  Identities=23%  Similarity=0.370  Sum_probs=59.7

Q ss_pred             cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHH
Q 010746          140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASR  212 (502)
Q Consensus       140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~  212 (502)
                      ..+++|.||.+++++|||++|++|++|+++|||+|+|+++.       +.++.|+|+|++++|.+|+.+|.++
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       4568899999999999999999875

>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=9.4e-13  Score=101.73  Aligned_cols=73  Identities=23%  Similarity=0.302  Sum_probs=64.1

Q ss_pred             CCccEEEEEEeeCCceeeeecCCChHHHHHHhh-cCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE-TRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~-tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..+.++.+|.||..+|++||||+|++|++|+++ ++|+|.++..+       +.++.|+|+|++++|.+|+.+|.+++.+
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 59999986552       4578999999999999999999999987


Q ss_pred             C
Q 010746          216 N  216 (502)
Q Consensus       216 ~  216 (502)
                      .
T Consensus        79 ~   79 (82)
T d2ctja1          79 K   79 (82)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.25  E-value=2.3e-12  Score=101.49  Aligned_cols=70  Identities=24%  Similarity=0.369  Sum_probs=63.8

Q ss_pred             ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ..++..|.||.++|++|||++|.+|++|+++|||+|.|++.+       +.++.|+|+|++++|.+|+.+|.+++.+
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            468999999999999999999999999999999999997652       4567899999999999999999998876

>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=99.24  E-value=3.5e-12  Score=98.13  Aligned_cols=64  Identities=17%  Similarity=0.254  Sum_probs=57.7

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhch
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANT  423 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~  423 (502)
                      ..+.||.+.+|.|||++|++|++|+++|||+|+|.+           +..|+|+|++++|+.|+.+|...+++..
T Consensus         3 ~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea~   66 (84)
T d2ba0a3           3 RIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEAH   66 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCSC
T ss_pred             EEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhcc
Confidence            568999999999999999999999999999999942           2479999999999999999998887743

>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=99.23  E-value=1.1e-11  Score=96.98  Aligned_cols=68  Identities=16%  Similarity=0.277  Sum_probs=60.8

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHH-hCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSA-TRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~-tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..++..|.||..+|++|||++|++|++|+++ ++++|.+++.          ...|+|+|++++|+.|+.+|.+++++.
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 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG----------EDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECSS----------SCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCCC----------CceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999 4899998532          347999999999999999999999874

>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=99.22  E-value=2.3e-12  Score=97.77  Aligned_cols=64  Identities=22%  Similarity=0.295  Sum_probs=56.6

Q ss_pred             ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHH
Q 010746          345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTL  417 (502)
Q Consensus       345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~  417 (502)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|.+...         +++.|+|.| ++++|+.|+.||..
T Consensus         6 ~~~t~~i~Ip~~~ig~vIG~gG~~I~~I~~~tGa~i~i~~~---------~~g~v~I~g~~~eav~~A~~~Ie~   70 (78)
T d2cpqa1           6 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE---------DTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET---------TTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEecC---------CCceEEEEECCHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999988642         346899999 79999999999853

>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=99.16  E-value=2.6e-11  Score=94.88  Aligned_cols=68  Identities=19%  Similarity=0.295  Sum_probs=61.4

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhc-CceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTET-RAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      ...++..+.||..+|++|||++|++|++|++++ +|+|.|..+          +..|+|+|++++|++|+.+|.+++.+
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            456899999999999999999999999999995 899999644          45799999999999999999999876

>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=99.10  E-value=3.1e-11  Score=92.72  Aligned_cols=62  Identities=26%  Similarity=0.293  Sum_probs=56.6

Q ss_pred             EEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN  216 (502)
Q Consensus       144 ~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~  216 (502)
                      -+.||.+.++.|||++|++|++|+++|||+|.|.+           +..|+|+|++++|.+|+.+|..++.+.
T Consensus         4 vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~-----------~g~v~I~G~~e~v~~A~~~I~~i~~ea   65 (84)
T d2ba0a3           4 IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ-----------NGLIWVNGDRRKVSIAEEAIYLIEQEA   65 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECT-----------TSEEEEESCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECC-----------CCEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            47899999999999999999999999999999953           347999999999999999999988774

>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=99.09  E-value=4.2e-11  Score=90.71  Aligned_cols=64  Identities=22%  Similarity=0.257  Sum_probs=56.9

Q ss_pred             CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHH
Q 010746          138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIA  210 (502)
Q Consensus       138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~  210 (502)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.+..+         .++.|+|.| ++++|++|+.+|.
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            456789999999999999999999999999999999988655         246799999 6999999998884

>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=98.81  E-value=2.4e-09  Score=81.67  Aligned_cols=63  Identities=21%  Similarity=0.189  Sum_probs=51.8

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEE-----cCHHHHHHHHHHHHHHHHh
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQIT-----GSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~-----G~~~~v~~A~~~I~~~l~~  421 (502)
                      ..+.||.+.+|.|||++|++|++|+++|||+|+|..++          ..|.+.     |.+.++..|..+|.+..+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~----------g~v~i~~~~~~~~~~a~~~a~~iI~aI~rG   72 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTEN----------SMVIVEPEAEGIPPVNLMKAAEVVKAISLG   72 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTT----------TEEEEEESSTTSCHHHHHHHHHHHHHHHHT
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCC----------CeEEEecCCccccHHHHHHHHHHHHHHhCC
Confidence            35899999999999999999999999999999996432          245554     5688889998888877654

>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=98.80  E-value=6.6e-11  Score=87.36  Aligned_cols=61  Identities=11%  Similarity=0.086  Sum_probs=46.7

Q ss_pred             EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHHh
Q 010746          350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRA  421 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~  421 (502)
                      .+.||.+.+|.|||++|++|+.|+++|||+|.|.+           +..|+|.|. ++.++.|..+|....++
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 77999999998766554

>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=98.76  E-value=5.3e-09  Score=79.92  Aligned_cols=63  Identities=14%  Similarity=0.242  Sum_probs=55.2

Q ss_pred             EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHhc
Q 010746          349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRAN  422 (502)
Q Consensus       349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~  422 (502)
                      ..+.||.+.++.|||++|++|+.|+++|||+|.|..+           ..|.|.| +.+.+..|+.+|....++.
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 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARN-----------GRIHLECPNEDLEAIAVMAIKIIDEEA   66 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETT-----------TEEEEECSCHHHHHHHHHHHHHHHHCS
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCC-----------cEEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999532           3799999 5889999999998887664

>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=98.70  E-value=2.7e-10  Score=84.01  Aligned_cols=61  Identities=11%  Similarity=0.098  Sum_probs=46.5

Q ss_pred             EEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (502)
Q Consensus       144 ~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~  215 (502)
                      .+.||.+.++.||||+|++|++|+++|||+|.|.++           ..|+|.|. .+++.+|..+|..+.++
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            378999999999999999999999999999999533           36999995 67899999999775554

>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=98.69  E-value=6.9e-09  Score=79.10  Aligned_cols=48  Identities=19%  Similarity=0.355  Sum_probs=41.0

Q ss_pred             EEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010746           46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (502)
Q Consensus        46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (502)
                      +.+.||.+++|.||||+|++|++|+++|||+|+|++.     +..+.+.+..+
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     35677777543

>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=98.61  E-value=2.1e-08  Score=76.48  Aligned_cols=61  Identities=13%  Similarity=0.209  Sum_probs=54.1

Q ss_pred             EEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746          144 RMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE  215 (502)
Q Consensus       144 ~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~  215 (502)
                      -+.||.+.++.|||++|++|+.|+++|||+|.|..+           -.|.|.|. .+.+..|+.+|..+..+
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           36999995 88899999999887766

>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=98.61  E-value=1.4e-09  Score=75.32  Aligned_cols=48  Identities=23%  Similarity=0.475  Sum_probs=16.0

Q ss_pred             EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010746           45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE   98 (502)
Q Consensus        45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e   98 (502)
                      ..+|.||.+++|.|||++|++||+|+++|||+|.|.+      +..|+|+|..+
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            4578999999999999999999999999999999974      46799988644

>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=98.56  E-value=1.7e-09  Score=74.79  Aligned_cols=46  Identities=26%  Similarity=0.445  Sum_probs=14.2

Q ss_pred             EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC
Q 010746          348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS  404 (502)
Q Consensus       348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~  404 (502)
                      ..+|.||.+++|.|||++|++||+|+++|||+|.|.           ++..|+|.|.
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           2356777764

>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=98.47  E-value=4.3e-08  Score=77.35  Aligned_cols=53  Identities=23%  Similarity=0.284  Sum_probs=47.4

Q ss_pred             ceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746          357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA  421 (502)
Q Consensus       357 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~  421 (502)
                      +.|.|||++|.+|+.|++.|||+|.|..            ..|.|.|++++++.|+.+|..++..
T Consensus        23 ~~GrIIG~gGktik~Ie~~Tg~~I~I~d------------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          23 IKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             HhcceeCCCcHHHHHHHHHHCCeEEEeC------------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            4789999999999999999999999942            2578899999999999999999865

>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=98.39  E-value=7.7e-08  Score=75.88  Aligned_cols=52  Identities=21%  Similarity=0.240  Sum_probs=46.7

Q ss_pred             eeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746          152 IGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE  215 (502)
Q Consensus       152 vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~  215 (502)
                      .|+|||++|.+|+.|++.|||.|.|..+            .|.|.|.++++..|+.+|..++.+
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            5899999999999999999999999432            478889999999999999999965

>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=4.5e-06  Score=67.77  Aligned_cols=75  Identities=17%  Similarity=0.343  Sum_probs=57.6

Q ss_pred             eEEEEEecCC------ceeeeeCCCchhHHHHHHHhCCeEEEecCCC----------CCCCC-CCCceEEEEEc-CHHHH
Q 010746          347 ITTRILVPSA------QIGCLIGRGGAIISEMRSATRASIRILTNEN----------VPKVA-YEDEEMVQITG-SLDVA  408 (502)
Q Consensus       347 ~~~~i~VP~~------~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~----------~P~~~-~~~~r~v~I~G-~~~~v  408 (502)
                      ++..|.||-+      ++|.|||.+|+++|+|+++|||+|.|-.+..          .+... .+..=-|.|++ +++.+
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            5778889876      4899999999999999999999999976432          01000 12233577888 67899


Q ss_pred             HHHHHHHHHHHHh
Q 010746          409 SSALSQVTLRLRA  421 (502)
Q Consensus       409 ~~A~~~I~~~l~~  421 (502)
                      ..|+.+|..+|..
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=97.92  E-value=1.8e-05  Score=64.13  Aligned_cols=76  Identities=25%  Similarity=0.331  Sum_probs=57.2

Q ss_pred             cEEEEEEeeCCc------eeeeecCCChHHHHHHhhcCceEEEeecCC----------CCcccCC-CCceEEEec-CHHH
Q 010746          140 LITVRMLVPADQ------IGCVIGKGGQVIQNIRTETRAQIRILKDEH----------LPLCALS-FDELLQVAG-EPAV  201 (502)
Q Consensus       140 ~~~~~llVp~~~------vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~~~~~-~er~v~I~G-~~~~  201 (502)
                      .++.+++||-+.      +|.|||.+|.++|.|+++|||+|.|--...          .+..... .+--|.|++ +.+.
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      899999999999999999999999975321          0111111 122466777 4778


Q ss_pred             HHHHHHHHHHHHhc
Q 010746          202 VRKALVQIASRLHE  215 (502)
Q Consensus       202 V~~A~~~I~~~l~~  215 (502)
                      +.+|+.+|..+|..
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=97.55  E-value=4.2e-05  Score=62.63  Aligned_cols=76  Identities=18%  Similarity=0.332  Sum_probs=55.4

Q ss_pred             EEEEEEeeC------CceeeeecCCChHHHHHHhhcCceEEEeecCCC------------Cccc-CCCCceEEEecCH--
Q 010746          141 ITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL------------PLCA-LSFDELLQVAGEP--  199 (502)
Q Consensus       141 ~~~~llVp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~er~v~I~G~~--  199 (502)
                      ++-+|+||.      +.+|.|||.+|.++|.|+++|||+|.|--....            |... ...+--|.|++..  
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            467888884      468999999999999999999999999764221            0000 1233447787752  


Q ss_pred             ----HHHHHHHHHHHHHHhcC
Q 010746          200 ----AVVRKALVQIASRLHEN  216 (502)
Q Consensus       200 ----~~V~~A~~~I~~~l~~~  216 (502)
                          ..+.+|+.+|..+|...
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                35888999999988653

>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=97.53  E-value=6.4e-05  Score=61.49  Aligned_cols=74  Identities=18%  Similarity=0.239  Sum_probs=52.7

Q ss_pred             eEEEEEecC------CceeeeeCCCchhHHHHHHHhCCeEEEecCCCC--------CC-----CCCCCceEEEEEcCH--
Q 010746          347 ITTRILVPS------AQIGCLIGRGGAIISEMRSATRASIRILTNENV--------PK-----VAYEDEEMVQITGSL--  405 (502)
Q Consensus       347 ~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~--------P~-----~~~~~~r~v~I~G~~--  405 (502)
                      ++.+|.||.      +++|.|||.+|.++|+|+++|||+|.|-.+...        ..     ...+++=-|.|++..  
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            456777874      578999999999999999999999999876421        00     001233357777742  


Q ss_pred             ----HHHHHHHHHHHHHHH
Q 010746          406 ----DVASSALSQVTLRLR  420 (502)
Q Consensus       406 ----~~v~~A~~~I~~~l~  420 (502)
                          ..+..|+.+|...|.
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

>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=94.92  E-value=0.0059  Score=43.09  Aligned_cols=41  Identities=22%  Similarity=0.206  Sum_probs=36.6

Q ss_pred             CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746           41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (502)
Q Consensus        41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~   81 (502)
                      .+.-.+.+.||.+..+..|||+|.|++-..+-||.+|.|-.
T Consensus        23 e~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~   63 (67)
T d2asba3          23 QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRG   63 (67)
T ss_dssp             TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEe
Confidence            34457889999999999999999999999999999999854

>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=94.66  E-value=0.0082  Score=42.48  Aligned_cols=40  Identities=30%  Similarity=0.394  Sum_probs=35.9

Q ss_pred             CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746           42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE   81 (502)
Q Consensus        42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~   81 (502)
                      +.-.+.+.||.+..+..|||+|.+++-..+-||.+|.|..
T Consensus        25 ~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          25 ENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CCCEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            3446889999999999999999999999999999999864

>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=94.49  E-value=0.011  Score=41.73  Aligned_cols=38  Identities=37%  Similarity=0.427  Sum_probs=35.6

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      .+.+.||.++.+..|||+|++++-..+-||.+|.|...
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            57789999999999999999999999999999999765

>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=94.26  E-value=0.01  Score=41.83  Aligned_cols=38  Identities=34%  Similarity=0.364  Sum_probs=36.0

Q ss_pred             EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746          142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD  179 (502)
Q Consensus       142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~  179 (502)
                      .+.+.||.++.+..|||+|.+++-..+-||.+|.|..+
T Consensus        27 ~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~e   64 (67)
T d2asba3          27 AARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD   64 (67)
T ss_dssp             EEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             EEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeC
Confidence            67789999999999999999999999999999999876

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

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: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=82.82  E-value=0.63  Score=33.93  Aligned_cols=55  Identities=13%  Similarity=0.062  Sum_probs=42.6

Q ss_pred             EEEecCCceeeeeCCCch-hHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 010746          350 RILVPSAQIGCLIGRGGA-IISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQV  415 (502)
Q Consensus       350 ~i~VP~~~vg~IIGk~G~-~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I  415 (502)
                      .+.||..++..+||++++ .++.|.+.+++.|.|-..           ..|-|.|. ++....+...|
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~N-----------GrIWi~~~~~~~~i~i~~aI   60 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLN-----------GKIWVKCEELSNTLACYRTI   60 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETT-----------TEEEEECSSHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecC-----------cEEEEECCCHHHHHHHHHHH
Confidence            467899999999999998 899999999999999432           36889994 55444443333

>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=80.87  E-value=0.22  Score=37.03  Aligned_cols=36  Identities=11%  Similarity=0.269  Sum_probs=29.1

Q ss_pred             eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEe
Q 010746           44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI   79 (502)
Q Consensus        44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i   79 (502)
                      ..+++.|....-|.|||++|+.|++|+++..-++.+
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            346788889999999999999999998876544433