Citrus Sinensis ID: 007844

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------
Protein Sequence
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEcccccccccEEEEEEccccccHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEcccEEEEEcccccHHHHHHHHcccEEEEccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEcccccHHHHHHHHccccEEEcccccccccEEEEEEEcccccccccHHHHHHHHHHHHHccccccccccccccccccEEEEEEEccccEEEEEccccccHHHHHHHHccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEcccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEcccEEEEEcccccEHHHHHHHcccEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEcccccEHHHHHHHcccEEEEccccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHEEEccccHHccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mmhhsnpygysskrrgplnlpddvvsfrlvcptpvvggligrsgsIISSIRRdtkcrihceggfpgsdHRVILVVGsgsidrrimFCENDVvveggevsstQEAVIRVFERMWEVEAevegdgdgddvaycGLLANTTKIGVvvgkggrnvtRMRIESgakivmlpppacaaiddQLIQITGATLAVKKALVAVTTCLQHlstmekspicfnrpiekvfysnssdphreffphlslvppltgnpsdnasefhsssadadrdhpgldkkgrKQEVALRMLFSgwtasgiigkrGAIVRSLQNASGALIsfaapltksgerVVTISALEyldtrhspvqNAAVLVFARSVevegqqgfssgenkgdAVAVSILVGADFvgcltgsgssavsemedvtgtdiklvggeqvlgcaaqnDVVIQISGEYKNVQNALSEVVGRLRhnlksgeilnearprspsgrvggpalhklhqsvalspefeqETIAVQGVdqfvlplnrsqtlqtegrrhatpttdgkpgsrmfeGSLELEKSLVHllptdmvdevgprscsdgmttasgednmltegvsqlglsdniigpstlqlpkg
Flexible Loop (DISEMBL)
mmhhsnpygysskrrgplNLPDDVVSFRLVCPTpvvggligrsgsiissiRRDTKCRIHCeggfpgsdhrvILVVGSGSIDRRIMFCENDVvveggevsstqeaVIRVFERMWEVEAEvegdgdgdDVAYCGLLanttkigvvvgkggrnvTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLstmekspicfnRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSssadadrdhpgldKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISfaapltksgeRVVTISALEYLDTRHSPVQNAAVLVFARSVEVEgqqgfssgenkGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLksgeilnearprspSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNrsqtlqtegrrhatpttdgkpgsrMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSqlglsdniigpstlqlpkg
Low Complexity Region (SEG)
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVggligrsgsiissirrDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWeveaevegdgdgddvaYCGLLAnttkigvvvgkggrnvtrMRIESGAKIVMLPPPACAAIDDQLIQITGatlavkkalvavttCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKG
Disordered region (IsUnstruct)
*******************LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYS****************************************************VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG**********GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN***************************************ETIAVQGVDQFVLPL********************************************************************************************
Disordered Region (DISOPRED)
************************VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFE********************CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML******AIDDQLIQITGATLAVKKALVAVTTCLQHLSTM**********IEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASE**********************EVALRMLFSGWTASGIIGKRGAIVRSLQN**************SGERVVTISALEYLDTRHSPVQNAAVLVF***********************VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL***************************************************************************************************************************************DNIIGP*T******
Disordered Region (DISEMBL)
************KRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSD******************LDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNE*********VGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQ*****************PGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKG
Disordered Region (DISPRO)
*********************DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLST*************K*FYSNSSDPHREFFPHLSLVP********************************KQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ*******KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPST******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKG
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	587	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.678	0.656	0.262	1e-30
Q5RB68	556	Insulin-like growth facto	no	no	0.562	0.593	0.224	2e-06
Q9UNW9	492	RNA-binding protein Nova-	yes	no	0.333	0.398	0.213	7e-06
Q5SF07	592	Insulin-like growth facto	no	no	0.630	0.625	0.218	9e-06
Q32PX7	639	Far upstream element-bind	yes	no	0.279	0.256	0.245	1e-05
Q91WJ8	651	Far upstream element-bind	no	no	0.247	0.222	0.252	1e-05
Q96AE4	644	Far upstream element-bind	no	no	0.247	0.225	0.252	1e-05
Q08CK7	598	Insulin-like growth facto	no	no	0.621	0.610	0.199	3e-05
Q756R8	316	Heterogeneous nuclear rnp	yes	no	0.373	0.693	0.221	3e-05
O42254	576	Insulin-like growth facto	no	no	0.626	0.638	0.198	5e-05

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

 Score =  135 bits (340), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 119/454 (26%), Positives = 216/454 (47%), Gaps = 56/454 (12%)

Query: 22  DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS-GSI 80
           D++V +R++CP  VVGG+IG+SG +I++IR +TK +I       G   RVI +  S    
Sbjct: 33  DELVVYRILCPIDVVGGVIGKSGKVINAIRHNTKAKIKVFDQLHGCSQRVITIYCSVKEK 92

Query: 81  DRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAE--VEGDGDGDDVAYCGLLANTT 138
              I F ++    E   +   Q+A+++V++ +   + E   + + D DD   C LL   +
Sbjct: 93  QEEIGFTKS----ENEPLCCAQDALLKVYDAIVASDEENNTKTNVDRDDNKECRLLVPFS 148

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVML------PPPACAAIDDQLIQITGATLAVKKALV 192
           +   ++GK G N+ R+R  + A + ++      P   CA   D ++ I+G   +VK+AL 
Sbjct: 149 QSSSLIGKAGENIKRIRRRTRASVKVVSKDVSDPSHVCAMEYDNVVVISGEPESVKQALF 208

Query: 193 AVTTCLQHLSTMEKSPI---CFNRPIEKVF----YSNSSDPHREFFPHLS-LVPPLTGNP 244
           AV+  +  ++  E  P+     + P   V      SNS  P   F+ +   ++    G P
Sbjct: 209 AVSAIMYKINPRENIPLDSTSQDVPAASVIVPSDLSNSVYPQTGFYSNQDHILQQGAGVP 268

Query: 245 SD----NASEFHSSSADADRDHP----------GLDKKGRKQEVALRMLFSGWTASGIIG 290
           S     + S+F   +  A    P          G     R +E+  ++L        +IG
Sbjct: 269 SYFNALSVSDFQGYAETAANPVPVFASSLPVTHGFGGSSRSEELVFKVLCPLCNIMRVIG 328

Query: 291 KRGAIVRSLQNASGALISFAAPLTKSG--ERVVTISALEYLDTRHSPVQNAAVLVFARSV 348
           K G+ ++ ++ ASG+ I      TK G  E V+ ++A E  D   S    A +L+     
Sbjct: 329 KGGSTIKRIREASGSCIEVNDSRTKCGDDECVIIVTATESPDDMKSMAVEAVLLL----- 383

Query: 349 EVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408
                Q + + E+  + V + +LV +  +GC+ G   S ++E+   T  +I +  G++  
Sbjct: 384 -----QEYINDED-AENVKMQLLVSSKVIGCVIGKSGSVINEIRKRTNANICISKGKK-- 435

Query: 409 GCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442
                 D ++++SGE  +V++AL ++V RLR ++
Sbjct: 436 ------DDLVEVSGEVSSVRDALIQIVLRLREDV 463

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 = 54.7 bits (130), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 93/415 (22%), Positives = 166/415 (40%), Gaps = 85/415 (20%)

Query: 27  FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMF 86
            R++ PT  VG +IG+ G  I +I + T+ R+          HR      SG+ ++ +  
Sbjct: 196 LRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDI--------HRK---ENSGAAEKPVTI 244

Query: 87  CENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGK 146
                  EG     T EA   + E M   + E +     +++    +LA+   +G ++GK
Sbjct: 245 ---HATPEG-----TSEACRMILEIM---QKEADETKLAEEIP-LKILAHNGLVGRLIGK 292

Query: 147 GGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206
            GRN+ ++  E+G KI +      +++ D  I     T+ VK  + A  +    +  M+K
Sbjct: 293 EGRNLKKIEHETGTKITI------SSLQDLSIYNPERTITVKGTVEACASA--EIEIMKK 344

Query: 207 SPICFNRPIEKVF----YSNSSDPHREF--FPHLSLVPPLTGNPSDNASEFHSSSADADR 260
               F   +  V     Y +S  PH +F  FPH    P                      
Sbjct: 345 LREAFENDMLAVNTHSGYFSSLYPHHQFGPFPHHHSYP---------------------- 382

Query: 261 DHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA-APLTKSGER 319
                     +QE+ + +         IIGK+GA ++ L   +GA I  A A      ER
Sbjct: 383 ----------EQEI-VNLFIPTQAVGAIIGKKGAHIKQLARFAGASIKIAPAEGPDVSER 431

Query: 320 VVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGC 379
           +V I+       +      A   +F +  E   +  F+  E     +   I V +   G 
Sbjct: 432 MVIITGPPEAQFK------AQGRIFGKLKE---ENFFNPKEEV--KLEAHIRVPSSTAGR 480

Query: 380 LTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434
           + G G   V+E++++T  ++ +V  +Q        +V+++I G +   Q A  ++
Sbjct: 481 VIGKGGKTVNELQNLTSAEV-IVPRDQT--PDENEEVIVRIIGHFFASQTAQRKI 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|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 49/229 (21%), Positives = 98/229 (42%), Gaps = 33/229 (14%)

Query: 14  RRGPLNLPDDVVS-------------FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60
           R+ PL  P +VV               +++ P+   G +IG+ G  I  ++++T   I  
Sbjct: 9   RKRPLETPPEVVCTKRSNTGEEGEYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL 68

Query: 61  EGG---FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEA 117
                 +PG+  RV LV G+      +     + V E  + + T+  V+ + +    +  
Sbjct: 69  SKSKDFYPGTTERVCLVQGTAEALNAVHSFIAEKVREIPQ-AMTKPEVVNILQPQTTM-- 125

Query: 118 EVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177
                 + D      L+   +  G+++GKGG  V  +  +SGA + +   P    + +++
Sbjct: 126 ------NPDRAKQAKLIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPEGINLQERV 179

Query: 178 IQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDP 226
           + ++G    V KA+ A+   +Q +    +S  C N     + Y+N + P
Sbjct: 180 VTVSGEPEQVHKAVSAI---VQKVQEDPQSSSCLN-----ISYANVAGP 220

May regulate RNA splicing or metabolism in a specific subset of developing neurons (By similarity). Binds single strand RNA.

Homo sapiens (taxid: 9606)

>sp|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 52.4 bits (124), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 95/435 (21%), Positives = 174/435 (40%), Gaps = 65/435 (14%)

Query: 27  FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMF 86
            R++ PT  VG +IG+ G  I +I + T+ R+          HR      SG+ ++ +  
Sbjct: 189 LRILVPTQFVGAIIGKEGLTIKNITKQTQSRVDI--------HR---KENSGAAEKPVTI 237

Query: 87  CENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGK 146
                  EG     T EA   + E M   + E +     ++V    +LA+   +G ++GK
Sbjct: 238 ---HATPEG-----TSEACRMILEIM---QKEADETKLAEEVP-LKILAHNGFVGRLIGK 285

Query: 147 GGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206
            GRN+ ++  E+G KI +      +++ D  I     T+ V+  + A       +  M+K
Sbjct: 286 EGRNLKKIEHETGTKITI------SSLQDLSIYNPERTITVRGTIEACANA--EIEIMKK 337

Query: 207 SPICFNRPIEKVFYSNSSDPHRE------FFPHLSLVPPLTG----------NPSDNASE 250
               F   +  V    +  P         F   LS++PP  G          +P    S 
Sbjct: 338 LREAFENDMLAVNQQANLIPGLNLSALGIFSTGLSVLPPPAGPRGVPPSPPYHPFATHSG 397

Query: 251 FHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA 310
           + SS        P        ++  + +         IIGK+GA ++ L   +GA I  A
Sbjct: 398 YFSSLYPHHHFGPFPHHHSYPEQETVSLFIPTQAVGAIIGKKGAHIKQLARFAGASIKIA 457

Query: 311 -APLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVS 369
            A      ER+V I+       +      A   +F +  E   +  F+  E     +   
Sbjct: 458 PAEGPDVSERMVIITGPPEAQFK------AQGRIFGKLKE---ENFFNPKEEV--KLEAH 506

Query: 370 ILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY---KN 426
           I V +   G + G G   V+E++++T  ++ +V  +Q        +V+++I G +   + 
Sbjct: 507 IRVPSSTAGRVIGKGGKTVNELQNLTSAEV-IVPRDQT--PDENEEVIVRIIGHFFASQT 563

Query: 427 VQNALSEVVGRLRHN 441
            Q  + E+V +++  
Sbjct: 564 AQRKIREIVQQVKQQ 578

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

Mus musculus (taxid: 10090)

>sp|Q32PX7|FUBP1_RAT Far upstream element-binding protein 1 OS=Rattus norvegicus GN=Fubp1 PE=1 SV=1

 Score = 52.4 bits (124), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/216 (24%), Positives = 92/216 (42%), Gaps = 52/216 (24%)

Query: 4   HSNPYGYSSKRRGPL---NLPD-----------------------DVVSFRLVCPTPVVG 37
           +SN YGY  ++R PL   + PD                        V++     P  +VG
Sbjct: 50  NSNDYGYGGQKR-PLEDGDQPDAKKVPPQNDSFGAQLPPMHQQQRSVMTEEYKVPDGMVG 108

Query: 38  GLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVE 94
            +IGR G  IS I++++ C+I      GG P    R  ++ G+                 
Sbjct: 109 FIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPE--------------- 150

Query: 95  GGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRM 154
              V S +  + ++ E+         GDG G+ V    ++   +K G+V+GKGG  + ++
Sbjct: 151 --SVQSAKRLLDQIVEKGRPAPGFHHGDGPGNAVQE--IMIPASKAGLVIGKGGETIKQL 206

Query: 155 RIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
           +  +G K+VM+         D+ ++ITG    V++A
Sbjct: 207 QERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 242

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Rattus norvegicus (taxid: 10116)

>sp|Q91WJ8|FUBP1_MOUSE Far upstream element-binding protein 1 OS=Mus musculus GN=Fubp1 PE=1 SV=1

 Score = 52.4 bits (124), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/170 (25%), Positives = 78/170 (45%), Gaps = 25/170 (14%)

Query: 24  VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGSGSI 80
           V++     P  +VG +IGR G  IS I++++ C+I      GG P    R  ++ G+   
Sbjct: 96  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPE- 151

Query: 81  DRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKI 140
                            V S +  + ++ E+         GDG G+ V    ++   +K 
Sbjct: 152 ----------------SVQSAKRLLDQIVEKGRPAPGFHHGDGPGNAVQE--IMIPASKA 193

Query: 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
           G+V+GKGG  + +++  +G K+VM+         D+ ++ITG    V++A
Sbjct: 194 GLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 243

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Mus musculus (taxid: 10090)

>sp|Q96AE4|FUBP1_HUMAN Far upstream element-binding protein 1 OS=Homo sapiens GN=FUBP1 PE=1 SV=3

 Score = 52.4 bits (124), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/170 (25%), Positives = 78/170 (45%), Gaps = 25/170 (14%)

Query: 24  VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGSGSI 80
           V++     P  +VG +IGR G  IS I++++ C+I      GG P    R  ++ G+   
Sbjct: 100 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPE- 155

Query: 81  DRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKI 140
                            V S +  + ++ E+         GDG G+ V    ++   +K 
Sbjct: 156 ----------------SVQSAKRLLDQIVEKGRPAPGFHHGDGPGNAVQE--IMIPASKA 197

Query: 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
           G+V+GKGG  + +++  +G K+VM+         D+ ++ITG    V++A
Sbjct: 198 GLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 247

Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription.

Homo sapiens (taxid: 9606)

>sp|Q08CK7|IF2B1_DANRE Insulin-like growth factor 2 mRNA-binding protein 1 OS=Danio rerio GN=igf2bp1 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 85/427 (19%), Positives = 169/427 (39%), Gaps = 62/427 (14%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRI 84
           +  RL+ PT  VG +IG+ G+ I +I + T+ +I          HR      +G+ ++ I
Sbjct: 199 IPLRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDV--------HR---KENAGAAEKPI 247

Query: 85  MFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVV 144
                        + ST E        + E+  +   D    D     +LA+   +G ++
Sbjct: 248 ------------SIHSTPEGCSAACRMILEIMNQEAKDTKTADEVPLKVLAHNNFVGRLI 295

Query: 145 GKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTM 204
           GK GRN+ ++  ++  KI + P      + D  +     T+ VK ++ A   CL     M
Sbjct: 296 GKEGRNLKKVEQDTDTKITISP------LQDLTLYNPERTITVKGSIEAC--CLAEQEIM 347

Query: 205 EKSPICFNRPIEKVFYSNSSDPHREFFPHLSL--VPPLTGNPSDNASEFHSSSADADRDH 262
           +K    ++  I       + +      P L+L  +     + +       +S        
Sbjct: 348 KKVREAYDNDIA------AMNQQTHLIPGLNLGAIGLFPPSSAMPPPALGNSVPG----- 396

Query: 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA-APLTKSGERVV 321
           P     G  ++  + +         +IGK+G  ++ L   +GA I  A A    S  R+V
Sbjct: 397 PPYGPMGASEQETVHVYIPAQAVGALIGKKGQHIKQLSRFAGASIKIAPAEAPDSKMRMV 456

Query: 322 TISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLT 381
            ++       +      A   ++ +  E    + F  G  +   +   I V A   G + 
Sbjct: 457 IVTGPPEAQFK------AQGRIYGKLKE----ENF-FGPKEEVKLETHIKVAAAAAGRVI 505

Query: 382 GSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY---KNVQNALSEVVGRL 438
           G G   V+E++++T  ++ +V  EQ       + V+++I G +   +  Q  + +++ ++
Sbjct: 506 GKGGKTVNELQNLTAAEV-VVPREQT--PDEHDQVIVKIIGHFYASQLAQRKIRDILTQV 562

Query: 439 RHNLKSG 445
           +   K G
Sbjct: 563 KQQQKGG 569

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability. May regulate mRNA stability in stress granules during the cellular stress response.

Danio rerio (taxid: 7955)

>sp|Q756R8|HEK2_ASHGO Heterogeneous nuclear rnp K-like protein 2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=HEK2 PE=3 SV=1

 Score = 50.8 bits (120), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/262 (22%), Positives = 113/262 (43%), Gaps = 43/262 (16%)

Query: 143 VVGKGGRNVTRMRIESGAKI-VMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201
           ++G+GG  +  +R  +G KI +     +C+   D+L+++TG+  AV  +L  V   L   
Sbjct: 47  ILGRGGNTIDNIRKANGVKIGISTKEKSCS---DRLLEVTGSIDAVANSLADVVKVLTAD 103

Query: 202 STMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLV-PPLTGNPSDNASEFHSSSADADR 260
            T E+                  +P +  F HL+ + PP    PS + +E          
Sbjct: 104 DTNEEDA--------------EPEPEQHIFKHLNFILPP----PSPDEAE---------- 135

Query: 261 DHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNA-SGALISFAAPLTKSGER 319
                D    KQ   LR++ +    S IIG  G+ ++ L +  S  L+     L  S +R
Sbjct: 136 -----DPMKVKQIGNLRLIVTNSQVSSIIGTAGSKIKKLIDTHSSKLVVSKTFLPDSQDR 190

Query: 320 VVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF--SSGENKGDAVAVSILVGADFV 377
           ++ I    + ++  + +++ +  +    V    ++ +   S  +K   V  ++ + A++V
Sbjct: 191 ILEIQG--FPNSIANCIKDISQTLIKDDVLDTKEKRYYPHSKHSKDIHVTATVAIPAEYV 248

Query: 378 GCLTGSGSSAVSEMEDVTGTDI 399
           G L G G + ++ +   T T I
Sbjct: 249 GALLGHGGNRIANLRKYTRTKI 270

RNA-binding protein involved in the correct localization of transcripts in the cell. RNA localization is a widespread mechanism for achieving localized protein synthesis. Involved in structural and functional organization of telomeric chromatin and regulates silencing at the HMR locus.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|O42254|IF2B1_CHICK Insulin-like growth factor 2 mRNA-binding protein 1 OS=Gallus gallus GN=IGF2BP1 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 88/443 (19%), Positives = 178/443 (40%), Gaps = 75/443 (16%)

Query: 14  RRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVIL 73
           ++ P+++P      RL+ PT  VG +IG+ G+ I +I + T+ +I          HR   
Sbjct: 190 KQQPVDIP-----LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDV--------HR--- 233

Query: 74  VVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGL 133
              +G+ ++ I             + ST E      + + E+  +   D    D     +
Sbjct: 234 KENAGAAEKAI------------SIHSTPEGCSAACKMILEIMQKEAKDTKTADEVPLKI 281

Query: 134 LANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVA 193
           LA+   +G ++GK GRN+ ++  ++  KI +      +++ D  +     T+ VK ++  
Sbjct: 282 LAHNNFVGRLIGKEGRNLKKVEQDTETKITI------SSLQDLTLYNPERTITVKGSI-- 333

Query: 194 VTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHRE-----FFPHLS-LVPPLTGNPSDN 247
              C      M+K    +   +  +   +   P         FP  S  VPP   + S  
Sbjct: 334 ENCCKAEQEIMKKVREAYENDVAAMSLQSHLIPGLNLAAVGLFPASSNAVPPPPSSVSGA 393

Query: 248 ASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALI 307
           A   +SS    +++              + +         IIGK+G  ++ L   + A I
Sbjct: 394 AP--YSSFMPPEQE-------------TVHVFIPAQAVGAIIGKKGQHIKQLSRFASASI 438

Query: 308 SFAAPLTKSGE-RVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAV 366
             A P T   + R+V I+       +      A   ++ +  E    + F  G  +   +
Sbjct: 439 KIAPPETPDSKVRMVVITGPPEAQFK------AQGRIYGKLKE----ENF-FGPKEEVKL 487

Query: 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY-- 424
              I V A   G + G G   V+E++++T  ++ +V  +Q      Q  V+++I G +  
Sbjct: 488 ETHIRVPASAAGRVIGKGGKTVNELQNLTAAEV-VVPRDQTPDENEQ--VIVKIIGHFYA 544

Query: 425 -KNVQNALSEVVGRLRHNLKSGE 446
            +  Q  + +++ +++   + G+
Sbjct: 545 SQMAQRKIRDILAQVKQQHQKGQ 567

RNA-binding factor that affects mRNA nuclear export, localization, stability and translation. Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability. May regulate mRNA stability in stress granules during the cellular stress response (By similarity). Acts as translational regulator that represses translation by blocking translation initiation. Promotes transport and localization of the beta-actin mRNA to actin-rich protrusions in primary fibroblasts and neurons. Binds to a conserved 54-nucleotide element in the 3'-UTR of the beta actin mRNA known as the 'zipcode'. Binds to the minimal 5'-ACACCC-3'sequence that is sufficient for localization of beta actin mRNA.

Gallus gallus (taxid: 9031)

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	587
255583245	688	nucleic acid binding protein, putative [	0.933	0.796	0.456	1e-128
356496890	602	PREDICTED: KH domain-containing protein	0.737	0.719	0.448	3e-93
225464083	648	PREDICTED: KH domain-containing protein	0.882	0.799	0.393	1e-92
356529691	611	PREDICTED: poly(rC)-binding protein 3-li	0.717	0.689	0.443	5e-92
297821485	633	KH domain-containing protein [Arabidopsi	0.756	0.701	0.430	3e-91
4314357	649	putative RNA-binding protein [Arabidopsi	0.889	0.804	0.382	1e-87
30681758	632	RNA-binding KH domain-containing protein	0.739	0.686	0.421	2e-87
224097168	404	predicted protein [Populus trichocarpa]	0.654	0.950	0.460	1e-86
357485457	596	Poly(rC)-binding protein [Medicago trunc	0.732	0.721	0.411	2e-83
356546743	663	PREDICTED: poly(rC)-binding protein 3-li	0.703	0.622	0.4	1e-75

>gi|255583245|ref|XP_002532387.1| nucleic acid binding protein, putative [Ricinus communis] gi|223527911|gb|EEF29999.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  465 bits (1196), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 286/626 (45%), Positives = 367/626 (58%), Gaps = 78/626 (12%)

Query: 1   MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60
           M HH +        R P+ L    V+FR+VC   ++GGLIGRSGS IS IRRDT C +HC
Sbjct: 1   MQHHRDRRRRPRPTRPPVMLQPGQVAFRVVCHASIIGGLIGRSGSAISQIRRDTGCTVHC 60

Query: 61  EGGFPGSDHRVILVVGSGSIDRRIMF----CENDVVVEGGE---VSSTQEAVIRVFERMW 113
           +    GSDHRVI +VG  S  +RI      C +    E  E   VS  QEAVIRV ERMW
Sbjct: 61  DEQVQGSDHRVITIVGPASPGKRITLNSTTCHDHNGAEEEEKELVSVAQEAVIRVCERMW 120

Query: 114 EVEAEVEGDGDGDDVA--------YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165
           EV+ + E  G  D+ +        YCGLLA+TT+IG VVGKGG+NV RMR ESGA I  L
Sbjct: 121 EVDGQRERRGGVDNNSNNSGLGEGYCGLLADTTQIGAVVGKGGKNVLRMRRESGADIRFL 180

Query: 166 PPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSD 225
           PPP CA+ DDQLIQITG+ LAVKKALVAVT CL      EK P    RP+E+  +  SSD
Sbjct: 181 PPPHCASKDDQLIQITGSILAVKKALVAVTDCLHDCPPYEKDPTLLMRPLERASHLASSD 240

Query: 226 PHREFFPHL-SLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWT 284
           PH EFFPHL SL+PPL+GN   +    H  S+DA  D P  D +  + EV+ R+L S   
Sbjct: 241 PHAEFFPHLSSLLPPLSGNSGTS----HPLSSDAGED-PNQDAEAVRHEVSFRLLCSNGA 295

Query: 285 ASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF 344
           A  IIGK+G IVR+LQN +GA I FAAP++ SGERVVTISALE L++ HSP QNAA+LVF
Sbjct: 296 AGSIIGKKGTIVRTLQNETGASIMFAAPMSMSGERVVTISALENLESWHSPAQNAAILVF 355

Query: 345 ARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAV--SEMEDVTGTDIKLV 402
           ARSVE + ++G  SG  +G  V   +LV +D V CL   G +    SEM +V+G DI+++
Sbjct: 356 ARSVEHDIEKGHPSGLIEGATVTARLLVASDAVCCLIEKGGTGNIDSEMIEVSGADIRIL 415

Query: 403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGG 462
            GEQ++ CA+++DVVI+I+GEYKNVQNAL  V G+LR                       
Sbjct: 416 DGEQIMACASEDDVVIEITGEYKNVQNALFMVTGKLR----------------------- 452

Query: 463 PALHKLHQSVALSPEFEQETIAVQGVDQFVL-------PLNRSQTLQTEGRRHATPTTDG 515
                      LSP+ +QET   + ++Q           L R Q+ Q   R H T   + 
Sbjct: 453 ----------GLSPDSDQETSLTRAMNQLGFSSSFNNASLPRLQSAQKFQREHTTAIKNQ 502

Query: 516 KPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASG--------------EDN 561
           +   + F G   LE+SL  LLP ++++EVG RS S G+   +               +D 
Sbjct: 503 ENSLQAFGGGSGLERSLHFLLPKEVLNEVGERSSSGGVRQTTSSGSHSSSGLAPGPIQDT 562

Query: 562 MLTEGVSQLGLSDNIIGPS-TLQLPK 586
            LT G++Q  LS+NI  PS  L +P+
Sbjct: 563 SLTRGINQPQLSNNIDFPSPALHMPQ 588

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496890|ref|XP_003517298.1| PREDICTED: KH domain-containing protein At4g18375-like [Glycine max]

 Score =  348 bits (894), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 201/448 (44%), Positives = 285/448 (63%), Gaps = 15/448 (3%)

Query: 11  SSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHR 70
           SSKR     LP  + +FRLVC    VGGLIG SGSI+S +RR+T C+IHCE     ++ R
Sbjct: 28  SSKRPVFKVLPGQI-AFRLVCHASTVGGLIGSSGSIVSQLRRETGCKIHCEDSLSSAEDR 86

Query: 71  VILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAE--VEGDGDGDDV 128
           VILV+GS S  + ++  +   V    EVSS QEAV+RVFER+W++EAE  V  +   +  
Sbjct: 87  VILVIGSLSPRKGLLLGDGGEV----EVSSAQEAVVRVFERVWDLEAEKGVNSNRAVNGE 142

Query: 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVK 188
            +  LLA+T++IG VVGKGG+N+T +R  +GAKI + PPP CA  D++L+QITG  LAVK
Sbjct: 143 VFSKLLAHTSQIGAVVGKGGKNITAIRNNTGAKIRVFPPPQCATKDEELVQITGGILAVK 202

Query: 189 KALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHL-SLVPPLTGNPSDN 247
           KAL++V+ CLQ    + K P+  + P        SSDP+ E FPHL SL+  + G     
Sbjct: 203 KALISVSHCLQDCPPLCKVPVTSSTPTVSSSDRLSSDPNAELFPHLNSLLTSMEG----- 257

Query: 248 ASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALI 307
               +  + +++ +    D KG + EV  R+L S   A  +IGKRGAIVR+L++ +GA I
Sbjct: 258 -LSIYERTTNSN-ETSNRDSKGAEHEVVFRLLCSNNVAGSVIGKRGAIVRALESKTGASI 315

Query: 308 SFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVA 367
            FAAPL++  ER+VTISA+E L++ +SP Q+A +LVFAR +E    +GF    +    V 
Sbjct: 316 IFAAPLSEHAERIVTISAVESLESCNSPAQDAVILVFARIIEDHIGKGFLQVSSMESPVT 375

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
             +LV    V C +G+    +SE+ +VTG DI+++ GE V   A+  DVV+QI+GEY+ V
Sbjct: 376 ARLLVATSTVNCFSGNEGQVISELREVTGADIQILHGESVPNGASDEDVVVQITGEYRCV 435

Query: 428 QNALSEVVGRLRHNLKSGEILNEARPRS 455
           QNAL ++  R+R NL   E++ EARP+S
Sbjct: 436 QNALYKITSRIRDNLSPNEVVAEARPKS 463

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464083|ref|XP_002269250.1| PREDICTED: KH domain-containing protein At4g18375-like [Vitis vinifera]

 Score =  347 bits (889), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 223/567 (39%), Positives = 320/567 (56%), Gaps = 49/567 (8%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRI 84
           V+FRL+C    +GG+IG+SG I+  ++ DT  RI  E     SDHRVILV+   S++RRI
Sbjct: 51  VAFRLLCHASRIGGVIGKSGVIVKQLQSDTGARIRVEDSPSTSDHRVILVIAPASVNRRI 110

Query: 85  MFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVV 144
               +    E  E S+ QEAV+RVFER+ EV A V+G   G  V  C LLA T+++G V+
Sbjct: 111 ALQGSS---EEVEASAAQEAVLRVFERILEVAAVVDGVPPGG-VVSCRLLAETSQVGSVI 166

Query: 145 GKGGRNVTRMRIESGAKIVMLPP---PACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201
           GKGG+ V ++R ESG+KI +L     P CAA  D++++I G  LAVKKALVAV+  LQ  
Sbjct: 167 GKGGKVVEKIRRESGSKIKVLTAEKLPTCAASTDEMVEIEGDVLAVKKALVAVSRRLQDC 226

Query: 202 STMEKSPICFNRPIEKVFYSNSSDPHREFFPHL-SLVPPLTGNPSDNASEFHSSSADADR 260
             ++K+ +   RP+E V   +  DP  + F    S++PP+  N    AS     S + +R
Sbjct: 227 PNVDKTKLIGGRPLEVVPQQSLPDPRVDLFQQRGSVLPPIPSNTISYASGSRPLSINTER 286

Query: 261 DHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERV 320
               LD K  +QEV  ++L S     G+IGK G IV++LQN +GA IS  AP+ +  ER+
Sbjct: 287 IS-TLDPKTSQQEVIFKILCSNDRVGGVIGKGGTIVKALQNEAGASISVGAPVAECDERL 345

Query: 321 VTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCL 380
           +TI+A E  ++R+SP QN  +LVF RS+E   ++G  SG +KG  V+  ++V ++ VGCL
Sbjct: 346 ITITASENPESRYSPAQNGVILVFNRSIEAGIEKGLDSG-SKGSPVSARLVVPSNQVGCL 404

Query: 381 TGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440
            G G + +SEM   +G  I+++G +QV  CA++ND V+QISGE+ NVQ+ L  + GRLR 
Sbjct: 405 MGKGGTIISEMRKASGAGIRIIGSDQVPKCASENDQVVQISGEFVNVQDGLYHITGRLRD 464

Query: 441 NLKSGEILNEARPR--------SPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFV 492
           NL   + LN A  R        SP GRV  PA   LH SV +SP F + T   Q +D   
Sbjct: 465 NLFPSKTLNGAGIRSSSAMNEISPYGRVRDPASFGLHSSVGVSPSFSRHTTLTQSMDHLG 524

Query: 493 LPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDG 552
           L    S +L         PT+                     L P+  V  V PR+   G
Sbjct: 525 L----SHSLD-------HPTSP-------------------RLWPSQTVTGVNPRNIKGG 554

Query: 553 MTTASGEDN-MLTEGVSQLGLSDNIIG 578
           +   SG  + ++T    ++ + +N+IG
Sbjct: 555 IELGSGSKSAIITNTTVEIVIPENVIG 581

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529691|ref|XP_003533422.1| PREDICTED: poly(rC)-binding protein 3-like [Glycine max]

 Score =  345 bits (884), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 192/433 (44%), Positives = 276/433 (63%), Gaps = 12/433 (2%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRI 84
           ++FRLVC   +VGGLIG SGSI+S +RR+T C+IHCE     ++ RVILV+GS S  + +
Sbjct: 50  IAFRLVCHASIVGGLIGSSGSIVSQLRRETACKIHCEDSLSSAEDRVILVIGSVSPRKGL 109

Query: 85  MFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAE--VEGDGDGDDVAYCGLLANTTKIGV 142
              +   V    EVSS QEA++RVFER+W +EAE  V  +   +   +  LLA+T++IG 
Sbjct: 110 QLGDGGEV----EVSSAQEAIVRVFERVWGLEAEKGVNSNRAVNSEVFSKLLAHTSQIGA 165

Query: 143 VVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLS 202
           VVGKGG+N+T +R  +GAKI + PPP CA  D++L+ ITG  LAVKKAL++V+ CLQ   
Sbjct: 166 VVGKGGKNITAIRNSTGAKIRVCPPPQCATKDEELVLITGGILAVKKALISVSHCLQDCP 225

Query: 203 TMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262
            + K P+  + P    F  +SSDP+ E FP L+ +  LT     +  E  ++S ++    
Sbjct: 226 PLCKVPVSSSIPTVSSFDRSSSDPNAELFPRLNSL--LTSMEGLSIYERTTNSNESSNR- 282

Query: 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVT 322
              D KG + EV  R+L S   A  +IGKRGAIVR+L++ +GA I FAAPL++  ER+VT
Sbjct: 283 ---DSKGGEHEVVFRLLCSNNVAGSVIGKRGAIVRALESKTGASIIFAAPLSEHAERIVT 339

Query: 323 ISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTG 382
           ISA+E L++ +SP Q+A +LVFAR +E    +GF    +    V   +LV    V   +G
Sbjct: 340 ISAIESLESCNSPAQDAVILVFARIIEDHIGKGFLQVSSMESPVTARLLVATSTVNSWSG 399

Query: 383 SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442
           +    + E+ +VTG DI+++ GE V   A+ +DVV+QI+GEY+ VQNAL ++  R+R NL
Sbjct: 400 NEGQVILELREVTGADIQILHGESVPNGASDDDVVVQITGEYRCVQNALYKITSRIRDNL 459

Query: 443 KSGEILNEARPRS 455
              E + EARP+S
Sbjct: 460 SPNEAVTEARPKS 472

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297821485|ref|XP_002878625.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297324464|gb|EFH54884.1| KH domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  342 bits (877), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 206/478 (43%), Positives = 288/478 (60%), Gaps = 34/478 (7%)

Query: 12  SKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRV 71
           SKRR  +++  D  + R+VC   V+GG+IG +G ++S +RR+T  +IHCE    GSDH V
Sbjct: 12  SKRRPVIHVLPDETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWV 71

Query: 72  ILVVGSGSIDRRIMFCENDVVVEGGE--------VSSTQEAVIRVFERMWEVEAEVEGDG 123
           + +VGS ++++ ++  +      GGE        VS+ Q A+IRV ER W V A  +G G
Sbjct: 72  VFIVGSTAVNKSVLLTDRVGDFSGGEHEDWVTCDVSAAQTALIRVLERSWVVLAAKDGGG 131

Query: 124 --DGDDV-AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI 180
             DG+D  AYCG+LA+  +IG V+G GG+NV  MR  SGA I +LPPP C    D+LIQI
Sbjct: 132 VVDGEDEEAYCGILADRNQIGAVLGLGGKNVEWMRRSSGAMIRVLPPPICGTNTDELIQI 191

Query: 181 TGATLAVKKALVAVTTCLQHLSTME--KSPICFNRPIEKVFYSNSSDPHREFFPHL-SLV 237
           TG  LAVKKALV V+TC+Q    +     P+C  +  E     NS DPH EFFP+L S V
Sbjct: 192 TGDVLAVKKALVMVSTCIQDNPPVNGYPQPLCI-KAYESSTDGNSEDPHSEFFPNLRSSV 250

Query: 238 PPLTGNPSDNASEFHSSSADADRDHPGL--DKKGRKQEVALRMLFSGWTASGIIGKRGAI 295
           P    N SD+AS        ++R  P +  +  G +++V  +++F+   A GIIGK+G I
Sbjct: 251 P----NASDSAS--------SNRHLPAVYDEGNGTERKVVFKIIFTSVVAGGIIGKQGTI 298

Query: 296 VRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG 355
           +R+LQN +GA IS  APL  SGERVVTISA E L++R+S  QNA  LVFARSVE++ ++G
Sbjct: 299 IRALQNETGASISIGAPLKVSGERVVTISARENLESRYSHAQNALALVFARSVEIDVEKG 358

Query: 356 FSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415
              G + G  V   +LV + F   L G+G+    E    TG D+ +    Q+L   ++N+
Sbjct: 359 LRPGLHNGAVVKTKLLVPSQFANSLVGNGN---REAIIATGADVHIPVDNQILEWISENE 415

Query: 416 VVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPR--SPSGRVGGPALHKLHQS 471
           VVI+I GEY +VQ AL+ V  +LR NL   ++L E R R  +P    G   ++ L QS
Sbjct: 416 VVIEIKGEYGHVQKALTHVSSKLRENLLPKKVLGEMRARVSNPYESAGTSQIYNLKQS 473

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4314357|gb|AAD15568.1| putative RNA-binding protein [Arabidopsis thaliana]

 Score =  330 bits (845), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 224/585 (38%), Positives = 319/585 (54%), Gaps = 63/585 (10%)

Query: 12  SKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRV 71
           SKRR  +++  D  + R+VC   V+GG+IG +G ++S +RR+T  +IHCE    GSDH V
Sbjct: 12  SKRRPVIHVLPDETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWV 71

Query: 72  ILVVGSGSIDRRIMFCENDVVVEGGE--------VSSTQEAVIRVFERMWEVEAEVEGDG 123
           + +VGS ++++ I+  +      GGE        VS+ Q A+IRV ER W V A  +G G
Sbjct: 72  VFIVGSTAVNQSILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGG 131

Query: 124 --DGDDV-AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI 180
             DG+D  AYCG+LA+  +IG V+G GG+NV  MR  SGA I +LPPP C   +D+LIQI
Sbjct: 132 VVDGEDEEAYCGILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPPPICGTKNDELIQI 191

Query: 181 TGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYS------NSSDPHREFFPHL 234
           TG  LAVKKALV V++ +Q+ + +   P     P+    Y       NS DPH EFFP+L
Sbjct: 192 TGDVLAVKKALVMVSSYIQNNAPLNGYP----PPLSIKGYESLSTDGNSEDPHSEFFPNL 247

Query: 235 SLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGA 294
                   +   NA+E  +S    +R  P       +++V  +++F+   A GIIGK+G 
Sbjct: 248 R------SSSLSNATEIVAS----NRHLPYDGGNSTERKVVFKIIFTSVVAGGIIGKQGT 297

Query: 295 IVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ 354
           I+R+LQN +GA IS  APL  SGERVVT+SA E L++R+S  QNA  LVFARSVE++ ++
Sbjct: 298 IIRALQNETGASISVGAPLKVSGERVVTVSARENLESRYSHAQNALALVFARSVEIDVEK 357

Query: 355 GFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414
           G   G + G  V   +LV + F     G+G+    E    TG D+ +  G QVL   ++N
Sbjct: 358 GLRPGLHNGAIVKTKLLVPSHFANSFNGNGN---REAIIATGADVHISVGNQVLEWISEN 414

Query: 415 DVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPR--SPSGRVGGPALHKLHQSV 472
           +VVI+I GEY +VQ AL+ V  +LR NL   ++L E R R  +P    GG +     Q  
Sbjct: 415 EVVIEIKGEYSHVQKALTHVSSKLRENLLPKKVLGEMRARVSNPYESAGGRS-----QIY 469

Query: 473 ALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEK-- 530
            L P  +              P N S   Q   R  +   +   P  +M     E+ K  
Sbjct: 470 NLQPSQQ--------------PSN-SIKPQDASRGDSLSVSAAVPDLKMVRSGAEVLKSN 514

Query: 531 SLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDN 575
           S++H      VDE+   +    +     ED  LT+G+ QL +S N
Sbjct: 515 SVMHTEVLKEVDELNDFTLPQSLLE---ED--LTQGMKQLQMSSN 554

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30681758|ref|NP_850026.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana] gi|330252232|gb|AEC07326.1| RNA-binding KH domain-containing protein [Arabidopsis thaliana]

 Score =  329 bits (844), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 198/470 (42%), Positives = 279/470 (59%), Gaps = 36/470 (7%)

Query: 12  SKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRV 71
           SKRR  +++  D  + R+VC   V+GG+IG +G ++S +RR+T  +IHCE    GSDH V
Sbjct: 12  SKRRPVIHVLPDETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWV 71

Query: 72  ILVVGSGSIDRRIMFCENDVVVEGGE--------VSSTQEAVIRVFERMWEVEAEVEGDG 123
           + +VGS ++++ I+  +      GGE        VS+ Q A+IRV ER W V A  +G G
Sbjct: 72  VFIVGSTAVNQSILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGG 131

Query: 124 --DGDDV-AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI 180
             DG+D  AYCG+LA+  +IG V+G GG+NV  MR  SGA I +LPPP C   +D+LIQI
Sbjct: 132 VVDGEDEEAYCGILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPPPICGTKNDELIQI 191

Query: 181 TGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYS------NSSDPHREFFPHL 234
           TG  LAVKKALV V++ +Q+ + +   P     P+    Y       NS DPH EFFP+L
Sbjct: 192 TGDVLAVKKALVMVSSYIQNNAPLNGYP----PPLSIKGYESLSTDGNSEDPHSEFFPNL 247

Query: 235 SLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGA 294
                   +   NA+E  +S    +R  P       +++V  +++F+   A GIIGK+G 
Sbjct: 248 R------SSSLSNATEIVAS----NRHLPYDGGNSTERKVVFKIIFTSVVAGGIIGKQGT 297

Query: 295 IVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ 354
           I+R+LQN +GA IS  APL  SGERVVT+SA E L++R+S  QNA  LVFARSVE++ ++
Sbjct: 298 IIRALQNETGASISVGAPLKVSGERVVTVSARENLESRYSHAQNALALVFARSVEIDVEK 357

Query: 355 GFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414
           G   G + G  V   +LV + F     G+G+    E    TG D+ +  G QVL   ++N
Sbjct: 358 GLRPGLHNGAIVKTKLLVPSHFANSFNGNGN---REAIIATGADVHISVGNQVLEWISEN 414

Query: 415 DVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPR--SPSGRVGG 462
           +VVI+I GEY +VQ AL+ V  +LR NL   ++L E R R  +P    GG
Sbjct: 415 EVVIEIKGEYSHVQKALTHVSSKLRENLLPKKVLGEMRARVSNPYESAGG 464

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097168|ref|XP_002310861.1| predicted protein [Populus trichocarpa] gi|222853764|gb|EEE91311.1| predicted protein [Populus trichocarpa]

 Score =  327 bits (838), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 189/410 (46%), Positives = 258/410 (62%), Gaps = 26/410 (6%)

Query: 15  RGPL-NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVIL 73
           R PL  L    V+FR+VC    +G LIG SGS+IS IR +T C +HCE    GS+HR I+
Sbjct: 15  RQPLIELQPGQVAFRVVCHASKIGALIGHSGSVISQIRLETGCLVHCEEAVKGSEHRAIV 74

Query: 74  VVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGL 133
           V GS S +R+I   E++ V    EVS+ QEAV+RV ERMWEV+A  +G   GD   YCGL
Sbjct: 75  VAGSASPERKIAVGEDETV----EVSAAQEAVVRVLERMWEVDAVKDG---GDCEGYCGL 127

Query: 134 LANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALV 192
           LANT++IG VVG+ GRN+ RM+  SGA I +LP P CA  +DQLIQITG+ T+AVKKA++
Sbjct: 128 LANTSQIGAVVGREGRNIKRMKRASGAHIWILPAPLCALKEDQLIQITGSSTVAVKKAVI 187

Query: 193 AVTTCLQHLSTMEKSPICFN-RPIEKVFYSNSSDPHREFFPHL-SLVPPLTGNPSDNASE 250
           A+T+CLQ     EK  +  +   + +    +S DPH EFFPHL SL+P  + N +     
Sbjct: 188 AITSCLQDCPPYEKDEVDLSLEAVRRRRSGSSGDPHAEFFPHLCSLLPTYSENIA----- 242

Query: 251 FHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA 310
                   D+DH    K   + +V  RM+     A  IIGK G++VR+LQN +GA I  A
Sbjct: 243 -------TDKDH---KKPNEQLQVQFRMICPHGAAGSIIGKGGSVVRALQNQTGASIILA 292

Query: 311 APLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSI 370
            P+T S  R+VT+SALE L++ HSP QNA +LVFARS+E + ++  S G  +   V  ++
Sbjct: 293 PPITNSDGRLVTVSALENLESSHSPAQNALLLVFARSIEHDIERARSLGLIEEITVTATL 352

Query: 371 LVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420
           L+ ++ V CL   G    SEM + TG DI+++ G+Q   CA+ NDVV+Q+
Sbjct: 353 LLPSNRVSCLIERGGRIDSEMIETTGADIQILQGDQFFYCASNNDVVLQV 402

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485457|ref|XP_003613016.1| Poly(rC)-binding protein [Medicago truncatula] gi|355514351|gb|AES95974.1| Poly(rC)-binding protein [Medicago truncatula]

 Score =  316 bits (809), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 188/457 (41%), Positives = 277/457 (60%), Gaps = 27/457 (5%)

Query: 3   HHSNPYGYSSKRRGP-LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61
           HH  P    + R+ P   L    ++FRLVC +  VGGLIG SGSI+S +RR+T C+IHCE
Sbjct: 16  HHPQPPLKRNNRKRPVFKLLPGQIAFRLVCHSSTVGGLIGSSGSIVSQLRRETGCKIHCE 75

Query: 62  GGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEG 121
               G+D RVILV+GS S  + I+  + ++     EVS+ QE V+RVF+R+W +E+E  G
Sbjct: 76  DAVVGTDDRVILVIGSMSDRKGIVLGDREM-----EVSNAQEGVVRVFDRVWGLESEKGG 130

Query: 122 DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT 181
           +G+     Y  LLA+++++G +VGKGG+N++ +R  SG+ I + P P CAA D++LI IT
Sbjct: 131 NGE----VYGKLLAHSSQVGAIVGKGGKNISNIRNNSGSNIRVCPAPHCAAKDEELILIT 186

Query: 182 GATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSD-----PHREFFPHL-S 235
           G +LAVKKAL+ V+ CLQ    M K  +  N P       NSSD      H + FPHL S
Sbjct: 187 GESLAVKKALIYVSYCLQDCPPMGK--VSLNTPPTI----NSSDRSTSYTHEDLFPHLNS 240

Query: 236 LVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAI 295
            +P + G   ++AS+  +++A+ +     LD KG    V  R+L S   A  +IGK+G+I
Sbjct: 241 WLPSMEGLSINDASK-QTTNANGNSS---LDSKGSGHAVVFRLLCSNNVAGSVIGKKGSI 296

Query: 296 VRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG 355
           VR+ +  +GA I FA PL +  ER+VTISA E L++ +SP Q+A +LVF R  E   + G
Sbjct: 297 VRTFEIRTGASIVFAPPLGQYEERIVTISAFENLESSNSPAQDAVILVFTRIAEDHIRNG 356

Query: 356 FSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415
           F         V   +L+    +  LTG+    +SE+  V+G DI+L+ GE +   A+ ND
Sbjct: 357 FQPATAVESPVTARLLITTSTLHLLTGNEGQVISELRQVSGADIQLLHGEPIPN-ASDND 415

Query: 416 VVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEAR 452
           VV+QI+G Y+ V+NAL ++   +R N  + E+L EA+
Sbjct: 416 VVVQITGGYRCVENALRKITSIIRDNPLTNELLAEAK 452

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546743|ref|XP_003541782.1| PREDICTED: poly(rC)-binding protein 3-like [Glycine max]

 Score =  290 bits (743), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 176/440 (40%), Positives = 263/440 (59%), Gaps = 27/440 (6%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRI 84
           V+FRL+C    +GG+IG+SGS+I ++++ T  +I  E     S  RVILV+   ++  ++
Sbjct: 45  VAFRLLCNASRIGGVIGKSGSVIKTLQQSTGAKIRIEDAPQESPDRVILVIADAALSCKV 104

Query: 85  MFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVV 144
           +    +VV    EVS  QEA+++VF+R+ EV AE+EG   GD V  C L+A++ + G V+
Sbjct: 105 LLRNEEVV----EVSKAQEALLKVFDRILEVAAEMEGVDVGDRVMSCRLVADSAQAGSVI 160

Query: 145 GKGGRNVTRMRIESGAKIVMLPP--PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLS 202
           GKGG+ V R++ E+G KI +L    P CA+  D++I+I G   +VKKALVAV+  LQ   
Sbjct: 161 GKGGKVVERIKKETGCKIRVLTDDLPLCASASDEMIEIEGRVSSVKKALVAVSQRLQDCP 220

Query: 203 TMEKSPICFNRPIEKVFYSNSSDPHREFFPH-----LSLVPPLTGN-------------- 243
           ++ +  +  N+P E V Y       RE         L++VP  T +              
Sbjct: 221 SVNRIKMMGNKPYEIVQYETLDALPREILTAAPRGTLTVVPHETVDHLLLRSSALSTLSS 280

Query: 244 -PSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNA 302
             +  A+  HS SA+ +R    L+ K  +QEV+ R+L S     G+IGK G IVR+LQ+ 
Sbjct: 281 SSNSYATRVHSLSAEVNRVS-SLEPKALQQEVSFRILCSNDRVGGVIGKGGNIVRALQSE 339

Query: 303 SGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENK 362
           +GA IS    + +  +R++TI+A E  ++R+SP Q AAVLVF+RS+EV  ++   SG NK
Sbjct: 340 TGATISIGPLVAECEDRLITIAASENPESRYSPAQKAAVLVFSRSIEVGFEKELDSGLNK 399

Query: 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422
           G  V V ++V +  VGCL G G   VSE+   TG +I+++G +QV  CA+ ND V+QISG
Sbjct: 400 GSTVTVRLVVPSSQVGCLIGKGGVIVSEIRKATGANIRIIGTDQVPKCASDNDQVVQISG 459

Query: 423 EYKNVQNALSEVVGRLRHNL 442
           E+ +VQ+AL    GRLR NL
Sbjct: 460 EFSSVQDALYNATGRLRDNL 479

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	587
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.761	0.707	0.352	8.7e-65
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.323	0.305	0.350	1.9e-23
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.798	0.728	0.231	8.5e-20
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.499	0.449	0.241	1.4e-13
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.381	0.467	0.251	7.7e-13
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.337	0.361	0.268	9.8e-13
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.347	0.353	0.248	2.7e-08
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.287	0.341	0.239	3.3e-06
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.248	0.240	0.254	2.6e-05
ZFIN|ZDB-GENE-050706-149	222	zgc:110045 "zgc:110045" [Danio	0.335	0.887	0.248	3e-05

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

 Score = 629 (226.5 bits), Expect = 8.7e-65, Sum P(2) = 8.7e-65
 Identities = 168/476 (35%), Positives = 239/476 (50%)

Query:    12 SKRRGPLNLPDDVVSFRLVCPTPVVXXXXXXXXXXXXXXXXDTKCRIHCEGGFPGSDHRV 71
             SKRR  +++  D  + R+VC   V+                +T  +IHCE    GSDH V
Sbjct:    12 SKRRPVIHVLPDETAIRVVCHASVIGGIIGSNGYVVSKLRRETGTKIHCESPVNGSDHWV 71

Query:    72 ILVVGSGSIDRRIMFCENDVVVEGGE--------VSSTQEAVIRVFERMWXXXXXXXXXX 123
             + +VGS ++++ I+  +      GGE        VS+ Q A+IRV ER W          
Sbjct:    72 VFIVGSTAVNQSILLTDRVGEFSGGEHEDWVTCEVSAAQTALIRVLERSWVVLAAKDGGG 131

Query:   124 XXXXX---XYCGLLAXXXXXXXXXXXXXXXXXXMRIESGAKIVMLPPPACAAIDDQLIQI 180
                      YCG+LA                  MR  SGA I +LPPP C   +D+LIQI
Sbjct:   132 VVDGEDEEAYCGILADRNQIGAVLGLGGKNVEWMRRNSGAMIRVLPPPICGTKNDELIQI 191

Query:   181 TGXXXXXXXXXXXXXXCLQHLSTMEKSPICFN-RPIEKVFYS-NSSDPHREFFPHLSLVP 238
             TG               +Q+ + +   P   + +  E +    NS DPH EFFP+L    
Sbjct:   192 TGDVLAVKKALVMVSSYIQNNAPLNGYPPPLSIKGYESLSTDGNSEDPHSEFFPNLR--- 248

Query:   239 PLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRS 298
                 +   NA+E  +S+     D  G +   RK  V  +++F+   A GIIGK+G I+R+
Sbjct:   249 ---SSSLSNATEIVASNRHLPYD--GGNSTERK--VVFKIIFTSVVAGGIIGKQGTIIRA 301

Query:   299 LQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSS 358
             LQN +GA IS  APL  SGERVVT+SA E L++R+S  QNA  LVFARSVE++ ++G   
Sbjct:   302 LQNETGASISVGAPLKVSGERVVTVSARENLESRYSHAQNALALVFARSVEIDVEKGLRP 361

Query:   359 GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI 418
             G + G  V   +LV + F     G+G+    E    TG D+ +  G QVL   ++N+VVI
Sbjct:   362 GLHNGAIVKTKLLVPSHFANSFNGNGNR---EAIIATGADVHISVGNQVLEWISENEVVI 418

Query:   419 QISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPR--SPSGRVGGPA-LHKLHQS 471
             +I GEY +VQ AL+ V  +LR NL   ++L E R R  +P    GG + ++ L  S
Sbjct:   419 EIKGEYSHVQKALTHVSSKLRENLLPKKVLGEMRARVSNPYESAGGRSQIYNLQPS 474

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

 Score = 278 (102.9 bits), Expect = 1.9e-23, Sum P(3) = 1.9e-23
 Identities = 73/208 (35%), Positives = 108/208 (51%)

Query:   250 EFHSSSADADRDHP---------G-LDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSL 299
             E+HS       DHP         G  ++   ++EVA R+L        +IGK GA+VR+L
Sbjct:   242 EYHSMEYHPQWDHPPPNPMPEDVGPFNRPVVEEEVAFRLLCPADKVGSLIGKGGAVVRAL 301

Query:   300 QNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSG 359
             QN SGA I  + P   S ER++ ISA E L+ RHS  Q+  + V  R VE+    GF   
Sbjct:   302 QNESGASIKVSDPTHDSEERIIVISARENLERRHSLAQDGVMRVHNRIVEI----GFEPS 357

Query:   360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419
                  AV   +LV + ++G L G G   +SEM   TG  I++   +Q     +Q+D ++Q
Sbjct:   358 A----AVVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESQHDEIVQ 413

Query:   420 ISGEYKNVQNALSEVVGRLRHNLKSGEI 447
             + G  K VQ+AL +++ RLR  +  G +
Sbjct:   414 VIGNLKTVQDALFQILCRLREAMFPGRL 441

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 265 (98.3 bits), Expect = 8.5e-20, P = 8.5e-20
 Identities = 117/506 (23%), Positives = 200/506 (39%)

Query:    10 YSSKRRGPLNLPDDVVSFRLVCPTPVVXXXXXXXXXXXXXXXXDTKCRIHCEGGFPGSDH 69
             Y S+ +   N  D VV +R++CP+ V+                +T+ RI     FPG   
Sbjct:    29 YESEEKKIDNKDDLVVVYRILCPSGVMGSVIGKSGKVINLIRQETRARIKVVDPFPGCSE 88

Query:    70 RVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWXXXXXXXXXXXXXXXX 129
             RVI +  S S  + I+  E   +     + S Q A+++V + +                 
Sbjct:    89 RVITIFCSVSEKKDIVDIEYSELDYSVPLCSAQAALLKVHDAIVASLATAAENTKIDRDD 148

Query:   130 Y--CGLLAXXXXXXXXXXXXXXXXXXMRIESGAKIVML------PPPACAAIDDQLIQIT 181
             +  C LL                   +R  + A + ++      P   CA   D ++ I+
Sbjct:   149 FRECRLLVPSSQCSIVIGKSGSIIKNIRGRTRANVKVVSKDVSDPSHTCAMDFDNIVMIS 208

Query:   182 GXXXXXXXXXXXXXXCLQHLS---------TMEKSPICFNRPIEKVFYSNSS-DPHRE-F 230
             G               +  +S         T+++ P     P +   Y  +   P ++  
Sbjct:   209 GETESVKKALFAVSAIMYKVSPREQIPLDTTVQEVPASIIIPSDLSIYPQAGLYPSQDSI 268

Query:   231 FPHLSLVPPLTGN-PS---DNASE-FHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA 285
             F H + V    G  P    +NA+      SA A     G     R +++A++++ S    
Sbjct:   269 FQHGANVSSFIGTLPQGYGENAANPVPVFSASALPVVHGFGGSSRSEKLAIKVICSSSKI 328

Query:   286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGER-VVTISALEYLDTRHSPVQNAAVLVF 344
               +IGK G  ++ ++ ASG+ I      T   +  V+T++A E  D   S    A VL+ 
Sbjct:   329 GRVIGKGGLTIKGIRQASGSHIEVNDSRTNHDDDCVITVTATESPDDLKSMAVEA-VLLL 387

Query:   345 ARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404
                +  E +          D V + +LV +  +GC+ G   S +SE+   T  DI +  G
Sbjct:   388 QEKINDEDE----------DKVKMQLLVSSKVIGCIIGKSGSIISEIRKRTKADIHISKG 437

Query:   405 EQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN-LKSGEILNEARPRSPSGRVGGP 463
                  CA  ND +++ISGE  NV++AL ++V RLR + L+  E  +  +P + S      
Sbjct:   438 NNTPKCADPNDELVEISGEVSNVRDALIQIVLRLRDDVLRDRETGSRNQPPARSENNNFF 497

Query:   464 ALHKLHQSVALSPEFEQETIAVQGVD 489
             +    +  +AL   F      V  VD
Sbjct:   498 SSSSSNTGLALPQSFMSSVPQVASVD 523

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

 Score = 209 (78.6 bits), Expect = 1.4e-13, P = 1.4e-13
 Identities = 75/310 (24%), Positives = 138/310 (44%)

Query:   154 MRIESGAKIVMLPP----PACAAIDDQLIQITGXXXXXXXXXXXXXXCLQHLSTMEKSPI 209
             MRIE+   I +LP     P C ++ ++++QI G               L+     ++S  
Sbjct:   201 MRIETKTHIRILPRESNLPRCVSLSEEIVQIVGELNAVKNALAIVSSRLRESQHRDRSNF 260

Query:   210 CFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLD--K 267
                    +  ++ + D +       S      GN  +N   F S  ++   + P +   +
Sbjct:   261 QGRSHSPERSFAAAGDDYMPQLRRQSSDRFPRGNFRNN--NFSSRQSNYAEEAPAVPVGE 318

Query:   268 KGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALE 327
                 +E+  ++L        ++G+   I+  LQN  G  +  + P+  S E+++TIS+ E
Sbjct:   319 NVYSEELVFQILCPADKIVRVVGESQGIIDLLQNEIGVDVRVSDPVAGSDEQIITISSEE 378

Query:   328 YLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSA 387
               D    P Q A + +  + +++          +K + +   +LV +    CL G   S 
Sbjct:   379 APDDPFFPAQEALLHIQTQIIDLI--------PDKDNLITTRLLVPSRDSICLEGKAGS- 429

Query:   388 VSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEI 447
             VSE+  +TGT ++++  E++  CA+ NDVVIQI+GE +  + AL E+   LR ++     
Sbjct:   430 VSEISRLTGTSVQILAREEIPRCASINDVVIQITGEIRAAREALVELTLLLRSHMFKELS 489

Query:   448 LNEARPRSPS 457
               E  P S S
Sbjct:   490 QKETPPASTS 499

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

 Score = 197 (74.4 bits), Expect = 7.7e-13, Sum P(2) = 7.7e-13
 Identities = 59/235 (25%), Positives = 108/235 (45%)

Query:   208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDK 267
             P+     + +V      +P R  F HL L    +      A    ++   + R++     
Sbjct:   205 PLVVREALYQVASLLHDNPSR--FQHLLLSSSSSSMHQPGAMLMSAALTSSHRNYAVRRD 262

Query:   268 KGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALE 327
                 +E  +  +       G+IGK G  +  ++  +GA I      T   + ++ IS+ E
Sbjct:   263 IADAREFCVCFICPAENVGGVIGKGGGFINQIRQETGATIRVNTSETDDDDCIIFISSKE 322

Query:   328 YLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGD-AVAVSILVGADFVGCLTGSGSS 386
             + + + SP  NAA+ +  R  E         G++  D A++  +LV +  +GCL G G +
Sbjct:   323 FYEDQ-SPAVNAAIRLQQRCSE-------KVGKDANDLAISTRLLVSSSQIGCLIGKGGA 374

Query:   387 AVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441
              +SEM  VT  +I+++  E V   A +++ ++QI+G       AL++V+ RLR N
Sbjct:   375 VISEMRSVTRANIRILQKEDVPKIAREDEEMVQITGSPDAAMKALTQVILRLRAN 429

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 = 200 (75.5 bits), Expect = 9.8e-13, P = 9.8e-13
 Identities = 57/212 (26%), Positives = 105/212 (49%)

Query:   232 PHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGK 291
             P L  + PL G+   +A ++        R+ P         E  +R++      + +IGK
Sbjct:   248 PRLVGLAPLMGSYGRDAGDWSRPLYQPPRNDPPAT------EFFIRLVSPVENIASVIGK 301

Query:   292 RGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFAR-SVEV 350
              GA++  L+  + A I   +  T+  + ++TISA E  +  +SP   A + +  + S +V
Sbjct:   302 GGALINQLRQETRATIKVDSSRTEGNDCLITISAREVFEDAYSPTIEAVMRLQPKCSDKV 361

Query:   351 EGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGC 410
             E   G  S   +       +LV +  +GC+ G G + ++EM  +T  +I+++G E +   
Sbjct:   362 ERDSGLVSFTTR-------LLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPKV 414

Query:   411 AAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442
             A+ +D ++QISGE    + AL ++  RLR N+
Sbjct:   415 ASDDDEMVQISGELDVAKEALIQITSRLRANV 446

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

 Score = 160 (61.4 bits), Expect = 2.7e-08, P = 2.7e-08
 Identities = 52/209 (24%), Positives = 90/209 (43%)

Query:   242 GNPSDNASEFHSSSADADRDHPGLDKK--GRKQEVALRMLFSGWTASGIIGKRGAIVRSL 299
             G P ++      S  + D    G +K+  G   E   RML        IIG++G +++ +
Sbjct:   154 GIP-EHLESLQKSEPEEDATVGGEEKRWPGWPGETVFRMLVPAQKVGSIIGRKGDVIKKI 212

Query:   300 QNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSG 359
                + A I        + ER V +S  E  ++   P  +  + V  R V+  G  G +S 
Sbjct:   213 VEETRARIKILDGPPGTTERAVMVSGKEEPESSLPPSMDGLLRVHMRIVD--GLDGEASQ 270

Query:   360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419
                   V+  +LV A   G L G     V  +++ +   ++++G E +   A Q+D V++
Sbjct:   271 APPPSKVSTRLLVPASQAGSLIGKQGGTVKAIQEASACIVRVLGSEDLPVFALQDDRVVE 330

Query:   420 ISGEYKNVQNALSEVVGRLRHNLKSGEIL 448
             + GE  +V  AL  +   LR  L    I+
Sbjct:   331 VVGEPTSVHRALELIASHLRKFLVDRSII 359

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:2120755 PEP "AT4G26000" [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 3.3e-06, P = 3.3e-06
 Identities = 41/171 (23%), Positives = 76/171 (44%)

Query:   273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTR 332
             +   RM+        IIG++G  ++ +   + A I        + +R+V IS  E  +  
Sbjct:    73 DCVFRMIVPVTKVGAIIGRKGDFIKKMCEETRARIKVLDGPVNTPDRIVLISGKEEPEAY 132

Query:   333 HSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVA-VSILVGADFVGCLTGSGSSAVSEM 391
              SP  +A + VF R   +         +N G   + V +LV +     L G   S +  +
Sbjct:   133 MSPAMDAVLRVFRRVSGLPDNDD-DDVQNAGSVFSSVRLLVASTQAINLIGKQGSLIKSI 191

Query:   392 EDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442
              + +G  ++++  E+    AAQ++ ++ + GE   +  AL  +VG LR  L
Sbjct:   192 VENSGASVRILSEEETPFYAAQDERIVDLQGEALKILKALEAIVGHLRRFL 242

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0048367 "shoot system development" evidence=IMP

GO:0048467 "gynoecium development" evidence=IMP

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

 Score = 117 (46.2 bits), Expect = 2.6e-05, Sum P(2) = 2.6e-05
 Identities = 42/165 (25%), Positives = 77/165 (46%)

Query:   264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG--ERVV 321
             G     R +E+  ++L        +IGK G+ ++ ++ ASG+ I      TK G  E V+
Sbjct:   302 GFGGSSRSEELVFKVLCPLCNIMRVIGKGGSTIKRIREASGSCIEVNDSRTKCGDDECVI 361

Query:   322 TISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLT 381
              ++A E  D   S    A +L+          Q + + E+  + V + +LV +  +GC+ 
Sbjct:   362 IVTATESPDDMKSMAVEAVLLL----------QEYINDED-AENVKMQLLVSSKVIGCVI 410

Query:   382 GSGSSAVSEMEDVTGTDIKLVGGE-----QVLG-CAAQNDVVIQI 420
             G   S ++E+   T  +I +  G+     +V G  ++  D +IQI
Sbjct:   411 GKSGSVINEIRKRTNANICISKGKKDDLVEVSGEVSSVRDALIQI 455

GO:0003676 "nucleic acid binding" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-050706-149 zgc:110045 "zgc:110045" [Danio rerio (taxid:7955)]

 Score = 124 (48.7 bits), Expect = 3.0e-05, P = 3.0e-05
 Identities = 53/213 (24%), Positives = 90/213 (42%)

Query:   264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTI 323
             G+ + G    + +R+L  G     IIGK+G  V+ ++  SGA I+ +     S ER+VTI
Sbjct:     7 GVSEGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISDG--SSPERIVTI 64

Query:   324 SALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF-SSGENKGDAVAVSILVGADFVGCLTG 382
                    T  S V   A  + A   E +      +S       V + ++  A   G L G
Sbjct:    65 -------TGASEVIFKAFAMIAEKFEEDILASMINSTVTSRPPVTLRLVFPASQCGSLIG 117

Query:   383 SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442
              G S + E+ + TG  +++ G   +L  + +  V I  SG    +   +  +   +  + 
Sbjct:   118 KGGSKIKEIRESTGAQVQVAG--DLLPDSTERAVTI--SGTPHAITQCVKHICTVMLESP 173

Query:   443 KSGEILNEARPRSPSGRVGGPALHKLHQSVALS 475
               G  +   RP+ PS   G   L + H + A +
Sbjct:   174 PKGATI-PYRPK-PSAGGGHTVLTQPHAATAFA 204

GO:0003723 "RNA binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	587
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	3e-12
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-08
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-08
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-07
pfam13014	42	pfam13014, KH_3, KH domain	3e-07
pfam00013	59	pfam00013, KH_1, KH domain	4e-07
pfam00013	59	pfam00013, KH_1, KH domain	2e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	8e-06
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	1e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	1e-05
pfam13014	42	pfam13014, KH_3, KH domain	2e-05
pfam13014	42	pfam13014, KH_3, KH domain	2e-05
smart00322	68	smart00322, KH, K homology RNA-binding domain	2e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	7e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-04
pfam00013	59	pfam00013, KH_1, KH domain	7e-04
smart00322	68	smart00322, KH, K homology RNA-binding domain	0.003

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

 Score = 61.3 bits (150), Expect = 3e-12
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGF-PGSDHRVILVVGS 77
          + RL+ P+   G +IG+ GS I  IR +T  +I       PGS  RV+ + G 
Sbjct: 1  TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK 53

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 = 50.6 bits (122), Expect = 2e-08
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALV 192
           LL  +++ G ++GKGG  +  +R E+GAKI +       +  ++++ I+G   AV+KAL+
Sbjct: 4   LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGS-TERVVTISGKPSAVQKALL 62

Query: 193 AVT 195
            + 
Sbjct: 63  LIL 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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 50.6 bits (122), Expect = 2e-08
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          + R++ P+ +VG +IG+ GS I  IR +T  +I       GS+ R++ + G+
Sbjct: 1  TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT 52

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

 Score = 47.9 bits (115), Expect = 2e-07
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 7/70 (10%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALIS-FAAPLTKSGERVVTISALEYLDTRHS 334
           LR+L     A  IIGK G+ ++ ++  +GA I    + L  S ERVVTIS       + S
Sbjct: 2   LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG------KPS 55

Query: 335 PVQNAAVLVF 344
            VQ A +L+ 
Sbjct: 56  AVQKALLLIL 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|221895 pfam13014, KH_3, KH domain

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 36 VGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVG 76
          VG +IG+ G  I  IR +T  +I      PGS  R++ + G
Sbjct: 2  VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 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|215657 pfam00013, KH_1, KH domain

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALV 192
           +L    K+G ++GKGG N+  +R E+G KI +          D  + I+G    V+KA  
Sbjct: 4   ILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDD------RDDTVTISGTPEQVEKAKE 57

Query: 193 AV 194
            +
Sbjct: 58  LI 59

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 = 45.2 bits (108), Expect = 2e-06
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          + R++ P   VG +IG+ GS I  IR +T  +I      P      + + G+
Sbjct: 1  TERILIPPDKVGRIIGKGGSNIKEIREETGVKIR----IPDDRDDTVTISGT 48

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

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

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          D V+  ++ P   VG +IG+ GS I  I  +T  +I   G  PGS+ RV+ + G 
Sbjct: 1  DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGP 53

Length = 68

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 370 ILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN 429
           +LV +   G + G G S + E+ + TG  I++             + V+ ISG+   VQ 
Sbjct: 4   LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQK 59

Query: 430 ALSEVV 435
           AL  ++
Sbjct: 60  ALLLIL 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|238053 cd00105, KH-I, K homology RNA-binding domain, type I

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194
            +G ++GKGG  +  +R E+GAKI +  P + +  +++++ ITG   AV+KA   +
Sbjct: 10  LVGRIIGKGGSTIKEIREETGAKIKI--PDSGSGSEERIVTITGTPEAVEKAKELI 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|221895 pfam13014, KH_3, KH domain

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 16/37 (43%), Positives = 23/37 (62%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           IIGK G  ++ ++  +GA I    P   SGER+VTI+
Sbjct: 5   IIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTIT 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|221895 pfam13014, KH_3, KH domain

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182
            +G ++GKGG  +  +R E+GAKI +  P       ++++ ITG
Sbjct: 1   LVGAIIGKGGETIKEIREETGAKIQI--PKPEPGSGERIVTITG 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 = 42.3 bits (100), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 4/58 (6%)

Query: 137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194
             K+G+++GKGG  + ++  E+G KI +  P      ++++++ITG    V+KA   +
Sbjct: 11  ADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG----SEERVVEITGPPENVEKAAELI 64

Length = 68

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

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISA 325
            R+L        IIGK G+ ++ ++  +GA I      + S ER+VTI+ 
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG 51

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 = 39.9 bits (94), Expect = 2e-04
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
             +LV +  VG + G G S + E+ + TG  IK+             + ++ I+G  + V
Sbjct: 2   ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAV 56

Query: 428 QNALSEV 434
           + A   +
Sbjct: 57  EKAKELI 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 = 37.9 bits (89), Expect = 7e-04
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 9/67 (13%)

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
             IL+  D VG + G G S + E+ + TG  I++             D  + ISG  + V
Sbjct: 2   ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPDDR---------DDTVTISGTPEQV 52

Query: 428 QNALSEV 434
           + A   +
Sbjct: 53  EKAKELI 59

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

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISA 325
           IIGK G+ ++ ++  +G  I    P   S ERVV I+ 
Sbjct: 17  IIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITG 52

Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	587
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	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
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.96
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.92
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.85
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.6
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.48
PRK13763	180	putative RNA-processing protein; Provisional	99.46
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.45
PRK13763	180	putative RNA-processing protein; Provisional	99.4
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.32
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.32
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.24
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.2
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.18
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.13
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.11
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.06
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.04
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.03
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.99
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.97
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.97
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.89
PF13014	43	KH_3: KH domain	98.83
PF13014	43	KH_3: KH domain	98.79
smart00322	69	KH K homology RNA-binding domain.	98.76
smart00322	69	KH K homology RNA-binding domain.	98.67
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.6
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.48
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.11
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	98.06
PRK08406	140	transcription elongation factor NusA-like protein;	97.93
KOG2113	394	consensus Predicted RNA binding protein, contains	97.9
KOG2113	394	consensus Predicted RNA binding protein, contains	97.66
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.65
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.62
PRK08406	140	transcription elongation factor NusA-like protein;	97.59
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.41
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.27
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.18
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.13
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.03
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.78
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.72
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.66
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.61
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.57
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.54
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.51
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.49
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.49
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.43
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.42
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.39
TIGR01953	341	NusA transcription termination factor NusA. This m	96.22
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.2
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.14
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.13
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.05
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.85
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.74
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	95.64
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.62
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.57
PRK00468	75	hypothetical protein; Provisional	95.5
TIGR01953	341	NusA transcription termination factor NusA. This m	95.33
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.28
PRK02821	77	hypothetical protein; Provisional	94.93
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.79
COG5176	269	MSL5 Splicing factor (branch point binding protein	94.77
PRK12328	374	nusA transcription elongation factor NusA; Provisi	94.58
PRK00468	75	hypothetical protein; Provisional	94.57
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.54
PRK12704	520	phosphodiesterase; Provisional	94.39
PRK01064	78	hypothetical protein; Provisional	94.34
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.32
COG1837	76	Predicted RNA-binding protein (contains KH domain)	94.3
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	94.14
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	94.09
PRK02821	77	hypothetical protein; Provisional	93.98
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	93.83
PRK00106	535	hypothetical protein; Provisional	93.78
PRK09202	470	nusA transcription elongation factor NusA; Validat	93.69
PRK01064	78	hypothetical protein; Provisional	93.58
PRK12704	520	phosphodiesterase; Provisional	93.38
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.33
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.24
PRK00106	535	hypothetical protein; Provisional	93.15
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	92.2
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	92.02
COG5176	269	MSL5 Splicing factor (branch point binding protein	91.88
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	91.3
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	90.7
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	89.43
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	88.42
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	88.07
PRK12705	508	hypothetical protein; Provisional	87.65
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	87.14
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	85.99
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	85.58
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	85.14
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	84.95
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	83.3
cd02410	145	archeal_CPSF_KH The archaeal cleavage and polyaden	81.13
PRK12705	508	hypothetical protein; Provisional	80.64
cd02414	77	jag_KH jag_K homology RNA-binding domain. The KH d	80.54

>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=9e-43  Score=375.74  Aligned_cols=370  Identities=28%  Similarity=0.453  Sum_probs=293.1

Q ss_pred             CCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCc
Q 007844           19 NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV   98 (587)
Q Consensus        19 ~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~   98 (587)
                      ..++...+|||||+.+.+|.||||+|.+||+||++|.++|+|.+..++++|||++|+|...+               ...
T Consensus        37 ~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~~~  101 (485)
T KOG2190|consen   37 TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------LNL  101 (485)
T ss_pred             CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------ccC
Confidence            33344445999999999999999999999999999999999999999999999999997322               247


Q ss_pred             cHHHHHHHHHHHHHHhhhhccCC-----C-CCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCC
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEG-----D-GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA  172 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~-----~-~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~  172 (587)
                      +++++|++++++.|.....+++.     . .....++++|||||.+++|+||||+|+.||+|+++|||+|+|.++ ..+.
T Consensus       102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~  180 (485)
T KOG2190|consen  102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN  180 (485)
T ss_pred             CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc
Confidence            88999999999999875332211     1 111226899999999999999999999999999999999999996 5566


Q ss_pred             CCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC---CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 007844          173 IDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK---SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNAS  249 (587)
Q Consensus       173 ~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~---~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~  249 (587)
                      .++|.|+|.|.+++|.+|+..|..+|++++.+.-   ....+|+|...              .+...+|........|+ 
T Consensus       181 ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~--------------~~~~~~~s~~~~~~~~~-  245 (485)
T KOG2190|consen  181 STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSAS--------------QGGPVLPSTAQTSPDAH-  245 (485)
T ss_pred             ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCccc--------------ccCccccccccCCcccc-
Confidence            6999999999999999999999999999653311   11223333100              00011111111100000 


Q ss_pred             ccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCc
Q 007844          250 EFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYL  329 (587)
Q Consensus       250 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p  329 (587)
                              .      +.......+..+++.+|.+.++.|||++|..|+.++.++++.|.+.....+   ++|+++..+.+
T Consensus       246 --------~------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~  308 (485)
T KOG2190|consen  246 --------P------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENP  308 (485)
T ss_pred             --------c------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCc
Confidence                    0      000223456788999999999999999999999999999999999977554   89999999999


Q ss_pred             CCCCChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccc
Q 007844          330 DTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLG  409 (587)
Q Consensus       330 ~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~  409 (587)
                      ++..+++++|+.+++.++.+.....      . ...++.+|+||++++||||||+|++|.+|++.|||.|+|...++.  
T Consensus       309 ~~~~s~a~~a~~~~~~~~~~~~~~~------~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~--  379 (485)
T KOG2190|consen  309 EDRYSMAQEALLLVQPRISENAGDD------L-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV--  379 (485)
T ss_pred             ccccccchhhhhhcccccccccccc------c-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc--
Confidence            9999999999999999987653211      1 467899999999999999999999999999999999999998773  


Q ss_pred             cCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcccCcc
Q 007844          410 CAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGE  446 (587)
Q Consensus       410 ~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~  446 (587)
                       ...+++.++|+|...+...|+++|..++........
T Consensus       380 -~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~  415 (485)
T KOG2190|consen  380 -SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG  415 (485)
T ss_pred             -CCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence             257899999999999999999999888776554443

>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=2.2e-42  Score=349.98  Aligned_cols=369  Identities=21%  Similarity=0.338  Sum_probs=272.2

Q ss_pred             CCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEecCCchhhhhhhccccccccCCCcc
Q 007844           21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVS   99 (587)
Q Consensus        21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~   99 (587)
                      ...+..+|+|||..++|+||||.|+|||.|...|.|+|+|.. ...|..||+|+|.+++|.                 .+
T Consensus       195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-----------------~s  257 (584)
T KOG2193|consen  195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-----------------TS  257 (584)
T ss_pred             cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-----------------hH
Confidence            356789999999999999999999999999999999999975 456889999999999987                 34


Q ss_pred             HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEE
Q 007844          100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLI  178 (587)
Q Consensus       100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V  178 (587)
                      .|+..++.|..+   ...+.    .-..++.+++|.++.+||+||||.|++||+|+++||++|.|++. .....+.||+|
T Consensus       258 ~Ac~~ILeimqk---EA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTI  330 (584)
T KOG2193|consen  258 KACKMILEIMQK---EAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTI  330 (584)
T ss_pred             HHHHHHHHHHHH---hhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceE
Confidence            455555544433   22221    12247899999999999999999999999999999999999986 44445679999


Q ss_pred             EEeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcC-CCCCCCCCCCCCCCccCCCCCC
Q 007844          179 QITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLS-LVPPLTGNPSDNASEFHSSSAD  257 (587)
Q Consensus       179 ~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~-~~P~~~~~~~~y~~~~~p~~~~  257 (587)
                      +++|+.|+|.+|..+|..+|++....+-..+...-++....    ..+.-..+|..+ +.||          .+.|....
T Consensus       331 tVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l----~~~~l~~f~ssS~~~~P----------h~~Ps~v~  396 (584)
T KOG2193|consen  331 TVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGL----NLPALGLFPSSSAVSPP----------HFPPSPVT  396 (584)
T ss_pred             EecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCccc----CccccCCCCcccccCCC----------CCCCCccc
Confidence            99999999999999999999986544421111000000000    000000111111 1111          00111100


Q ss_pred             CCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC-CCCCCccEEEEEecCCcCCCCChH
Q 007844          258 ADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPV  336 (587)
Q Consensus       258 ~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~er~V~IsG~~~p~~~~~~a  336 (587)
                      +...-+.+  ....+...++|+||...+|.|||++|.+||.|.+.+||.|+|.++ .++..+|.|+|+|.  |+    +.
T Consensus       397 ~a~p~~~~--hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGp--pe----aq  468 (584)
T KOG2193|consen  397 FASPYPLF--HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGP--PE----AQ  468 (584)
T ss_pred             cCCCchhh--hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCC--hH----HH
Confidence            00000000  112244578999999999999999999999999999999999975 67789999999998  33    23


Q ss_pred             HHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCc
Q 007844          337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV  416 (587)
Q Consensus       337 ~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r  416 (587)
                      -+|.-+||.++.|..+-     .+...-...+.+.||...+|+||||||.+++++|+.|+|.+.|+.+. .|.  .++..
T Consensus       469 fKAQgrifgKikEenf~-----~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~v  540 (584)
T KOG2193|consen  469 FKAQGRIFGKIKEENFF-----LPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQV  540 (584)
T ss_pred             HhhhhhhhhhhhhhccC-----CchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--cccee
Confidence            37777888888664321     11234567888999999999999999999999999999999998754 553  56778


Q ss_pred             EEEEcCCHHHHHHHHHHHHHHHhhccc
Q 007844          417 VIQISGEYKNVQNALSEVVGRLRHNLK  443 (587)
Q Consensus       417 ~V~I~G~~~~V~~A~~~I~~~Lr~~~~  443 (587)
                      +|.|.|.+.+.+.|+..|.+.+.++.-
T Consensus       541 ivriiGhfyatq~aQrki~~iv~qvkq  567 (584)
T KOG2193|consen  541 IVRIIGHFYATQNAQRKIAHIVNQVKQ  567 (584)
T ss_pred             eeeeechhhcchHHHHHHHHHHHHHHH
Confidence            999999999999999999998887553

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

Probab=100.00  E-value=6e-41  Score=355.64  Aligned_cols=341  Identities=22%  Similarity=0.293  Sum_probs=262.7

Q ss_pred             CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      ..++-+.-||..++|.||||+|+.|..|+.++||+|.+.....+..+|-+.++|..++++.                 |.
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~-----------------aK  114 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV-----------------AK  114 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH-----------------HH
Confidence            4567788899999999999999999999999999999877666778999999999998654                 33


Q ss_pred             HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEee
Q 007844          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG  182 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G  182 (587)
                      ..+-.+..+......-.  .......++.+|+||.+.+|.||||+|++||.|++++||++.+.++-......++.+.|+|
T Consensus       115 ~li~evv~r~~~~~~~~--~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG  192 (600)
T KOG1676|consen  115 QLIGEVVSRGRPPGGFP--DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG  192 (600)
T ss_pred             HhhhhhhhccCCCCCcc--ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence            33334444432110000  1122457899999999999999999999999999999999999987333344889999999


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007844          183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH  262 (587)
Q Consensus       183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~  262 (587)
                      +++.|+.|..+|.++|++...   ...     .                           ....|+.             
T Consensus       193 dp~~ve~a~~lV~dil~e~~~---~~~-----g---------------------------~~~~~g~-------------  224 (600)
T KOG1676|consen  193 DPDKVEQAKQLVADILREEDD---EVP-----G---------------------------SGGHAGV-------------  224 (600)
T ss_pred             CHHHHHHHHHHHHHHHHhccc---CCC-----c---------------------------cccccCc-------------
Confidence            999999999999999986210   000     0                           0000000             


Q ss_pred             CCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC-CCCCCccEEEEEecCCcCCCCChHHHHHH
Q 007844          263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV  341 (587)
Q Consensus       263 ~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~er~V~IsG~~~p~~~~~~a~~Av~  341 (587)
                            ......+++|.||...||.||||+|++||+|+.+||++|+|.+. .+.+.||.+.|.|+.      ..+..|..
T Consensus       225 ------~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~  292 (600)
T KOG1676|consen  225 ------RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAE  292 (600)
T ss_pred             ------CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHH
Confidence                  00123388999999999999999999999999999999999876 448899999999994      55567777


Q ss_pred             HHHhhhhcccccCCCCCCCC-CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEE
Q 007844          342 LVFARSVEVEGQQGFSSGEN-KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI  420 (587)
Q Consensus       342 ~i~~~v~e~~~~~g~~~g~~-~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I  420 (587)
                      +|.+.+.+.....+...+.. ........+.||.+.||.||||+|++||.|.++|||++.+.+.  .| ..+..+++++|
T Consensus       293 lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p-~~~~~ektf~I  369 (600)
T KOG1676|consen  293 LINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PP-NGNPKEKTFVI  369 (600)
T ss_pred             HHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CC-CCCccceEEEE
Confidence            77666655433222211100 0112278899999999999999999999999999999999886  23 36778999999


Q ss_pred             cCCHHHHHHHHHHHHHHHhhcccCc
Q 007844          421 SGEYKNVQNALSEVVGRLRHNLKSG  445 (587)
Q Consensus       421 ~G~~~~V~~A~~~I~~~Lr~~~~~~  445 (587)
                      +|+..+|+.|+.||..++-.....-
T Consensus       370 rG~~~QIdhAk~LIr~kvg~~~~n~  394 (600)
T KOG1676|consen  370 RGDKRQIDHAKQLIRDKVGDIAPNT  394 (600)
T ss_pred             ecCcccchHHHHHHHHHhcccCCCC
Confidence            9999999999999999998754433

>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=1.5e-32  Score=264.50  Aligned_cols=336  Identities=17%  Similarity=0.284  Sum_probs=210.7

Q ss_pred             CCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCcc
Q 007844           20 LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVS   99 (587)
Q Consensus        20 ~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~   99 (587)
                      ..-..+.+|||+.++.+|+||||+|+|||+|+.+.+|.|.|.|+  ..+|||++|+...+.+                  
T Consensus        43 ~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti------------------  102 (390)
T KOG2192|consen   43 FKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI------------------  102 (390)
T ss_pred             hhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH------------------
Confidence            34457999999999999999999999999999999999999887  5689999999866442                  


Q ss_pred             HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEE
Q 007844          100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ  179 (587)
Q Consensus       100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~  179 (587)
                        -+.|.+|+.++.+.-.       ..+++.+||||+.+++|.|||++|++||+|++++.|+++|... .|+.++||+|.
T Consensus       103 --~~ilk~iip~lee~f~-------~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv~l  172 (390)
T KOG2192|consen  103 --GEILKKIIPTLEEGFQ-------LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRVVL  172 (390)
T ss_pred             --HHHHHHHhhhhhhCCC-------CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceEEE
Confidence              2334445544433221       2347899999999999999999999999999999999999995 88999999999


Q ss_pred             EeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCC-----CCc-CCCCCCCCCCCCCCCccCC
Q 007844          180 ITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFF-----PHL-SLVPPLTGNPSDNASEFHS  253 (587)
Q Consensus       180 I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~-----p~~-~~~P~~~~~~~~y~~~~~p  253 (587)
                      |.|.+.+|..++..|.+.|.+.+.+...     +|+...++.....-....+     |.. ..+|+.++...        
T Consensus       173 ~~g~~k~v~~~i~~il~~i~e~pikgsa-----~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp--------  239 (390)
T KOG2192|consen  173 IGGKPKRVVECIKIILDLISESPIKGSA-----QPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP--------  239 (390)
T ss_pred             ecCCcchHHHHHHHHHHHhhcCCcCCcC-----CcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC--------
Confidence            9999999999999999999997765543     2222112211100000000     000 11111111000        


Q ss_pred             CCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCC
Q 007844          254 SSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRH  333 (587)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~  333 (587)
                                    .......-  +.+.  .    -|+-|..-.       --+.|........    .|-+-. +..+ 
T Consensus       240 --------------p~~~~sdl--may~--r----~GrpG~ryd-------g~vdFs~detw~s----aidtw~-~Sew-  284 (390)
T KOG2192|consen  240 --------------PPPRGSDL--MAYD--R----RGRPGDRYD-------GMVDFSADETWPS----AIDTWS-PSEW-  284 (390)
T ss_pred             --------------CCCCcccc--ceec--c----CCCCCcccc-------ccccccccccCCC----cCCCcC-cccc-
Confidence                          00000000  0000  0    011111000       0011111000000    000000 0000 


Q ss_pred             ChHHHHHHHHHhhhhcccccCCCCC-CCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCC
Q 007844          334 SPVQNAAVLVFARSVEVEGQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAA  412 (587)
Q Consensus       334 ~~a~~Av~~i~~~v~e~~~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~  412 (587)
                      .+   |-.--...--+.....+... |.-.....|.+|.||++.-|.||||+|+.|++|++++||.|++....+     +
T Consensus       285 qm---aYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikideple-----G  356 (390)
T KOG2192|consen  285 QM---AYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLE-----G  356 (390)
T ss_pred             cc---ccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCC-----C
Confidence            00   00000000000000000000 111246789999999999999999999999999999999999976443     7


Q ss_pred             CCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          413 QNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       413 ~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      +.+|+++|+|+.++++.|++++...++.+
T Consensus       357 sedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  357 SEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             CCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence            88999999999999999999999988853

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

Probab=99.96  E-value=3.8e-28  Score=258.41  Aligned_cols=246  Identities=20%  Similarity=0.299  Sum_probs=194.5

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK  206 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~  206 (587)
                      ..++.+.-||..++|.||||+|+.|..|+.+|||+|+|...  ......|.|.++|.+++|+.|+.+|.+++....    
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~--~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~----  125 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD--PSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR----  125 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCC--CCCcccccccccCCcccHHHHHHhhhhhhhccC----
Confidence            46778899999999999999999999999999999998774  234578999999999999999999999986521    


Q ss_pred             CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeeccccc
Q 007844          207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS  286 (587)
Q Consensus       207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG  286 (587)
                      .+.                    .+++                                  .....+++.+|.||.+++|
T Consensus       126 ~~~--------------------~~~~----------------------------------~q~~~~ttqeI~IPa~k~G  151 (600)
T KOG1676|consen  126 PPG--------------------GFPD----------------------------------NQGSVETTQEILIPANKCG  151 (600)
T ss_pred             CCC--------------------Cccc----------------------------------cCCccceeeeeccCcccee
Confidence            000                    0000                                  1113567999999999999


Q ss_pred             ccccccchhhHhhhhhcCceEEeeCC--CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc---ccCCCCCCCC
Q 007844          287 GIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE---GQQGFSSGEN  361 (587)
Q Consensus       287 ~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~---~~~g~~~g~~  361 (587)
                      .||||+|++||.|++.+||++.+..+  ......+.+.|+|..      ..+..|-.++++.+.+..   +..+...+..
T Consensus       152 lIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp------~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~  225 (600)
T KOG1676|consen  152 LIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP------DKVEQAKQLVADILREEDDEVPGSGGHAGVR  225 (600)
T ss_pred             eEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH------HHHHHHHHHHHHHHHhcccCCCccccccCcC
Confidence            99999999999999999999887643  223367789999983      445566666666665321   1111111222


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      .....+.+|.||...||.||||+|++||+|+.+|||+|+|.++++ |   ...+|.+.|.|+.++|+.|.++|.+.|++.
T Consensus       226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d~ie~Aa~lI~eii~~~  301 (600)
T KOG1676|consen  226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVDQIEHAAELINEIIAEA  301 (600)
T ss_pred             ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHHHHHHHHHHHHHHHHHH
Confidence            234569999999999999999999999999999999999988766 3   578999999999999999999999999864


Q ss_pred             c
Q 007844          442 L  442 (587)
Q Consensus       442 ~  442 (587)
                      .
T Consensus       302 ~  302 (600)
T KOG1676|consen  302 E  302 (600)
T ss_pred             h
Confidence            3

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

Probab=99.96  E-value=6.4e-29  Score=252.32  Aligned_cols=239  Identities=17%  Similarity=0.291  Sum_probs=195.0

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS  207 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~  207 (587)
                      +..+|+|||..++|.||||.|++||.|...|-|+|.|... ...+..|+.|+|.|++|...+|+.+|.+++......+  
T Consensus       198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrk-en~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~--  274 (584)
T KOG2193|consen  198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRK-ENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDD--  274 (584)
T ss_pred             CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeec-ccCCcccCceEEecCccchHHHHHHHHHHHHHhhhcc--
Confidence            4679999999999999999999999999999999999986 5568899999999999999999999999997632211  


Q ss_pred             CcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccc
Q 007844          208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG  287 (587)
Q Consensus       208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~  287 (587)
                                                                                   ....++.++|+..+.+||+
T Consensus       275 -------------------------------------------------------------k~~~e~pLk~lAHN~lvGR  293 (584)
T KOG2193|consen  275 -------------------------------------------------------------KVAEEIPLKILAHNNLVGR  293 (584)
T ss_pred             -------------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence                                                                         1235678899999999999


Q ss_pred             cccccchhhHhhhhhcCceEEeeCC---CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcc------------cc
Q 007844          288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV------------EG  352 (587)
Q Consensus       288 IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~------------~~  352 (587)
                      +|||.|.+||+|..+||++|.|...   ..-..||+|++.|+-      .....|..+|.+++.+.            .+
T Consensus       294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi------Eac~~AE~eImkKlre~yEnDl~a~s~q~~l  367 (584)
T KOG2193|consen  294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI------EACVQAEAEIMKKLRECYENDLAAMSLQCHL  367 (584)
T ss_pred             hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH------HHHHHHHHHHHHHHHHHHhhhHHHhhccCCC
Confidence            9999999999999999999999863   334569999999973      33345555555554322            11


Q ss_pred             cCCC-------------------CCC----C-------CCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844          353 QQGF-------------------SSG----E-------NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (587)
Q Consensus       353 ~~g~-------------------~~g----~-------~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~  402 (587)
                      .+++                   ++.    .       .......++|.||...+|.|||++|.+||.|.+.+||.|+|.
T Consensus       368 ~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa  447 (584)
T KOG2193|consen  368 PPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA  447 (584)
T ss_pred             CcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeec
Confidence            1110                   010    0       012556789999999999999999999999999999999998


Q ss_pred             CCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       403 ~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      +.+-    .+..+|+|+|+|.+++..+|+..|..+|.+
T Consensus       448 ppE~----pdvseRMViItGppeaqfKAQgrifgKikE  481 (584)
T KOG2193|consen  448 PPEI----PDVSERMVIITGPPEAQFKAQGRIFGKIKE  481 (584)
T ss_pred             CCCC----CCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence            8653    357899999999999999999999999995

>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=2.6e-26  Score=227.62  Aligned_cols=241  Identities=20%  Similarity=0.294  Sum_probs=171.4

Q ss_pred             CCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEe---CCCCCCCceEEEEecCCchhhhhhhcccccccc
Q 007844           18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGSGSIDRRIMFCENDVVVE   94 (587)
Q Consensus        18 ~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~---~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e   94 (587)
                      +...++.+++|||||+..+|.||||+|++|.+|+++|||+|+++   |.+|++.||||.|.|+.+++.            
T Consensus        32 n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~------------   99 (402)
T KOG2191|consen   32 NTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN------------   99 (402)
T ss_pred             cCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH------------
Confidence            34445569999999999999999999999999999999999996   578999999999999876521            


Q ss_pred             CCCccHHHHHHHHHHHHHHhhhhccCC------CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-
Q 007844           95 GGEVSSTQEAVIRVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-  167 (587)
Q Consensus        95 ~~~~~~A~~Al~~i~~~i~~~~~~~~~------~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-  167 (587)
                              .-+..|.++|.+.....+.      ....++.-.++++||++.+|.||||+|.+||.|++++||.|+|++. 
T Consensus       100 --------av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqk  171 (402)
T KOG2191|consen  100 --------AVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQK  171 (402)
T ss_pred             --------HHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccC
Confidence                    1122333344333222221      1123445679999999999999999999999999999999999954 


Q ss_pred             CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCC
Q 007844          168 PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDN  247 (587)
Q Consensus       168 p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y  247 (587)
                      |..-...||+|++.|++++..+|+.+|.++|.+++.......   .++....                      +....|
T Consensus       172 pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln---~sya~vs----------------------GpvaNs  226 (402)
T KOG2191|consen  172 PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLN---ISYANVS----------------------GPVANS  226 (402)
T ss_pred             CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceec---cchhccc----------------------Cccccc
Confidence            555667899999999999999999999999999765443211   0110000                      001111


Q ss_pred             CCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC
Q 007844          248 ASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP  312 (587)
Q Consensus       248 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~  312 (587)
                      ++...|+....         .......+.-.-|+....|..-|.+|.++-.|-.-+|+.+.+.+.
T Consensus       227 nPtGspya~~~---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  227 NPTGSPYAYQA---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             CCCCCCCCCCC---------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence            11111111000         011122233355888999999999999999999999998888753

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

Probab=99.92  E-value=5.7e-24  Score=211.10  Aligned_cols=250  Identities=21%  Similarity=0.290  Sum_probs=197.2

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK  206 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~  206 (587)
                      .+.+|+|||+..+|.||||+|++|.+|+.+|||+|++++. .++++++||+|.|+|+.+++......|.++|++.+....
T Consensus        38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~  117 (402)
T KOG2191|consen   38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA  117 (402)
T ss_pred             ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence            4899999999999999999999999999999999999988 889999999999999999999999999999998543211


Q ss_pred             CCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeeccccc
Q 007844          207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS  286 (587)
Q Consensus       207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG  286 (587)
                      .+....                                                     ++........++++||+..+|
T Consensus       118 k~v~~~-----------------------------------------------------~pqt~~r~kqikivvPNstag  144 (402)
T KOG2191|consen  118 KPVDIL-----------------------------------------------------QPQTPDRIKQIKIVVPNSTAG  144 (402)
T ss_pred             CCcccc-----------------------------------------------------CCCCccccceeEEeccCCccc
Confidence            100000                                                     000111223588999999999


Q ss_pred             ccccccchhhHhhhhhcCceEEeeCCCC---CCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc-------cC--
Q 007844          287 GIIGKRGAIVRSLQNASGALISFAAPLT---KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-------QQ--  354 (587)
Q Consensus       287 ~IIGk~G~~Ik~I~~~tga~I~i~~~~~---~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~-------~~--  354 (587)
                      .||||+|.+||.|++++||+|+|.+.++   .-.+|+||++|..      ....+|+.+|++++.|++-       ..  
T Consensus       145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~------e~~~~A~~~IL~Ki~eDpqs~scln~sya~  218 (402)
T KOG2191|consen  145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP------EQNMKAVSLILQKIQEDPQSGSCLNISYAN  218 (402)
T ss_pred             ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH------HHHHHHHHHHHHHhhcCCcccceeccchhc
Confidence            9999999999999999999999995433   3468999999984      5566899999999987521       00  


Q ss_pred             --C----CCC-C-------CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEE
Q 007844          355 --G----FSS-G-------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI  420 (587)
Q Consensus       355 --g----~~~-g-------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I  420 (587)
                        |    +.+ |       ...+...+....|+....|..-|.+|.++-.+...+|+.+.+...-+.-  .+...+ +.+
T Consensus       219 vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m--~g~gy~-~n~  295 (402)
T KOG2191|consen  219 VSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTM--AGYGYN-TNI  295 (402)
T ss_pred             ccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccc--cccccc-ccc
Confidence              0    001 0       0123456677889999999999999999999999999999998866622  233344 889


Q ss_pred             cCCHHHHHHHHHHHHHHHh
Q 007844          421 SGEYKNVQNALSEVVGRLR  439 (587)
Q Consensus       421 ~G~~~~V~~A~~~I~~~Lr  439 (587)
                      .|...++..|-.+|..+..
T Consensus       296 ~g~~ls~~aa~g~L~~~~~  314 (402)
T KOG2191|consen  296 LGLGLSILAAEGVLAAKVA  314 (402)
T ss_pred             cchhhhhhhhhhHHHHhhc
Confidence            9999999999998877554

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

Probab=99.85  E-value=8.5e-20  Score=197.76  Aligned_cols=164  Identities=27%  Similarity=0.408  Sum_probs=138.6

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc-
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-  352 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~-  352 (587)
                      .++||+|+...+|.||||+|..||+|+.++.++|+|.+...++.+|+|+|+|+... ...+++++|+.+.++.+..... 
T Consensus        43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~~~~  121 (485)
T KOG2190|consen   43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFKLEE  121 (485)
T ss_pred             ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhcccc
Confidence            35999999999999999999999999999999999999999999999999995322 2567889999999988865311 


Q ss_pred             --cCCCCCC-CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007844          353 --QQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN  429 (587)
Q Consensus       353 --~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~  429 (587)
                        ....+.+ ......++.+|+||.+++|+||||+|+.||+|++.|||+|+|.+. .+|.   .++|.|+|.|.+++|.+
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              1111111 122236899999999999999999999999999999999999986 6665   67788999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 007844          430 ALSEVVGRLRHNL  442 (587)
Q Consensus       430 A~~~I~~~Lr~~~  442 (587)
                      |+..|..+|+++.
T Consensus       198 al~~Is~~L~~~~  210 (485)
T KOG2190|consen  198 ALVQISSRLLENP  210 (485)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999999965

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

Probab=99.60  E-value=3.3e-15  Score=144.94  Aligned_cols=149  Identities=21%  Similarity=0.313  Sum_probs=126.5

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS  207 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~  207 (587)
                      .+.++||+.++.+|.||||+|++||+|+.+++|.|+|..    ....+|+|+|+-+.+-|-.-++.|...|++..     
T Consensus        47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd----s~~peri~tisad~~ti~~ilk~iip~lee~f-----  117 (390)
T KOG2192|consen   47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD----SSGPERILTISADIETIGEILKKIIPTLEEGF-----  117 (390)
T ss_pred             ceeEEEEEecccccceeccccccHHHHhhhccceeeccC----CCCCceeEEEeccHHHHHHHHHHHhhhhhhCC-----
Confidence            689999999999999999999999999999999999976    35579999999999999999999999998731     


Q ss_pred             CcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccc
Q 007844          208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG  287 (587)
Q Consensus       208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~  287 (587)
                                                                                   .+...+.++|+|..+++|.
T Consensus       118 -------------------------------------------------------------~~~~pce~rllihqs~ag~  136 (390)
T KOG2192|consen  118 -------------------------------------------------------------QLPSPCELRLLIHQSLAGG  136 (390)
T ss_pred             -------------------------------------------------------------CCCCchhhhhhhhhhhccc
Confidence                                                                         1123467899999999999


Q ss_pred             cccccchhhHhhhhhcCceEEeeC-CCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc
Q 007844          288 IIGKRGAIVRSLQNASGALISFAA-PLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (587)
Q Consensus       288 IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~  352 (587)
                      |||++|++||++++++.|+.+|.. -.+.+++|+|.|.|..      ..+...+..+.+.+.|..+
T Consensus       137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~------k~v~~~i~~il~~i~e~pi  196 (390)
T KOG2192|consen  137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKP------KRVVECIKIILDLISESPI  196 (390)
T ss_pred             eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCc------chHHHHHHHHHHHhhcCCc
Confidence            999999999999999999999885 4788999999999873      3445555566666666543

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.48  E-value=1.8e-13  Score=130.37  Aligned_cols=138  Identities=17%  Similarity=0.190  Sum_probs=95.5

Q ss_pred             EEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEE---ecCCchhhhhhhccccccccCCCccHHHHHH
Q 007844           29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILV---VGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (587)
Q Consensus        29 iLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I---~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al  105 (587)
                      +.||.+++|.|||++|++|+.|+++|||+|++.+.     +..|.|   +++++.+                 ..|++.+
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i-----------------~kA~~~I   59 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAV-----------------MKAREVV   59 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHH-----------------HHHHHHH
Confidence            45799999999999999999999999999999763     245777   3333332                 2233333


Q ss_pred             HHHHHHHHhhhhccCCCCCCCCceEEEE-Eeec---------ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCC
Q 007844          106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD  175 (587)
Q Consensus       106 ~~i~~~i~~~~~~~~~~~~~~~~vt~rl-lVp~---------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~d  175 (587)
                      ..+..   ....+..- .--...+++++ -|+.         ..+|.|||++|++++.|++.|||+|.|.         +
T Consensus        60 ~~i~~---gf~~e~A~-~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~  126 (172)
T TIGR03665        60 KAIGR---GFSPEKAL-KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G  126 (172)
T ss_pred             HHHHc---CCCHHHHH-HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence            22211   00000000 00001223332 2222         3689999999999999999999999994         3


Q ss_pred             cEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          176 QLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       176 r~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      +.|.|.|++++++.|..+|.+++.+.
T Consensus       127 ~~v~i~G~~~~~~~A~~~i~~li~~~  152 (172)
T TIGR03665       127 KTVGIIGDPEQVQIAREAIEMLIEGA  152 (172)
T ss_pred             CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence            67999999999999999999999653

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=99.46  E-value=4.6e-13  Score=128.56  Aligned_cols=142  Identities=16%  Similarity=0.199  Sum_probs=98.0

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEe----cCCchhhhhhhccccccccCCCccH
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS  100 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~----G~~e~~~~a~~~~~~~~~e~~~~~~  100 (587)
                      +...+-||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|.    ++++..                 ..
T Consensus         3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i-----------------~k   60 (180)
T PRK13763          3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAV-----------------LK   60 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHH-----------------HH
Confidence            567889999999999999999999999999999999863     2556675    333332                 22


Q ss_pred             HHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEE-----ee-----cceeeeeeecCchHHHHHHhhhCCeEEecCCCCC
Q 007844          101 TQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC  170 (587)
Q Consensus       101 A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rll-----Vp-----~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~  170 (587)
                      |++.+..+..   .-..+... ..-.+.+.+++.     .+     ...+|.|||++|++++.|++.|||+|.|..    
T Consensus        61 A~~~I~ai~~---gf~~e~A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----  132 (180)
T PRK13763         61 ARDIVKAIGR---GFSPEKAL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----  132 (180)
T ss_pred             HHHHHHHHhc---CCCHHHHH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----
Confidence            3333222211   00001000 000012222221     11     136899999999999999999999999954    


Q ss_pred             CCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       171 ~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                           +.|.|.|+++++..|...|..++++.
T Consensus       133 -----~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        133 -----KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             -----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence                 45899999999999999999999663

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.45  E-value=4.1e-13  Score=127.98  Aligned_cols=140  Identities=19%  Similarity=0.207  Sum_probs=98.2

Q ss_pred             EEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEe-cCCcCCCCChHHHHHHHHHhhhhcccccCCC
Q 007844          278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISA-LEYLDTRHSPVQNAAVLVFARSVEVEGQQGF  356 (587)
Q Consensus       278 i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG-~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~  356 (587)
                      +.||.+.+|.|||++|++|+.|+++||++|.+++.     +..|.|.. +.+|    ..++.|...|........+...+
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~----~~i~kA~~~I~~i~~gf~~e~A~   72 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP----LAVMKAREVVKAIGRGFSPEKAL   72 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH----HHHHHHHHHHHHHHcCCCHHHHH
Confidence            56899999999999999999999999999999953     24688841 1111    34455555554432210100000


Q ss_pred             CCCCCCCCceEEEEEeCc---------ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHH
Q 007844          357 SSGENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV  427 (587)
Q Consensus       357 ~~g~~~~~~~t~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V  427 (587)
                        ..-.....-.-+.|+.         ..+|+|||++|++++.|++.|||+|.|..            ..|.|.|+++++
T Consensus        73 --~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~  138 (172)
T TIGR03665        73 --KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQV  138 (172)
T ss_pred             --HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHH
Confidence              0000111122234444         47999999999999999999999999952            679999999999


Q ss_pred             HHHHHHHHHHHhh
Q 007844          428 QNALSEVVGRLRH  440 (587)
Q Consensus       428 ~~A~~~I~~~Lr~  440 (587)
                      +.|.++|...|..
T Consensus       139 ~~A~~~i~~li~~  151 (172)
T TIGR03665       139 QIAREAIEMLIEG  151 (172)
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999997754

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=99.40  E-value=2e-12  Score=124.10  Aligned_cols=145  Identities=19%  Similarity=0.228  Sum_probs=99.7

Q ss_pred             EEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccC
Q 007844          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ  354 (587)
Q Consensus       275 ~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~  354 (587)
                      ...+.||.+.+|.|||++|.+|+.|+++||++|++.+.     +..|.|.-...++  ...+..|...+..-......+.
T Consensus         4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d--~~~i~kA~~~I~ai~~gf~~e~   76 (180)
T PRK13763          4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED--PLAVLKARDIVKAIGRGFSPEK   76 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC--HHHHHHHHHHHHHHhcCCCHHH
Confidence            56788999999999999999999999999999999954     2567776211001  1334455555443332100000


Q ss_pred             CCCCCCCCCCceEEE-EEeC---------cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCH
Q 007844          355 GFSSGENKGDAVAVS-ILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY  424 (587)
Q Consensus       355 g~~~g~~~~~~~t~~-l~VP---------~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~  424 (587)
                      .+-  . .......+ +.|.         ...+|+|||++|++++.|++.|||+|.|..            ..|.|.|++
T Consensus        77 A~~--l-~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~  141 (180)
T PRK13763         77 ALR--L-LDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDP  141 (180)
T ss_pred             HHH--H-hCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCH
Confidence            000  0 01111111 1221         147999999999999999999999999953            349999999


Q ss_pred             HHHHHHHHHHHHHHhhc
Q 007844          425 KNVQNALSEVVGRLRHN  441 (587)
Q Consensus       425 ~~V~~A~~~I~~~Lr~~  441 (587)
                      ++++.|...|...++.+
T Consensus       142 ~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        142 EQVEIAREAIEMLIEGA  158 (180)
T ss_pred             HHHHHHHHHHHHHHcCC
Confidence            99999999999988654

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=99.32  E-value=3.7e-12  Score=101.71  Aligned_cols=65  Identities=31%  Similarity=0.534  Sum_probs=59.3

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHH
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVT  195 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~  195 (587)
                      ++||+||.+.+|+||||+|++|++|+++|||+|.+.+. ......+|+|+|+|++++|.+|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence            37899999999999999999999999999999999985 334678999999999999999999873

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=99.32  E-value=3.3e-12  Score=102.04  Aligned_cols=65  Identities=28%  Similarity=0.473  Sum_probs=59.0

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV  435 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~  435 (587)
                      +.+|+||.+.+|+|||++|++|++|+++|||+|++.+..+    ....+|.|+|+|+++++++|+.+|.
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~   65 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLIL   65 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhhC
Confidence            3689999999999999999999999999999999987554    2577899999999999999999983

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

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

Probab=99.24  E-value=5.1e-11  Score=126.69  Aligned_cols=275  Identities=20%  Similarity=0.226  Sum_probs=172.9

Q ss_pred             CCCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccC
Q 007844           16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG   95 (587)
Q Consensus        16 ~~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~   95 (587)
                      +..+...+++.+.+.|++..+-.+|||.|++|+.|++.|+++|.+.+...+ ++++.++.|-+..               
T Consensus        59 ~~e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~---------------  122 (608)
T KOG2279|consen   59 TEEQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQ---------------  122 (608)
T ss_pred             ceecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCC---------------
Confidence            345667789999999999999999999999999999999999999765333 5677777665433               


Q ss_pred             CCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCC
Q 007844           96 GEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD  175 (587)
Q Consensus        96 ~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~d  175 (587)
                        +++|..++..   .+..           +..+...+-+|...++.|+|++|.+++.|+.-++|+|.+..+  .-...+
T Consensus       123 --v~~a~a~~~~---~~~~-----------~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~  184 (608)
T KOG2279|consen  123 --VCKAKAAIHQ---ILTE-----------NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLS  184 (608)
T ss_pred             --CChHHHHHHH---HHhc-----------CCcccccccchhhhcccccccchhhhcchhcccccccccccc--cccccc
Confidence              4555444332   2221           126667789999999999999999999999999999999874  334578


Q ss_pred             cEEEEeecHHHHHHHHHHHHHHHhcCCCCCC-C------CcccCCCccccccCCCCCCCCCCCCC------cCCCCCCCC
Q 007844          176 QLIQITGATLAVKKALVAVTTCLQHLSTMEK-S------PICFNRPIEKVFYSNSSDPHREFFPH------LSLVPPLTG  242 (587)
Q Consensus       176 r~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~-~------~~~~~~P~~~~~~~~~~~~~~~~~p~------~~~~P~~~~  242 (587)
                      +...|.|...-++.|..++.+.+.+.-..-+ .      ..+...|...+. .....+.....+|      .++.|..++
T Consensus       185 ~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~-~~m~~~~~s~~~h~~~~t~~s~spg~~~  263 (608)
T KOG2279|consen  185 RLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRR-EDMTEPGGAGEPHLWKNTSSSMSPGAPL  263 (608)
T ss_pred             cceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccc-hhhcccccCCccccCccchhccCCCCCC
Confidence            9999999999999999999998876421111 0      111111111110 0000000000011      012222111


Q ss_pred             CCCCCCCccCCCCCCCCC--CCCCCC-ccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCC--
Q 007844          243 NPSDNASEFHSSSADADR--DHPGLD-KKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG--  317 (587)
Q Consensus       243 ~~~~y~~~~~p~~~~~~~--~~~~~~-~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~--  317 (587)
                      ...  .++.........+  ..+..+ .........++|-+|...+|.+||+.|++++.+...+++.+.|........  
T Consensus       264 ~~~--eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~  341 (608)
T KOG2279|consen  264 VTK--EGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVL  341 (608)
T ss_pred             ccc--CCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhh
Confidence            110  0000000000000  000000 011223346778899999999999999999999999999999875322221  


Q ss_pred             -ccEEEEEecC
Q 007844          318 -ERVVTISALE  327 (587)
Q Consensus       318 -er~V~IsG~~  327 (587)
                       -.++.+.|+.
T Consensus       342 ~~qic~~egkq  352 (608)
T KOG2279|consen  342 QLQICVNEGKQ  352 (608)
T ss_pred             hhhhheecchh
Confidence             2567777773

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

Probab=99.20  E-value=5.5e-11  Score=126.43  Aligned_cols=230  Identities=18%  Similarity=0.216  Sum_probs=168.0

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME  205 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~  205 (587)
                      ...+.+++.|+...+.+++||.|++|+.|+..++++|.+..+   ....+++..+.|-+.++.+|...+..++.++.   
T Consensus        65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e---d~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~---  138 (608)
T KOG2279|consen   65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE---DVGDERVLLISGFPVQVCKAKAAIHQILTENT---  138 (608)
T ss_pred             hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc---cCCcccchhhccCCCCCChHHHHHHHHHhcCC---
Confidence            346889999999999999999999999999999999999774   22345556666689999999999999996631   


Q ss_pred             CCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccc
Q 007844          206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA  285 (587)
Q Consensus       206 ~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~v  285 (587)
                                                                                         .+...+.+|...+
T Consensus       139 -------------------------------------------------------------------pvk~~lsvpqr~~  151 (608)
T KOG2279|consen  139 -------------------------------------------------------------------PVSEQLSVPQRSV  151 (608)
T ss_pred             -------------------------------------------------------------------cccccccchhhhc
Confidence                                                                               1234456889999


Q ss_pred             cccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc--------------
Q 007844          286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE--------------  351 (587)
Q Consensus       286 G~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~--------------  351 (587)
                      ++|+|++|.+++.|+.-++|+|.+..+......+...|.+..      +....|-..+.+++.++.              
T Consensus       152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qq------k~~~~a~~~~~~~~~edeelv~~~~e~~q~rv  225 (608)
T KOG2279|consen  152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQ------KEVAAAKHLILEKVSEDEELVKRIAESAQTRV  225 (608)
T ss_pred             ccccccchhhhcchhcccccccccccccccccccceeccccc------chHHHHHhhhhccccchhHHhhhchhhcccCC
Confidence            999999999999999999999999977444456777777764      222223333333332210              


Q ss_pred             -------------------------------ccCCCCC-----------------------CC--CCCCceEEEEEeCcc
Q 007844          352 -------------------------------GQQGFSS-----------------------GE--NKGDAVAVSILVGAD  375 (587)
Q Consensus       352 -------------------------------~~~g~~~-----------------------g~--~~~~~~t~~l~VP~~  375 (587)
                                                     ...+.+.                       +.  ......-.+|.||..
T Consensus       226 prk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~  305 (608)
T KOG2279|consen  226 PRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEI  305 (608)
T ss_pred             CCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcc
Confidence                                           0011000                       00  012335567899999


Q ss_pred             cccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHH
Q 007844          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVG  436 (587)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~  436 (587)
                      .+|.|||..|+.++.....|++.+.|--......  --.-.++.+.|+..-+..++.|+..
T Consensus       306 lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~--v~~~qic~~egkqh~~n~vl~ml~~  364 (608)
T KOG2279|consen  306 LSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR--VLQLQICVNEGKQHYENSVLEMLTV  364 (608)
T ss_pred             cccchhhhhhhhhhhhhhccCccceEEeccccch--hhhhhhheecchhHHHHHHHhhhhc
Confidence            9999999999999999999999999875322100  0011568899999999999999884

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.18  E-value=4.2e-11  Score=94.56  Aligned_cols=61  Identities=20%  Similarity=0.330  Sum_probs=55.9

Q ss_pred             EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007844          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV  435 (587)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~  435 (587)
                      .+|.||.+++++|||++|++|++|++.|||+|.|++..       ..++.|+|+|+.++|..|+.+|.
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            57899999999999999999999999999999998743       46799999999999999999873

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

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=99.13  E-value=3.8e-11  Score=94.20  Aligned_cols=60  Identities=27%  Similarity=0.422  Sum_probs=54.9

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV  434 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I  434 (587)
                      |.+|.||.+++++|||++|++|++|+++|||+|+|++.       + ++..|+|+|++++|++|+.+|
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            67899999999999999999999999999999999763       2 356999999999999999987

; 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 ....

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

Probab=99.11  E-value=1.8e-10  Score=90.65  Aligned_cols=59  Identities=15%  Similarity=0.255  Sum_probs=53.7

Q ss_pred             eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 007844          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV  435 (587)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~  435 (587)
                      .+..+.||.+++|+|||++|++|++|+++|||+|.|.+           ++.|.|+|+ .++++.|+.+|.
T Consensus         2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I~   61 (61)
T cd02393           2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMIE   61 (61)
T ss_pred             eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHhC
Confidence            46789999999999999999999999999999999964           467999999 999999999873

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

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

Probab=99.06  E-value=4e-10  Score=89.20  Aligned_cols=62  Identities=26%  Similarity=0.489  Sum_probs=56.6

Q ss_pred             EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007844          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV  434 (587)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I  434 (587)
                      .+|.||.+++++|||++|++|++|++.|||+|.|+....     ...++.|+|.|+.+++..|+.+|
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            579999999999999999999999999999999987543     35789999999999999999887

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=99.04  E-value=2e-10  Score=90.07  Aligned_cols=60  Identities=23%  Similarity=0.418  Sum_probs=54.7

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I  194 (587)
                      |.+|.||.+++++|||++|++|++|+++|||+|.|...    + .+..|+|+|+.++|.+|+.+|
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            67899999999999999999999999999999999762    2 445999999999999999886

; 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=99.03  E-value=4e-10  Score=88.96  Aligned_cols=60  Identities=27%  Similarity=0.354  Sum_probs=55.2

Q ss_pred             EEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (587)
Q Consensus       131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I  194 (587)
                      .+|.||..++++|||++|++|++|+++|||+|.|...    ...++.|+|+|+.++|.+|+.+|
T Consensus         2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~----~~~~~~v~I~G~~~~v~~A~~~i   61 (62)
T cd02394           2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP----GSKSDTITITGPKENVEKAKEEI   61 (62)
T ss_pred             eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC----CCCCCEEEEEcCHHHHHHHHHHh
Confidence            4689999999999999999999999999999999773    25789999999999999999886

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=98.99  E-value=2.2e-09  Score=123.33  Aligned_cols=288  Identities=17%  Similarity=0.154  Sum_probs=196.1

Q ss_pred             CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      ..+..++.+-......+||++|.+++.++.++.+.|++++.....  ....|.|......                 .+.
T Consensus       199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~~-----------------~~~  259 (753)
T KOG2208|consen  199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSSS-----------------SIN  259 (753)
T ss_pred             eeEEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhccccccce-----------------ehh
Confidence            357888999999999999999999999999999999998753322  2233444332210                 011


Q ss_pred             HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEee
Q 007844          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG  182 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G  182 (587)
                      --+...+.++.             .+....+.++....-.++|..|..+..|+...--...+.+.   +.+.+..+.+.|
T Consensus       260 ~~i~~~~~~le-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---~~s~~~~~~~~~  323 (753)
T KOG2208|consen  260 VEIQEALTRLE-------------SEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---YPSKDDSIVLSG  323 (753)
T ss_pred             hhhHHHHHHhc-------------ChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---ccccceeEeecc
Confidence            11111222221             12333466777777889999999999999887655555542   344667788888


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007844          183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH  262 (587)
Q Consensus       183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~  262 (587)
                      ....+..+...-...+....                                                            
T Consensus       324 ~~~~~~~~~~~~~~~~~~~~------------------------------------------------------------  343 (753)
T KOG2208|consen  324 FEVGAVLAKRDKTLLLKNSE------------------------------------------------------------  343 (753)
T ss_pred             cccchhhhhhHHHHHHHHhh------------------------------------------------------------
Confidence            87777766655444443310                                                            


Q ss_pred             CCCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHH
Q 007844          263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVL  342 (587)
Q Consensus       263 ~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~  342 (587)
                              .......+.+-...+..|+||+|.+|.+|++++.+.+.+..  .++....++++|..      .....|...
T Consensus       344 --------~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~------~~~~ka~~~  407 (753)
T KOG2208|consen  344 --------ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVS------ANDEKAVED  407 (753)
T ss_pred             --------ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccc------cchhHHHHH
Confidence                    11235556788899999999999999999999999999986  23456678888874      222334433


Q ss_pred             HHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhC-CeEEEcCCCcccccCCCCCcEEEEc
Q 007844          343 VFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTG-TDIKLVGGEQVLGCAAQNDVVIQIS  421 (587)
Q Consensus       343 i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG-a~I~i~~~~~~p~~~~~~~r~V~I~  421 (587)
                      +.....+-.           .......+.+|...+.+|||.+|..|++|...+| .+|+.+..       ......+++.
T Consensus       408 v~~~~~ei~-----------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-------~~~~~~~~~~  469 (753)
T KOG2208|consen  408 VEKIIAEIL-----------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-------NNSSDMVTIR  469 (753)
T ss_pred             HHHHHHhhh-----------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-------CcccccceEe
Confidence            333332210           1145677999999999999999999999999999 66666553       2345667888


Q ss_pred             CCHHHHHHHHHHHHHHHh
Q 007844          422 GEYKNVQNALSEVVGRLR  439 (587)
Q Consensus       422 G~~~~V~~A~~~I~~~Lr  439 (587)
                      |....+..++.+......
T Consensus       470 ~~~~dv~~~~~~~~~~~~  487 (753)
T KOG2208|consen  470 GISKDVEKSVSLLKALKA  487 (753)
T ss_pred             ccccccchhHHHHHhhhh
Confidence            887777776666654443

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

Probab=98.97  E-value=2.2e-09  Score=84.57  Aligned_cols=58  Identities=26%  Similarity=0.343  Sum_probs=52.8

Q ss_pred             eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHH
Q 007844          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV  194 (587)
Q Consensus       129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I  194 (587)
                      .+..+-||.+++|+||||+|++|++|+++|||+|.|..        ++.|.|+|+ .+++.+|+.+|
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            45678899999999999999999999999999999965        467999999 99999999886

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

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

Probab=98.97  E-value=1.9e-09  Score=85.23  Aligned_cols=62  Identities=31%  Similarity=0.532  Sum_probs=56.2

Q ss_pred             EEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007844          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (587)
Q Consensus       131 ~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I  194 (587)
                      .++.||..++++|||++|++|++|+++|||+|.|...  .....++.|.|.|..+++..|+.+|
T Consensus         2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~--~~~~~~~~v~i~G~~~~v~~a~~~i   63 (64)
T cd00105           2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDS--GSGSEERIVTITGTPEAVEKAKELI   63 (64)
T ss_pred             EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCC--CCCCCceEEEEEcCHHHHHHHHHHh
Confidence            5799999999999999999999999999999999873  2246789999999999999999876

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.

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.89  E-value=3.4e-09  Score=121.79  Aligned_cols=301  Identities=16%  Similarity=0.165  Sum_probs=196.9

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHH
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA  104 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~A  104 (587)
                      ....+-+-......|+||+|.+|.+|+++++|.|.+...  +..+..+.+++..+++                 ..|.+.
T Consensus       347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~-----------------~ka~~~  407 (753)
T KOG2208|consen  347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND-----------------EKAVED  407 (753)
T ss_pred             eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch-----------------hHHHHH
Confidence            445556677889999999999999999999999999874  4566789999888763                 445566


Q ss_pred             HHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhC-CeEEecCCCCCCCCCCcEEEEeec
Q 007844          105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESG-AKIVMLPPPACAAIDDQLIQITGA  183 (587)
Q Consensus       105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etG-a~I~I~~~p~~~~~~dr~V~I~G~  183 (587)
                      +..++..+...            .+.-.+++|...+..|||.+|..|..|..++| ..|....    .......+++.|.
T Consensus       408 v~~~~~ei~n~------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~----~~~~~~~~~~~~~  471 (753)
T KOG2208|consen  408 VEKIIAEILNS------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN----NNNSSDMVTIRGI  471 (753)
T ss_pred             HHHHHHhhhcc------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC----CCcccccceEecc
Confidence            66655554331            34455899999999999999999999999999 5555544    2345556788888


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCC
Q 007844          184 TLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHP  263 (587)
Q Consensus       184 ~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~  263 (587)
                      ...+..+..+...+........                                                          
T Consensus       472 ~~dv~~~~~~~~~~~~~a~~~~----------------------------------------------------------  493 (753)
T KOG2208|consen  472 SKDVEKSVSLLKALKADAKNLK----------------------------------------------------------  493 (753)
T ss_pred             ccccchhHHHHHhhhhhhhcch----------------------------------------------------------
Confidence            8888887766665554321100                                                          


Q ss_pred             CCCccCCCcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHH
Q 007844          264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV  343 (587)
Q Consensus       264 ~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i  343 (587)
                            .....+.+...|..+.+..+|+.|..+....++....+..+     ..+..++|.|...      .+.+|...+
T Consensus       494 ------~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~i~i~gk~~------~v~~a~~~L  556 (753)
T KOG2208|consen  494 ------FRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEKITIEGKLE------LVLEAPAEL  556 (753)
T ss_pred             ------hhhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccceeeeccccc------chhhhHHHH
Confidence                  01122334556777777777777776666665555433322     3456788888752      222333333


Q ss_pred             HhhhhcccccCCCCCCCCCCCceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC
Q 007844          344 FARSVEVEGQQGFSSGENKGDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG  422 (587)
Q Consensus       344 ~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G  422 (587)
                      ...+...            .......+.+|. .+.-++++++....+..+...|+.+.+++.       ....+.++|.|
T Consensus       557 ~~~~~~~------------~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~-------~~~~~e~~i~g  617 (753)
T KOG2208|consen  557 KALIEAL------------IKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRS-------PTSSDEVSIKG  617 (753)
T ss_pred             Hhcchhh------------hhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCC-------CCchhhhccch
Confidence            3333111            112233444454 455566666666666666666678877763       34566899999


Q ss_pred             CHHHHHHHHHHHHHHHh---hcccCccccccCCCC
Q 007844          423 EYKNVQNALSEVVGRLR---HNLKSGEILNEARPR  454 (587)
Q Consensus       423 ~~~~V~~A~~~I~~~Lr---~~~~~~~~~~~~~~~  454 (587)
                      ....++.|...+.....   .+...+-+++....+
T Consensus       618 ~~~~v~aa~~~~~~i~~~~~~~~~~~~~i~~~~~~  652 (753)
T KOG2208|consen  618 AKDEVKAAKGRLEEIVEYLSAYATTNTKIPDKFHR  652 (753)
T ss_pred             hHHHHHHhhccchhhhhhcccccceeeecccccce
Confidence            99999999988877555   344444344333333

>PF13014 KH_3: KH domain

Probab=98.83  E-value=5.9e-09  Score=76.07  Aligned_cols=42  Identities=40%  Similarity=0.727  Sum_probs=38.5

Q ss_pred             ccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEec
Q 007844           35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG   76 (587)
Q Consensus        35 ~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G   76 (587)
                      ++|+|||++|++|++|+++|||+|+|++ ..++..+|+|+|+|
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            4799999999999999999999999988 55678899999987

>PF13014 KH_3: KH domain

Probab=98.79  E-value=7e-09  Score=75.68  Aligned_cols=43  Identities=33%  Similarity=0.630  Sum_probs=37.9

Q ss_pred             cccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC
Q 007844          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG  422 (587)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G  422 (587)
                      +||+|||++|++|++|+++|||+|+|++. ..   ....++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~-~~---~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPPE-NE---PGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECCc-cC---CCCCceEEEEEC
Confidence            58999999999999999999999999982 21   357899999998

>smart00322 KH K homology RNA-binding domain

Probab=98.76  E-value=3.7e-08  Score=78.02  Aligned_cols=68  Identities=29%  Similarity=0.521  Sum_probs=60.4

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr  439 (587)
                      ..+.++.||.++++++||++|++|++|++.||++|.+....       .....|+|.|+.++++.|+.+|...++
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            35789999999999999999999999999999999997532       257899999999999999999988763

>smart00322 KH K homology RNA-binding domain

Probab=98.67  E-value=1.2e-07  Score=74.97  Aligned_cols=67  Identities=27%  Similarity=0.487  Sum_probs=60.3

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      .++.++.||...++.+||++|++|++|++++|++|.+...    .....++.|.|+.+++..|..+|.+.+
T Consensus         2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~----~~~~~~v~i~g~~~~v~~a~~~i~~~~   68 (69)
T smart00322        2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED----GSEERVVEITGPPENVEKAAELILEIL   68 (69)
T ss_pred             ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC----CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999999999999763    225789999999999999999998876

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

Probab=98.60  E-value=2.8e-07  Score=87.71  Aligned_cols=141  Identities=16%  Similarity=0.208  Sum_probs=98.6

Q ss_pred             CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCc---hhh--hhh---hcccccccc
Q 007844           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGS---IDR--RIM---FCENDVVVE   94 (587)
Q Consensus        23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e---~~~--~a~---~~~~~~~~e   94 (587)
                      ....+.+.+|.+..+.+||+.|++.+.|.+.++++|.++.     .+..|.|.....   ...  +|.   ..++..   
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---   77 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG---   77 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC---
Confidence            4456779999999999999999999999999999999953     456788876532   111  000   001111   


Q ss_pred             CCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEE-----ee------cceeeeeeecCchHHHHHHhhhCCeEE
Q 007844           95 GGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN------TTKIGVVVGKGGRNVTRMRIESGAKIV  163 (587)
Q Consensus        95 ~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rll-----Vp------~~~vG~IIGkgG~~Ik~I~~etGa~I~  163 (587)
                         +++- +|+.. ++.                .+.|.+.     +.      ....|+|||++|.+-+.|++-|||+|.
T Consensus        78 ---F~pe-~A~~L-L~d----------------~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~  136 (194)
T COG1094          78 ---FPPE-KALKL-LED----------------DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYIS  136 (194)
T ss_pred             ---CCHH-HHHHH-hcC----------------CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEE
Confidence               1111 11111 100                2222211     11      124599999999999999999999999


Q ss_pred             ecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          164 MLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       164 I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      |.         +..|.|-|.+++|+.|...|..++...
T Consensus       137 V~---------g~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         137 VY---------GKTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             Ee---------CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence            94         468999999999999999999999764

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

Probab=98.48  E-value=1.1e-06  Score=83.76  Aligned_cols=143  Identities=19%  Similarity=0.226  Sum_probs=98.6

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ  353 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~  353 (587)
                      ....+.||.+..+.+||+.|...+.|.+.+++++.++..     +..|+|..++.-.++ ...+.|...+..      +.
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~Dp-~~~~ka~d~VkA------Ig   75 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDP-LALLKARDVVKA------IG   75 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCCh-HHHHHHHHHHHH------Hh
Confidence            356688999999999999999999999999999999833     456888776311111 122233222211      12


Q ss_pred             CCCCCC----CCCCCceEEEEEe------C----cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEE
Q 007844          354 QGFSSG----ENKGDAVAVSILV------G----ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ  419 (587)
Q Consensus       354 ~g~~~g----~~~~~~~t~~l~V------P----~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~  419 (587)
                      .|+++.    +-.....-..+.+      +    ....|+|||++|.+.+-|++.|||.|-|..            .+|.
T Consensus        76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVa  143 (194)
T COG1094          76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVA  143 (194)
T ss_pred             cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEE
Confidence            233320    0001111111111      1    236799999999999999999999999963            6799


Q ss_pred             EcCCHHHHHHHHHHHHHHHhh
Q 007844          420 ISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       420 I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      |-|.+++|+.|.+.|...+..
T Consensus       144 iiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         144 IIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             EecChhhhHHHHHHHHHHHcC
Confidence            999999999999999998775

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

Probab=98.11  E-value=6.5e-06  Score=73.71  Aligned_cols=68  Identities=19%  Similarity=0.370  Sum_probs=53.7

Q ss_pred             ccccccccCCCchhHHHHHhhCCeEEEcCCCcc-----------ccc-CCCCCcEEEEcCCH---HHHHHHHHHHHHHHh
Q 007844          375 DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGC-AAQNDVVIQISGEY---KNVQNALSEVVGRLR  439 (587)
Q Consensus       375 ~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~-----------p~~-~~~~~r~V~I~G~~---~~V~~A~~~I~~~Lr  439 (587)
                      +++|.|||++|++||+|+++|||+|.|..+...           |.+ ..++.-.|.|++..   +++++|+.+|...|.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            689999999999999999999999999875210           111 12344789999975   899999999999888


Q ss_pred             hcc
Q 007844          440 HNL  442 (587)
Q Consensus       440 ~~~  442 (587)
                      ...
T Consensus        95 ~~~   97 (120)
T cd02395          95 PAI   97 (120)
T ss_pred             cCC
Confidence            543

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=98.06  E-value=1.7e-05  Score=71.07  Aligned_cols=64  Identities=25%  Similarity=0.352  Sum_probs=51.7

Q ss_pred             ceeeeeeecCchHHHHHHhhhCCeEEecCC-CC--------------CCCCCCcEEEEeecH---HHHHHHHHHHHHHHh
Q 007844          138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PA--------------CAAIDDQLIQITGAT---LAVKKALVAVTTCLQ  199 (587)
Q Consensus       138 ~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~--------------~~~~~dr~V~I~G~~---e~V~~A~~~I~~~L~  199 (587)
                      +.+|.|||++|++||+|+++|||+|.|..+ ..              .....+-.|.|++..   +++.+|+.+|..++.
T Consensus        15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~   94 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK   94 (120)
T ss_pred             CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999864 00              001223578899975   999999999999997


Q ss_pred             cC
Q 007844          200 HL  201 (587)
Q Consensus       200 e~  201 (587)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            53

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=97.93  E-value=2.6e-05  Score=71.87  Aligned_cols=102  Identities=13%  Similarity=0.122  Sum_probs=69.1

Q ss_pred             EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHH
Q 007844           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (587)
Q Consensus        26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al  105 (587)
                      .+.++|+...+|+.||++|++|+.|++..|-+|+|-....+           ++                          
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-----------~~--------------------------   75 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-----------PE--------------------------   75 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-----------HH--------------------------
Confidence            45678899999999999999999999999988887442111           00                          


Q ss_pred             HHHHHHHHhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEec
Q 007844          106 IRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (587)
Q Consensus       106 ~~i~~~i~~~~~~~~~-~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~  165 (587)
                       ..+..+.....-.+- -...+....+.+.|+....|.+|||+|++|+.++.-++-++.|.
T Consensus        76 -~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         76 -EFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             -HHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence             011111110000000 00011235667789999999999999999999999999887763

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

Probab=97.90  E-value=1.2e-05  Score=80.72  Aligned_cols=149  Identities=18%  Similarity=0.253  Sum_probs=104.7

Q ss_pred             cceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHh---hhh
Q 007844          272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV  348 (587)
Q Consensus       272 ~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~---~v~  348 (587)
                      +.++..+.||..+++.|.|++|.+||.|+.+|...|+-+...   .+-++.++|..  +    -+..|-..|..   .+.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~--e----dv~~aRrei~saaeH~~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRH--E----DVRRARREIPSAAEHFG   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCc--h----hHHHHhhcCccccceee
Confidence            566777889999999999999999999999999998766331   23567888873  1    11122221111   000


Q ss_pred             cccccCCCC---CCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH
Q 007844          349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK  425 (587)
Q Consensus       349 e~~~~~g~~---~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~  425 (587)
                      --...+.+.   .+...+.+.+..+.+|-+.+|.+.|..|.+|+.||+.+...|.-+-+        ..+.++-++|.+.
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 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPK  166 (394)
T ss_pred             eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCc
Confidence            000001111   12233567888999999999999999999999999999999987653        4578899999999


Q ss_pred             H-HHHHH-HHHHHH
Q 007844          426 N-VQNAL-SEVVGR  437 (587)
Q Consensus       426 ~-V~~A~-~~I~~~  437 (587)
                      + +++|. ..|...
T Consensus       167 nC~kra~s~eie~t  180 (394)
T KOG2113|consen  167 NCVKRARSCEIEQT  180 (394)
T ss_pred             chhhhccccchhhh
Confidence            8 77776 555543

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

Probab=97.66  E-value=8.3e-05  Score=74.87  Aligned_cols=154  Identities=18%  Similarity=0.185  Sum_probs=109.0

Q ss_pred             CCCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccC
Q 007844           16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG   95 (587)
Q Consensus        16 ~~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~   95 (587)
                      .+...+ +.++..+-||...++.|.|++|-+||.|+.+|...|+-+-.   -.|-+..++|..+.+++|..++.-.    
T Consensus        18 ~~~~~p-~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~edv~~aRrei~sa----   89 (394)
T KOG2113|consen   18 YRTSIG-QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHEDVRRARREIPSA----   89 (394)
T ss_pred             cCCCCC-CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCchhHHHHhhcCccc----
Confidence            333444 88899999999999999999999999999999999986432   1346788899999988887765321    


Q ss_pred             CCccHHHHHHHHHHHHHHhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCC
Q 007844           96 GEVSSTQEAVIRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID  174 (587)
Q Consensus        96 ~~~~~A~~Al~~i~~~i~~~~~~~~~-~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~  174 (587)
                           |    .++-..+.......+- ........+...-+|-..+|.|.|..|.+|++|++.++..|.-.-  .|   .
T Consensus        90 -----a----eH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v--~~---~  155 (394)
T KOG2113|consen   90 -----A----EHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV--RC---G  155 (394)
T ss_pred             -----c----ceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec--cC---C
Confidence                 1    0100000000000000 011234566777889999999999999999999999999988766  23   6


Q ss_pred             CcEEEEeecHHH-HHHHH
Q 007844          175 DQLIQITGATLA-VKKAL  191 (587)
Q Consensus       175 dr~V~I~G~~e~-V~~A~  191 (587)
                      +-+..++|-+.+ +.+|.
T Consensus       156 ~~Vf~Vtg~~~nC~kra~  173 (394)
T KOG2113|consen  156 EPVFCVTGAPKNCVKRAR  173 (394)
T ss_pred             CceEEEecCCcchhhhcc
Confidence            678889999888 44444

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.65  E-value=0.00017  Score=82.11  Aligned_cols=93  Identities=13%  Similarity=0.205  Sum_probs=71.1

Q ss_pred             ChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCC
Q 007844          334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ  413 (587)
Q Consensus       334 ~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~  413 (587)
                      ..+.++...|++.+.+....+   ...........++.||.+++|.|||+||.+||+|+++|||+|.|.+          
T Consensus       549 ~~A~~g~~~Il~~m~~al~~p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------  615 (719)
T TIGR02696       549 KQARDARLAILDVMAEAIDTP---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----------  615 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHhCc---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence            344566666766665432222   1122345678889999999999999999999999999999999853          


Q ss_pred             CCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          414 NDVVIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       414 ~~r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                       +..|.|.+ +.+.+++|+.+|...++.
T Consensus       616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 -DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence             57788887 567899999999998884

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.62  E-value=0.00025  Score=80.69  Aligned_cols=93  Identities=18%  Similarity=0.228  Sum_probs=73.0

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..+++..+.+..... .+-....+....+.||.+.++.|||+||.+||.|.++|||+|.|..        +..|
T Consensus       549 ~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~V  619 (719)
T TIGR02696       549 KQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGTV  619 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcEE
Confidence            456667777766655443333 2222334667788999999999999999999999999999999954        5778


Q ss_pred             EEeec-HHHHHHHHHHHHHHHhc
Q 007844          179 QITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .|.+. .+++.+|+.+|..++..
T Consensus       620 ~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       620 YIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             EEEeCCHHHHHHHHHHHHHhhCc
Confidence            88886 99999999999999974

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=97.59  E-value=0.00026  Score=65.21  Aligned_cols=102  Identities=16%  Similarity=0.163  Sum_probs=71.2

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhh--hccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVE  351 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v--~e~~  351 (587)
                      ..+.++|+...+|..||++|++|+.|++..|-+|.+-.-..+                    ..+-+..++..+  .+..
T Consensus        32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d--------------------~~~fI~n~l~Pa~V~~v~   91 (140)
T PRK08406         32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD--------------------PEEFIKNIFAPAAVRSVT   91 (140)
T ss_pred             CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC--------------------HHHHHHHHcCCCEEEEEE
Confidence            366788999999999999999999999999988877642111                    011111111111  0000


Q ss_pred             ccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844          352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (587)
Q Consensus       352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~  402 (587)
                      ..       .........+.|+.+..|..|||+|++|+.++..+|-++.|.
T Consensus        92 I~-------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         92 IK-------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             EE-------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            00       012345677889999999999999999999999999998774

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.41  E-value=0.00045  Score=63.57  Aligned_cols=102  Identities=14%  Similarity=0.152  Sum_probs=68.5

Q ss_pred             EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHHH
Q 007844           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEA  104 (587)
Q Consensus        26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~A  104 (587)
                      -+=++|....+|+.||++|++|+.|++..|-+|+|-+...+           ++. +.+             .++||.  
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-----------~~~fI~N-------------~l~PA~--   87 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-----------LEEFVAN-------------KLAPAE--   87 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-----------HHHHHHH-------------cCCCce--
Confidence            44467788899999999999999999988988887442111           111 000             011110  


Q ss_pred             HHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEec
Q 007844          105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (587)
Q Consensus       105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~  165 (587)
                             +.....     ...++.....+.|+..+.+..|||+|++|+..++-++-++.|.
T Consensus        88 -------V~~V~i-----~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        88 -------VKNVTV-----SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             -------EEEEEE-----EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence                   000000     0011245677889999999999999999999999999887763

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=97.27  E-value=0.00076  Score=77.76  Aligned_cols=94  Identities=21%  Similarity=0.267  Sum_probs=69.6

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..++++.+.....+...+...-.+....+-||.+.++.|||+||++||+|.++|||+|.|..        +..|
T Consensus       521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------dG~V  592 (684)
T TIGR03591       521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------DGTV  592 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------CeEE
Confidence            34555666666655544333222222334667788999999999999999999999999999999954        4667


Q ss_pred             EEeec-HHHHHHHHHHHHHHHhc
Q 007844          179 QITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .|.+. .+.+.+|..+|..+..+
T Consensus       593 ~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       593 KIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             EEEECcHHHHHHHHHHHHhhhcc
Confidence            77765 88999999999988653

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

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

Probab=97.18  E-value=0.0017  Score=69.59  Aligned_cols=73  Identities=19%  Similarity=0.259  Sum_probs=59.0

Q ss_pred             ceEEEEEeec------ceeeeeeecCchHHHHHHhhhCCeEEecCC----C--------C--CCCCCCcEEEEeec-HHH
Q 007844          128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP----P--------A--CAAIDDQLIQITGA-TLA  186 (587)
Q Consensus       128 ~vt~rllVp~------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~----p--------~--~~~~~dr~V~I~G~-~e~  186 (587)
                      .++.|+.||.      +.+|+|||.+|.|.|+|+++|||+|.|..+    +        .  -....+=-|.|+++ .|.
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            6778888886      489999999999999999999999999863    0        0  11123345788888 889


Q ss_pred             HHHHHHHHHHHHhc
Q 007844          187 VKKALVAVTTCLQH  200 (587)
Q Consensus       187 V~~A~~~I~~~L~e  200 (587)
                      |.+|+..|..+|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999986

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.13  E-value=0.0011  Score=76.62  Aligned_cols=67  Identities=18%  Similarity=0.298  Sum_probs=56.6

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                      ......++.||.+.++.|||+||++||+|+++|||+|.|.+           +-.|.|.+ ..+.+++|..+|......
T Consensus       548 ~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       548 YAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             cCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            35678889999999999999999999999999999999954           35566665 566899999999887664

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).

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.03  E-value=0.0014  Score=60.28  Aligned_cols=101  Identities=14%  Similarity=0.124  Sum_probs=69.4

Q ss_pred             EEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhcccc
Q 007844          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG  352 (587)
Q Consensus       275 ~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~~  352 (587)
                      .+-++|....+|..||++|.+|+.|++..|-+|.+-.-..+..                    +-+..++  .++.....
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~--------------------~fI~N~l~PA~V~~V~i   93 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLE--------------------EFVANKLAPAEVKNVTV   93 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCHH--------------------HHHHHcCCCceEEEEEE
Confidence            5557789999999999999999999988898887764211100                    0000000  00000000


Q ss_pred             cCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEc
Q 007844          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (587)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~  402 (587)
                      .       .........+.||.+..+..|||+|++|+...+.+|-++.|.
T Consensus        94 ~-------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~  136 (141)
T TIGR01952        94 S-------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID  136 (141)
T ss_pred             E-------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence            0       012345678999999999999999999999999999988764

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.

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.78  E-value=0.0044  Score=59.90  Aligned_cols=101  Identities=19%  Similarity=0.250  Sum_probs=66.8

Q ss_pred             EEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHH
Q 007844           28 RLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIR  107 (587)
Q Consensus        28 riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~  107 (587)
                      -..+-.+.+|..||++|++|+.|+++.|-+|+|-...++           ++.                   ...+||.-
T Consensus        79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~P  128 (190)
T COG0195          79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALAP  128 (190)
T ss_pred             EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcCc
Confidence            334445778999999999999999999977877433211           100                   01111110


Q ss_pred             HHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844          108 VFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (587)
Q Consensus       108 i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~  166 (587)
                      +  ++......     ..+.. ...+.||.++.+..|||+|.+++.+.+-||-++.|..
T Consensus       129 a--~v~~V~~~-----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         129 A--EVLSVNIK-----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             c--eEeEEEEE-----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            0  00000000     00112 7788899999999999999999999999999999965

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.72  E-value=0.0027  Score=74.03  Aligned_cols=94  Identities=14%  Similarity=0.195  Sum_probs=71.5

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCe-EEecCCCCCCCCCCcE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQL  177 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~-I~I~~~p~~~~~~dr~  177 (587)
                      ..|.++..+++..+.+.....-.+-....+....|-||.+.++.|||.||.+||.|.++||++ |.+..        +-.
T Consensus       655 ~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg~  726 (891)
T PLN00207        655 LQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DGT  726 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Cee
Confidence            456667777766655443222111222346778899999999999999999999999999999 88854        467


Q ss_pred             EEEeec-HHHHHHHHHHHHHHHhc
Q 007844          178 IQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       178 V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      |.|.+. .+.+.+|+.+|..++.+
T Consensus       727 V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        727 VKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhcC
Confidence            888885 99999999999999864

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

Probab=96.66  E-value=0.004  Score=69.73  Aligned_cols=99  Identities=13%  Similarity=0.161  Sum_probs=74.4

Q ss_pred             ChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCC
Q 007844          334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ  413 (587)
Q Consensus       334 ~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~  413 (587)
                      .++..|.++|+..+.+....+ . ...........++.|+.+.++-+||++|.+|++|.++|||+|.|.           
T Consensus       522 ~QAk~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------  588 (692)
T COG1185         522 EQAKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------  588 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------
Confidence            445566667777775432111 0 001123456778899999999999999999999999999999995           


Q ss_pred             CCcEEEEcCCH-HHHHHHHHHHHHHHhhcccCc
Q 007844          414 NDVVIQISGEY-KNVQNALSEVVGRLRHNLKSG  445 (587)
Q Consensus       414 ~~r~V~I~G~~-~~V~~A~~~I~~~Lr~~~~~~  445 (587)
                      ++-+|.|.++. +.+++|+..|.+.+++..+..
T Consensus       589 ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~  621 (692)
T COG1185         589 DDGTVKIAASDGESAKKAKERIEAITREVEVGE  621 (692)
T ss_pred             CCCcEEEEecchHHHHHHHHHHHHHHhhccccc
Confidence            25678888888 679999999999999877654

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

Probab=96.61  E-value=0.0024  Score=67.20  Aligned_cols=67  Identities=18%  Similarity=0.292  Sum_probs=55.8

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr  439 (587)
                      ....-+.|-+++||.+||++|+.|+.||..|.++|+|.+.        +.+..|+|.|...--.+|+..|..-++
T Consensus        46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence            3445567888999999999999999999999999999874        348899999999988888777755443

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

Probab=96.57  E-value=0.0049  Score=66.09  Aligned_cols=76  Identities=17%  Similarity=0.335  Sum_probs=57.6

Q ss_pred             ceEEEEEeCc------ccccccccCCCchhHHHHHhhCCeEEEcCC---------Cccccc--CCCCCcEEEEcCCH-HH
Q 007844          365 AVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGG---------EQVLGC--AAQNDVVIQISGEY-KN  426 (587)
Q Consensus       365 ~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~---------~~~p~~--~~~~~r~V~I~G~~-~~  426 (587)
                      ..+.+|.||-      ++||.|||..|.|.|+|+++|||+|.|-.+         .+.+.+  ..+++--+.|+.+. ++
T Consensus       137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek  216 (554)
T KOG0119|consen  137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK  216 (554)
T ss_pred             ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence            5677777774      689999999999999999999999999761         111111  13445567777765 47


Q ss_pred             HHHHHHHHHHHHhh
Q 007844          427 VQNALSEVVGRLRH  440 (587)
Q Consensus       427 V~~A~~~I~~~Lr~  440 (587)
                      |++|..+|...|.+
T Consensus       217 i~~Ai~vienli~~  230 (554)
T KOG0119|consen  217 IKKAIAVIENLIQS  230 (554)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999888885

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.54  E-value=0.0045  Score=72.28  Aligned_cols=92  Identities=14%  Similarity=0.181  Sum_probs=66.9

Q ss_pred             HHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCe-EEEcCCCcccccCCCC
Q 007844          336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQN  414 (587)
Q Consensus       336 a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~i~~~~~~p~~~~~~  414 (587)
                      +.++...|++.|.+....+ .. ...........+.||.++++.|||.||.+||+|+++||++ |.+.+           
T Consensus       657 A~~g~~~Il~~M~~~i~~p-r~-~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-----------  723 (891)
T PLN00207        657 AKDGRKHILAEMSKCSPPP-SK-RLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-----------  723 (891)
T ss_pred             HHHHHHHHHHHHHHHHhhh-hh-hhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------
Confidence            4455555666654432111 00 1123456788899999999999999999999999999999 86643           


Q ss_pred             CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          415 DVVIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       415 ~r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                      +-.|.|.+ +.+.+++|+.+|.....+
T Consensus       724 dg~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        724 DGTVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            56788877 667899999999988764

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

Probab=96.51  E-value=0.0017  Score=68.38  Aligned_cols=67  Identities=21%  Similarity=0.281  Sum_probs=54.2

Q ss_pred             CCCCCCCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhh
Q 007844           17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMF   86 (587)
Q Consensus        17 ~~~~~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~   86 (587)
                      +-....+++.+++-+-+.+||.|||++|++|+.||..|+++|++...   ..|-.|+|.|..+-..+|+.
T Consensus        39 ~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka  105 (629)
T KOG0336|consen   39 SAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKA  105 (629)
T ss_pred             ccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHh
Confidence            44566678999999999999999999999999999999999999653   34567888887654444433

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

Probab=96.49  E-value=0.012  Score=58.76  Aligned_cols=81  Identities=20%  Similarity=0.292  Sum_probs=58.2

Q ss_pred             CCceEEEEEeCc------ccccccccCCCchhHHHHHhhCCeEEEcCCCc------------ccccCC---CCCcEEEEc
Q 007844          363 GDAVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ------------VLGCAA---QNDVVIQIS  421 (587)
Q Consensus       363 ~~~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~------------~p~~~~---~~~r~V~I~  421 (587)
                      ....+.+|+||-      ++||+|+|+.|.++|+++++|||+|-|-.+.-            .|+|..   .--.+|+..
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~  168 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE  168 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence            456888899886      49999999999999999999999999976432            233322   123677888


Q ss_pred             CCHHHHHHHHHHHHHHHhhccc
Q 007844          422 GEYKNVQNALSEVVGRLRHNLK  443 (587)
Q Consensus       422 G~~~~V~~A~~~I~~~Lr~~~~  443 (587)
                      .++..+..=+..-.+.|+++++
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcC
Confidence            8887766644444555555553

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

Probab=96.49  E-value=0.0028  Score=63.34  Aligned_cols=40  Identities=20%  Similarity=0.500  Sum_probs=36.1

Q ss_pred             CCcEEEEEEeccC------ccceeccCCChHHHHHHhHhCceEEEe
Q 007844           22 DDVVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE   61 (587)
Q Consensus        22 ~~~v~~riLvP~~------~vG~IIGk~G~~Ik~IreeTga~I~V~   61 (587)
                      +-.++.||+||.+      +||+|+|.+|.++|+|+++|+|+|.|-
T Consensus        89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            3466889999996      799999999999999999999999995

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

Probab=96.43  E-value=0.011  Score=66.39  Aligned_cols=95  Identities=20%  Similarity=0.240  Sum_probs=71.5

Q ss_pred             ccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcE
Q 007844           98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL  177 (587)
Q Consensus        98 ~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~  177 (587)
                      +..|..|-++++..+.+.-.+...+...-.+-...+-|+...+.-+||++|.+|++|.++|||+|.|..        |..
T Consensus       521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------dGt  592 (692)
T COG1185         521 LEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------DGT  592 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--------CCc
Confidence            345667777777666544332211111222445667889999999999999999999999999999953        567


Q ss_pred             EEEeec-HHHHHHHHHHHHHHHhc
Q 007844          178 IQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       178 V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      |.|.+. .+.+.+|+..|..+.++
T Consensus       593 v~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         593 VKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             EEEEecchHHHHHHHHHHHHHHhh
Confidence            889888 69999999999999976

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

Probab=96.42  E-value=0.0044  Score=48.66  Aligned_cols=37  Identities=22%  Similarity=0.261  Sum_probs=34.5

Q ss_pred             cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC   60 (587)
Q Consensus        24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V   60 (587)
                      ...+.+.|+.+..|.+|||+|.+|+.+++.++.+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999998876

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.

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

Probab=96.39  E-value=0.004  Score=63.86  Aligned_cols=70  Identities=19%  Similarity=0.284  Sum_probs=58.0

Q ss_pred             eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ...-++|+....++|||++|.|-++|+++|+++|.++.. .  ...+.++.+.+..++|.+|...|...|.+.
T Consensus        57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p-~--~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP-N--TNKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC-C--CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            445589999999999999999999999999999999772 1  234555555556999999999999999774

>TIGR01953 NusA transcription termination factor NusA

Probab=96.22  E-value=0.013  Score=62.01  Aligned_cols=95  Identities=21%  Similarity=0.269  Sum_probs=63.9

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i  112 (587)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+..+   .       +.+|             ++||.         +
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~---f-------i~na-------------l~Pa~---------v  290 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE---F-------IANA-------------LSPAK---------V  290 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------cCCce---------E
Confidence            558999999999999999999 778887433211100   0       0000             11110         0


Q ss_pred             HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~  166 (587)
                      .......      ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus       291 ~~v~i~~------~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       291 ISVEVLD------EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             EEEEEEc------CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence            0000000      01246789999999999999999999999999999999965

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.

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.20  E-value=0.0038  Score=60.30  Aligned_cols=101  Identities=20%  Similarity=0.230  Sum_probs=68.8

Q ss_pred             EEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHh--hhhccccc
Q 007844          276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEGQ  353 (587)
Q Consensus       276 ~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~--~v~e~~~~  353 (587)
                      +-..+-.+.+|..||++|.+|+.|.++.|-+|.|-.-.+                   .++ +-+..++.  ++....+.
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~-------------------d~~-~fI~nal~Pa~v~~V~~~  137 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE-------------------DPA-EFIKNALAPAEVLSVNIK  137 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC-------------------CHH-HHHHHhcCcceEeEEEEE
Confidence            344566788999999999999999999997666543211                   111 11111111  11100000


Q ss_pred             CCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCC
Q 007844          354 QGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (587)
Q Consensus       354 ~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~  404 (587)
                              ..+...+.+.||.++.+..|||+|.+++-+.+-||-+|.|...
T Consensus       138 --------~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~  180 (190)
T COG0195         138 --------EDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI  180 (190)
T ss_pred             --------eCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence                    0012278899999999999999999999999999999999763

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.14  E-value=0.016  Score=61.78  Aligned_cols=96  Identities=17%  Similarity=0.252  Sum_probs=64.7

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i  112 (587)
                      +-+|+.||++|+.|+.|.++. |-+|+|-....+..+   .       +.+|             ++||.  +..+    
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---f-------i~na-------------l~Pa~--v~~v----  295 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---F-------VANA-------------LSPAK--VVSV----  295 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--EEEE----
Confidence            568999999999999999999 778887433211100   0       0000             11110  0000    


Q ss_pred             HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                         ... +     ...-.+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus       296 ---~i~-~-----~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        296 ---EVD-D-----EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             ---EEE-c-----CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence               000 0     113467899999999999999999999999999999999763

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.13  E-value=0.012  Score=63.34  Aligned_cols=95  Identities=23%  Similarity=0.232  Sum_probs=63.6

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i  112 (587)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+..+   .       +.+|             ++||.     +    
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~---f-------I~Na-------------LsPA~-----V----  324 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPAT---Y-------IANA-------------LSPAR-----V----  324 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------cCCce-----e----
Confidence            558999999999999999999 778887433211100   0       0000             11110     0    


Q ss_pred             HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~  166 (587)
                      .......      ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus       325 ~~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        325 DEVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             eEEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            0000000      01235689999999999999999999999999999999966

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.05  E-value=0.015  Score=61.62  Aligned_cols=95  Identities=16%  Similarity=0.214  Sum_probs=64.4

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i  112 (587)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+..+   .       +.+|             ++||.  +..+    
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---f-------I~Na-------------l~Pa~--V~~V----  301 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---F-------IARA-------------LAPAI--ISSV----  301 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--eeEE----
Confidence            558999999999999999999 777877433211100   0       0000             11110  0000    


Q ss_pred             HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                         ..  +     +..-.+.+.||..+.+..|||+|.+++....-||.+|.|..-
T Consensus       302 ---~i--~-----~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        302 ---KI--E-----EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             ---EE--c-----CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence               00  0     113467889999999999999999999999999999999864

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

Probab=95.85  E-value=0.012  Score=60.61  Aligned_cols=70  Identities=24%  Similarity=0.306  Sum_probs=58.6

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      .....+.|++.+.+.|||++|.+.+.|+++|+++|.++.+.+      ..+.++.+-+.-++|.+|.+.|.-.|-.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids  125 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDS  125 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence            356678999999999999999999999999999999988432      4566666777888999999999776654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.74  E-value=0.013  Score=67.94  Aligned_cols=94  Identities=20%  Similarity=0.245  Sum_probs=67.8

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..++++.+.+.....-.+-....+....+.|+.+.++.+||.||.+||+|.++||++|.+..        +-.|
T Consensus       524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------~G~v  595 (693)
T PRK11824        524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------DGTV  595 (693)
T ss_pred             HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC--------CceE
Confidence            35666667777666554322211111222445566779999999999999999999999999888743        5678


Q ss_pred             EEeec-HHHHHHHHHHHHHHHhc
Q 007844          179 QITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .|.+. .+.+.+|..+|..+..+
T Consensus       596 ~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        596 KIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             EEEcccHHHHHHHHHHHHHhccc
Confidence            88885 89999999999888754

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

Probab=95.64  E-value=0.015  Score=45.65  Aligned_cols=37  Identities=22%  Similarity=0.362  Sum_probs=34.4

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEE
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL  401 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i  401 (587)
                      .....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus        24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            3688999999999999999999999999999998876

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=95.62  E-value=0.018  Score=66.83  Aligned_cols=93  Identities=14%  Similarity=0.224  Sum_probs=65.6

Q ss_pred             hHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCC
Q 007844          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (587)
Q Consensus       335 ~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~  414 (587)
                      .+.++...|++.|.+..... .. ...........+.||.+.++.+||.||.+||+|+++||+.|.+.           +
T Consensus       525 ~a~~g~~~I~~~M~~aI~~~-r~-~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d  591 (693)
T PRK11824        525 QAKEGRLHILGKMNEAISEP-RA-ELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------D  591 (693)
T ss_pred             HHHHHHHHHHHHHHHHhcCC-hh-hhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------C
Confidence            34455566666665432111 00 01122445667788999999999999999999999999988663           2


Q ss_pred             CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          415 DVVIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       415 ~r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                      +-.|.|.+ ..+.+++|+++|.....+
T Consensus       592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        592 DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            56688887 567899999999987764

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.57  E-value=0.024  Score=57.01  Aligned_cols=65  Identities=18%  Similarity=0.168  Sum_probs=55.1

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHHhhcc
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHNL  442 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~-~V~~A~~~I~~~Lr~~~  442 (587)
                      -..+.||.++++.+||++|.+|+.|.+.+++.|.|-.           +-.|.|++... ++.+|+.+|...-++..
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence            3568899999999999999999999999999998843           56788888876 78899999987666543

>PRK00468 hypothetical protein; Provisional

Probab=95.50  E-value=0.014  Score=47.80  Aligned_cols=35  Identities=29%  Similarity=0.442  Sum_probs=31.1

Q ss_pred             CCCcEEEEEEeccCccceeccCCChHHHHHHhHhC
Q 007844           21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK   55 (587)
Q Consensus        21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTg   55 (587)
                      .++.+.+++-|..+.+|.||||+|.+|+.||.--.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            45668999999999999999999999999997654

>TIGR01953 NusA transcription termination factor NusA

Probab=95.33  E-value=0.046  Score=57.85  Aligned_cols=96  Identities=20%  Similarity=0.273  Sum_probs=63.9

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~  361 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+..+-                +..|+.-  .++......       .
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~f----------------i~nal~P--a~v~~v~i~-------~  297 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEF----------------IANALSP--AKVISVEVL-------D  297 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhcCC--ceEEEEEEE-------c
Confidence            458999999999999999998 7777665322111000                0011000  000000000       0


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCC
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~  404 (587)
                       .......+.||.++.+..|||+|.+++...+.||.+|.|...
T Consensus       298 -~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~  339 (341)
T TIGR01953       298 -EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE  339 (341)
T ss_pred             -CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence             122578899999999999999999999999999999999763

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.28  E-value=0.039  Score=60.86  Aligned_cols=94  Identities=21%  Similarity=0.298  Sum_probs=63.1

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i  112 (587)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+..   ..|.       +|             ++||.     +    
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~---~fi~-------na-------------l~pa~-----v----  292 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPA---QFII-------NA-------------LSPAE-----V----  292 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH---HHHH-------Hh-------------CCCCE-----E----
Confidence            448999999999999999999 77887743321100   0000       00             11110     0    


Q ss_pred             HhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (587)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~  166 (587)
                      .....  +     ...-.+.+.||..+.+..|||+|.+|+..++-||.+|.|..
T Consensus       293 ~~v~~--~-----~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~  339 (470)
T PRK09202        293 SSVVV--D-----EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT  339 (470)
T ss_pred             EEEEE--e-----CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence            00000  0     00236779999999999999999999999999999999976

>PRK02821 hypothetical protein; Provisional

Probab=94.93  E-value=0.025  Score=46.56  Aligned_cols=36  Identities=17%  Similarity=0.272  Sum_probs=31.5

Q ss_pred             CCCcEEEEEEeccCccceeccCCChHHHHHHhHhCc
Q 007844           21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC   56 (587)
Q Consensus        21 ~~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga   56 (587)
                      .++.+.+.|-|..+.+|.||||+|.+|+.||.--.+
T Consensus        27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            345688999999999999999999999999987654

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.79  E-value=0.076  Score=56.60  Aligned_cols=97  Identities=20%  Similarity=0.198  Sum_probs=64.7

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~  361 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+..+-                +..|+.-  .++.....        .
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~f----------------i~nal~P--a~v~~v~i--------~  298 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEF----------------VANALSP--AKVVSVEV--------D  298 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhCCC--ceEEEEEE--------E
Confidence            568999999999999999998 7777665322111000                0001000  00000000        0


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~  405 (587)
                      ........+.||.++.+.-|||+|.+++.-.+.||.+|.|...+
T Consensus       299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~  342 (362)
T PRK12327        299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES  342 (362)
T ss_pred             cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence            02235788999999999999999999999999999999997643

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

Probab=94.77  E-value=0.077  Score=51.06  Aligned_cols=42  Identities=26%  Similarity=0.442  Sum_probs=35.4

Q ss_pred             CCcEEEEEEecc------CccceeccCCChHHHHHHhHhCceEEEeCC
Q 007844           22 DDVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG   63 (587)
Q Consensus        22 ~~~v~~riLvP~------~~vG~IIGk~G~~Ik~IreeTga~I~V~~~   63 (587)
                      +-.+.-++.||.      ++||.|||..|+|.|+|++.|+|+|-|...
T Consensus       145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~  192 (269)
T COG5176         145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS  192 (269)
T ss_pred             cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence            335566788875      689999999999999999999999999654

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=94.58  E-value=0.14  Score=54.49  Aligned_cols=98  Identities=13%  Similarity=0.059  Sum_probs=66.1

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~  361 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+..+-                +..|+.-  .++.....        .
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~f----------------I~Nal~P--a~V~~V~i--------~  304 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIF----------------IARALAP--AIISSVKI--------E  304 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhCCC--ceeeEEEE--------c
Confidence            568999999999999999998 7777665321111000                0011000  00000000        0


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcc
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV  407 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~  407 (587)
                       .......+.||.++.+..|||+|.+++-..+.||.+|.|..-+..
T Consensus       305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~  349 (374)
T PRK12328        305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSK  349 (374)
T ss_pred             -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCC
Confidence             123477899999999999999999999999999999999886653

>PRK00468 hypothetical protein; Provisional

Probab=94.57  E-value=0.041  Score=45.11  Aligned_cols=33  Identities=27%  Similarity=0.446  Sum_probs=29.2

Q ss_pred             CCCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (587)
Q Consensus       125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e  157 (587)
                      .+..+.++|.+..+.+|.||||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv   58 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV   58 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence            345688999999999999999999999999864

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.54  E-value=0.094  Score=56.70  Aligned_cols=95  Identities=22%  Similarity=0.213  Sum_probs=62.9

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~  361 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+...-                +..|+.-  .++.....        .
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~f----------------I~NaLsP--A~V~~V~i--------~  330 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPATY----------------IANALSP--ARVDEVRL--------V  330 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHHH----------------HHHhcCC--ceeeEEEE--------E
Confidence            568999999999999999998 7677665321110000                0011000  00100000        0


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~  403 (587)
                      ........+.||.++.+.-|||+|.+++--.+.||.+|.|.+
T Consensus       331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence            012246789999999999999999999999999999999865

>PRK12704 phosphodiesterase; Provisional

Probab=94.39  E-value=0.11  Score=58.32  Aligned_cols=63  Identities=14%  Similarity=0.235  Sum_probs=48.2

Q ss_pred             CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHH
Q 007844          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVG  436 (587)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~  436 (587)
                      ......|.+|+ ++-|+||||.|.+|+-+...||+.|.|.+          +...|.|+| +|---+.|...+..
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~  272 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEK  272 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHH
Confidence            34566688898 89999999999999999999999999953          346777888 55544445444433

>PRK01064 hypothetical protein; Provisional

Probab=94.34  E-value=0.048  Score=45.02  Aligned_cols=34  Identities=26%  Similarity=0.527  Sum_probs=30.8

Q ss_pred             CCcEEEEEEeccCccceeccCCChHHHHHHhHhC
Q 007844           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK   55 (587)
Q Consensus        22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTg   55 (587)
                      ++.+.+++-|.....|.+|||+|.+|+.||.-..
T Consensus        27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~   60 (78)
T PRK01064         27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV   60 (78)
T ss_pred             CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence            5678999999999999999999999999998653

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

Probab=94.32  E-value=0.058  Score=44.16  Aligned_cols=32  Identities=25%  Similarity=0.443  Sum_probs=29.2

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e  157 (587)
                      +..+.++|-+.....|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            55788999999999999999999999999964

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

Probab=94.30  E-value=0.048  Score=44.64  Aligned_cols=33  Identities=27%  Similarity=0.458  Sum_probs=30.1

Q ss_pred             CCcEEEEEEeccCccceeccCCChHHHHHHhHh
Q 007844           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT   54 (587)
Q Consensus        22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeT   54 (587)
                      +..+.++|-+.....|.||||+|.+|+.||---
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            667889999999999999999999999998754

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=94.14  E-value=1.8  Score=42.54  Aligned_cols=86  Identities=19%  Similarity=0.317  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec
Q 007844          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA  183 (587)
Q Consensus       104 Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~  183 (587)
                      .+.+|++.+........-    +..-.+.+.++....-.|+..+|..++.|....||+|.+..       .+..|.|+|+
T Consensus         5 l~~~Il~d~W~l~v~e~v----~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-------~~~~i~I~g~   73 (210)
T PF14611_consen    5 LAERILRDCWNLEVSEEV----DELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-------SENRIRITGT   73 (210)
T ss_pred             HHHHHHHHhcCCccccee----eccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-------CCcEEEEEcc
Confidence            345666666655432211    11223444556888899999999999999888999999977       5678999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 007844          184 TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       184 ~e~V~~A~~~I~~~L~e  200 (587)
                      ...+..+...|.+++..
T Consensus        74 k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   74 KSTAEYIEASINEILSN   90 (210)
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999999965

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=94.09  E-value=0.13  Score=57.53  Aligned_cols=61  Identities=15%  Similarity=0.265  Sum_probs=47.0

Q ss_pred             CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHH
Q 007844          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEV  434 (587)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I  434 (587)
                      ......|.+|+ ++-|+||||.|.+|+-+...||+.|.|.+          +...|+|+| +|---+.|...+
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l  264 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMAL  264 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHH
Confidence            44566788999 89999999999999999999999999953          346677888 554444444433

>PRK02821 hypothetical protein; Provisional

Probab=93.98  E-value=0.089  Score=43.30  Aligned_cols=32  Identities=25%  Similarity=0.435  Sum_probs=28.5

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e  157 (587)
                      +..+.+.|.|....+|.||||+|.+|+.||.-
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl   59 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTV   59 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence            34578899999999999999999999999975

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=93.83  E-value=0.12  Score=52.07  Aligned_cols=62  Identities=21%  Similarity=0.267  Sum_probs=53.0

Q ss_pred             EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhcC
Q 007844          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e~  201 (587)
                      .+-||..+++.+||++|.+|+.|.++++++|.|-.        +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus       148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            36789999999999999999999999999999954        356888888 668888888888777663

>PRK00106 hypothetical protein; Provisional

Probab=93.78  E-value=0.16  Score=56.78  Aligned_cols=61  Identities=16%  Similarity=0.296  Sum_probs=47.4

Q ss_pred             CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHH
Q 007844          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEV  434 (587)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I  434 (587)
                      ......|.+|+ ++-|+||||.|.+|+-+...||+.+.|.+          +...|+|+| +|---+.|...+
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~l  285 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTL  285 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHH
Confidence            44566788999 89999999999999999999999999953          446777888 554444444433

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=93.69  E-value=0.04  Score=60.70  Aligned_cols=96  Identities=20%  Similarity=0.242  Sum_probs=63.9

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~  361 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+...  +              +..|+.-  .++.....        .
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~--f--------------i~nal~p--a~v~~v~~--------~  298 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQ--F--------------IINALSP--AEVSSVVV--------D  298 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHH--H--------------HHHhCCC--CEEEEEEE--------e
Confidence            457999999999999999998 777766532111000  0              0011000  00000000        0


Q ss_pred             CCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (587)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~  405 (587)
                       .......+.||..+.+.-|||+|.+++...+.||.+|.|...+
T Consensus       299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~  341 (470)
T PRK09202        299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE  341 (470)
T ss_pred             -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence             1224788999999999999999999999999999999997643

>PRK01064 hypothetical protein; Provisional

Probab=93.58  E-value=0.096  Score=43.23  Aligned_cols=33  Identities=27%  Similarity=0.503  Sum_probs=29.3

Q ss_pred             CCCceEEEEEeecceeeeeeecCchHHHHHHhh
Q 007844          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (587)
Q Consensus       125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e  157 (587)
                      .+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus        26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l   58 (78)
T PRK01064         26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL   58 (78)
T ss_pred             CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence            345788999999999999999999999999864

>PRK12704 phosphodiesterase; Provisional

Probab=93.38  E-value=0.3  Score=54.75  Aligned_cols=63  Identities=16%  Similarity=0.308  Sum_probs=48.8

Q ss_pred             EEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          131 CGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       131 ~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      ..+-+|+ .+-|.||||.|.+|+.+..-||++|.|..       +..+|.|+|. +---+.|...+...+.+
T Consensus       212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            3455566 88999999999999999999999999966       4567889984 54445666666666654

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.33  E-value=0.33  Score=54.40  Aligned_cols=65  Identities=15%  Similarity=0.295  Sum_probs=49.6

Q ss_pred             eEEEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       129 vt~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .+..+-+|+ .+-|.||||.|.+|+.+..-||+++-|..       +...|+|+|. +---+-|...+..++.+
T Consensus       204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~fdp~rreia~~~l~~li~d  270 (514)
T TIGR03319       204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPVRREIARMALEKLIQD  270 (514)
T ss_pred             eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence            344456666 78999999999999999999999999976       4466788884 55555566666666654

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.24  E-value=0.96  Score=44.46  Aligned_cols=127  Identities=13%  Similarity=0.086  Sum_probs=85.4

Q ss_pred             EEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCC
Q 007844          277 RMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF  356 (587)
Q Consensus       277 ~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~  356 (587)
                      .+.++....-.+...+|..++.|....||+|.+...     +..+.|+|++       .+.+.+......+.        
T Consensus        29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k-------~~~~~i~~~i~~~l--------   88 (210)
T PF14611_consen   29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK-------STAEYIEASINEIL--------   88 (210)
T ss_pred             EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH-------HHHHHHHHHHHHHH--------
Confidence            344557777888999999999998889999999843     4579999984       22233333333322        


Q ss_pred             CCCCCCCCceEEEEEeCccccccccc----CCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEc-----CCHHHH
Q 007844          357 SSGENKGDAVAVSILVGADFVGCLTG----SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKNV  427 (587)
Q Consensus       357 ~~g~~~~~~~t~~l~VP~~~vG~IIG----kgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~-----G~~~~V  427 (587)
                            ....+.+|.++.-..-.-.+    .....+++|++.|++.|+..+.+          ..+.|+     -....+
T Consensus        89 ------~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~~~~~~~  152 (210)
T PF14611_consen   89 ------SNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASPENEKRA  152 (210)
T ss_pred             ------hhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeeccccchH
Confidence                  13356666666432211111    13667999999999999886532          234444     466789


Q ss_pred             HHHHHHHHHHHh
Q 007844          428 QNALSEVVGRLR  439 (587)
Q Consensus       428 ~~A~~~I~~~Lr  439 (587)
                      +.|++++...+.
T Consensus       153 ~~a~RlL~~a~~  164 (210)
T PF14611_consen  153 DRAKRLLLWALD  164 (210)
T ss_pred             HHHHHHHHHhcc
Confidence            999999998775

>PRK00106 hypothetical protein; Provisional

Probab=93.15  E-value=0.4  Score=53.71  Aligned_cols=66  Identities=12%  Similarity=0.306  Sum_probs=50.6

Q ss_pred             ceEEEEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      ..+..+-+|+ .+-|.||||.|.+|+.+..-||+++-|..       +...|.|+|. +---+-|...+..++.+
T Consensus       224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            3444566677 78999999999999999999999999976       4466789984 65555566666666654

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

Probab=92.20  E-value=0.085  Score=61.87  Aligned_cols=64  Identities=19%  Similarity=0.056  Sum_probs=52.9

Q ss_pred             cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC-CCCCCCceEEEEecCCchhhhhhhc
Q 007844           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFC   87 (587)
Q Consensus        24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~~~~eRvI~I~G~~e~~~~a~~~   87 (587)
                      ....++-+|...+.+|||++|+||+.+|.-||+.|+|.. -..+..||-+++.|.++.++-+..-
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~ 1403 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSP 1403 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcc
Confidence            345567789999999999999999999999999999986 3344679999999999877655544

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

Probab=92.02  E-value=0.46  Score=52.27  Aligned_cols=93  Identities=17%  Similarity=0.230  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEE
Q 007844          100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ  179 (587)
Q Consensus       100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~  179 (587)
                      .|.+|-..|++.+...-...-.......++...|-|+.+....+||.+|...|+|..|||+.-++         ++..+.
T Consensus       568 ~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------De~t~~  638 (760)
T KOG1067|consen  568 KAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------DEGTFS  638 (760)
T ss_pred             hhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------cCceEE
Confidence            34455555555544333222222233457888899999999999999999999999999966665         456677


Q ss_pred             Eeec-HHHHHHHHHHHHHHHhcC
Q 007844          180 ITGA-TLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       180 I~G~-~e~V~~A~~~I~~~L~e~  201 (587)
                      |--. ..+.++|...|..++...
T Consensus       639 i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  639 IFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             EEecCHHHHHHHHHHHHHHhcCc
Confidence            7666 889999999999998763

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

Probab=91.88  E-value=0.24  Score=47.79  Aligned_cols=43  Identities=16%  Similarity=0.222  Sum_probs=36.8

Q ss_pred             CCCceEEEEEeec------ceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          125 GDDVAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       125 ~~~~vt~rllVp~------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                      .....+-++.||-      +.||.|||..|+|+|+|++.|+|+|.|-..
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            3446777888885      589999999999999999999999999763

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

Probab=91.30  E-value=0.13  Score=60.31  Aligned_cols=72  Identities=18%  Similarity=-0.021  Sum_probs=60.7

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ....++.+|-....+|||++|.+|+.++.-|||.|.|.+-..    ....||.+.+.|.++.+..|...|.-.+.+
T Consensus      1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~----~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP----DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC----ccchhhhcccCCCChhhhhhhccccceeec
Confidence            345567899999999999999999999999999999987332    135689999999999999999888765553

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=90.70  E-value=0.13  Score=41.75  Aligned_cols=35  Identities=17%  Similarity=0.273  Sum_probs=29.9

Q ss_pred             CCcEEEEEEeccCccceeccCCChHHHHHHhHhCc
Q 007844           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC   56 (587)
Q Consensus        22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga   56 (587)
                      .+...+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus        26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            45567788889999999999999999999987654

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

Probab=89.43  E-value=0.56  Score=36.61  Aligned_cols=35  Identities=17%  Similarity=0.274  Sum_probs=28.0

Q ss_pred             cEEEEEEeccCccceeccCCChHHHHHHhHhCceE
Q 007844           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI   58 (587)
Q Consensus        24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I   58 (587)
                      .....+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35555666666789999999999999999998554

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.

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

Probab=88.42  E-value=0.4  Score=38.63  Aligned_cols=36  Identities=25%  Similarity=0.360  Sum_probs=28.3

Q ss_pred             EEEEeccCc-----cceeccCCChHHHHHHhHh-CceEEEeC
Q 007844           27 FRLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCEG   62 (587)
Q Consensus        27 ~riLvP~~~-----vG~IIGk~G~~Ik~IreeT-ga~I~V~~   62 (587)
                      ..+.|-+..     +|..||++|+.|+.|.++. |-+|+|-.
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            345666666     9999999999999999999 88888743

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

Probab=88.07  E-value=0.3  Score=46.87  Aligned_cols=56  Identities=27%  Similarity=0.367  Sum_probs=49.1

Q ss_pred             CcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          373 GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       373 P~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      -+..+|+|+||+|.+---|.+.|.++|.+.+            ..|.|-|..+++..|...|+..|-.
T Consensus       176 lsRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG  231 (252)
T KOG3273|consen  176 LSRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG  231 (252)
T ss_pred             HHHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence            3468999999999999999999999998863            6799999999999999998876543

>PRK12705 hypothetical protein; Provisional

Probab=87.65  E-value=0.9  Score=50.64  Aligned_cols=62  Identities=15%  Similarity=0.262  Sum_probs=43.9

Q ss_pred             EEEeec-ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       132 rllVp~-~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .+-+|+ ++-|.||||.|.+|+.+...||+.+.|..-       .+.|.|++. +.--+.|...+..++.+
T Consensus       201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-------p~~V~ls~fdp~rreia~~~l~~Li~d  264 (508)
T PRK12705        201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-------PEAVVISSFNPIRREIARLTLEKLLAD  264 (508)
T ss_pred             eeecCChHhhccccCccchhHHHHHHhhCCceEecCC-------ccchhhcccCccchHHHHHHHHHHHhc
Confidence            344555 789999999999999999999999999763       344556665 44444455555555543

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

Probab=87.14  E-value=1.5  Score=48.40  Aligned_cols=90  Identities=14%  Similarity=0.136  Sum_probs=63.5

Q ss_pred             HHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCc
Q 007844          337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV  416 (587)
Q Consensus       337 ~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r  416 (587)
                      .+|-..|++.|......+-..  ..+...+..++.|+.+....+||.+|...|.|..+||+.-.+            ++.
T Consensus       570 ~~ar~~Il~~m~k~i~~Pr~~--~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~  635 (760)
T KOG1067|consen  570 REARLQILDIMEKNINSPRGS--DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEG  635 (760)
T ss_pred             hHHHHHHHHHHHhhcCCcccC--ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCc
Confidence            344556666665432211111  123467888999999999999999999999999999955444            245


Q ss_pred             EEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          417 VIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       417 ~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                      +++|.- ++.+.++|+++|.+.+..
T Consensus       636 t~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  636 TFSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             eEEEEecCHHHHHHHHHHHHHHhcC
Confidence            566554 566789999999987764

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

Probab=85.99  E-value=0.5  Score=45.39  Aligned_cols=56  Identities=29%  Similarity=0.388  Sum_probs=50.2

Q ss_pred             cceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       137 ~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      +..+|.|+||+|.+--.|++-|-++|.+.         +..|.|-|..++++-|...|+.+|...
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVla---------d~kIHiLG~~~niriAR~avcsLIlGs  232 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA---------DSKIHILGAFQNIRIARDAVCSLILGS  232 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEec---------CceEEEeecchhhHHHHHhhHhhhccC
Confidence            45679999999999999999999999994         467999999999999999999999764

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

Probab=85.58  E-value=0.81  Score=36.86  Aligned_cols=39  Identities=21%  Similarity=0.291  Sum_probs=30.5

Q ss_pred             EEEEEeCccc-----ccccccCCCchhHHHHHhh-CCeEEEcCCC
Q 007844          367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVGGE  405 (587)
Q Consensus       367 t~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-Ga~I~i~~~~  405 (587)
                      ...+.|-+..     +|..||++|+.|+.|+++. |-+|+|-.-+
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s   48 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS   48 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence            4566777777     9999999999999999999 9999997643

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

Probab=85.14  E-value=1.3  Score=34.46  Aligned_cols=35  Identities=11%  Similarity=0.260  Sum_probs=29.1

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeE
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI  399 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I  399 (587)
                      .....+.+.....|.+||++|++|+.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35666777776789999999999999999998655

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

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=84.95  E-value=0.59  Score=37.86  Aligned_cols=34  Identities=26%  Similarity=0.342  Sum_probs=28.7

Q ss_pred             cceEEEEEeecccccccccccchhhHhhhhhcCc
Q 007844          272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGA  305 (587)
Q Consensus       272 ~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga  305 (587)
                      ....+.+.+..+..|.||||+|.+++.||.-.+.
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~   60 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA   60 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence            3457778899999999999999999999876554

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=83.30  E-value=0.73  Score=37.71  Aligned_cols=33  Identities=27%  Similarity=0.428  Sum_probs=28.6

Q ss_pred             EEEEeccCccceeccCCChHHHHHHhHhCceEE
Q 007844           27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH   59 (587)
Q Consensus        27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~   59 (587)
                      ..+.+.....|.|||++|++|++|+++.+-.+.
T Consensus        27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~   59 (78)
T PF07650_consen   27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE   59 (78)
T ss_dssp             EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence            467889999999999999999999998876553

; 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 ....

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

Probab=81.13  E-value=3.2  Score=38.34  Aligned_cols=38  Identities=24%  Similarity=0.415  Sum_probs=33.6

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                      +-.+.|-...-|.+|||+|.++++|..+||=.-.|.+.
T Consensus        77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt  114 (145)
T cd02410          77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT  114 (145)
T ss_pred             CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence            34577888889999999999999999999999888875

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.

>PRK12705 hypothetical protein; Provisional

Probab=80.64  E-value=2.3  Score=47.45  Aligned_cols=40  Identities=18%  Similarity=0.336  Sum_probs=35.2

Q ss_pred             CceEEEEEeCc-ccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (587)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~  403 (587)
                      ......+.+|+ ++-|+||||.|.+|+-+...||+.|.|.+
T Consensus       196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd  236 (508)
T PRK12705        196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD  236 (508)
T ss_pred             hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence            34556678888 89999999999999999999999999975

>cd02414 jag_KH jag_K homology RNA-binding domain

Probab=80.54  E-value=1.6  Score=35.73  Aligned_cols=34  Identities=15%  Similarity=0.255  Sum_probs=27.0

Q ss_pred             EEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844           27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC   60 (587)
Q Consensus        27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V   60 (587)
                      +.+-+..+..|.+|||+|++++.||--++.-++-
T Consensus        26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~   59 (77)
T cd02414          26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR   59 (77)
T ss_pred             EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence            3455567889999999999999999888765443

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	587
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-27
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-20
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-12
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	1e-07
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	7e-04
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-25
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	2e-21
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	8e-07
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-24
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-23
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	1e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	5e-06
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-23
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-20
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	9e-14
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	2e-07
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	1e-21
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-09
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-07
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-06
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-10
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	6e-07
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	1e-06
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	1e-10
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	6e-07
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	2e-06
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	3e-09
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	4e-08
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-06
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	8e-04
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-09
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	6e-07
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	1e-06
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	3e-08
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-07
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	4e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	9e-08
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	3e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	2e-04
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-05
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	6e-05
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	2e-04
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	1e-07
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	4e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	5e-05
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	6e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-04
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	2e-07
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-05
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	6e-05
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	5e-07
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	3e-06
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	2e-04
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	8e-04
1we8_A	104	Tudor and KH domain containing protein; structural	2e-06
1we8_A	104	Tudor and KH domain containing protein; structural	6e-05
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	6e-06
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	4e-05
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	3e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	6e-05
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	1e-04
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	2e-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 =  108 bits (270), Expect = 2e-27
 Identities = 31/182 (17%), Positives = 75/182 (41%), Gaps = 12/182 (6%)

Query: 21  PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH---CEGGFPGSDHRVILVVGS 77
                  +++ P+   G +IG+ G  I  ++++T   I     +  +PG+  RV L+ G+
Sbjct: 2   LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61

Query: 78  GSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANT 137
                 +     + + E  +  +  E              + +   + D      ++   
Sbjct: 62  IEALNAVHGFIAEKIREMPQNVAKTEP---------VSILQPQTTVNPDRANQVKIIVPN 112

Query: 138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTC 197
           +  G+++GKGG  V  +  +SGA + +   P    + ++++ ++G     +KA+  +   
Sbjct: 113 STAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQK 172

Query: 198 LQ 199
           +Q
Sbjct: 173 IQ 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 = 87.6 bits (217), Expect = 3e-20
 Identities = 38/174 (21%), Positives = 71/174 (40%), Gaps = 9/174 (5%)

Query: 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA---PLTKSGERVVTISA-LE 327
            +  L++L   + A  IIGK G  +  LQ  +GA I  +        + ERV  I   +E
Sbjct: 4   SQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIE 63

Query: 328 YLDTRHSPVQNAAVLVFARSVEVEGQ--QGFSSGENKGDAVAVSILVGADFVGCLTGSGS 385
            L+  H  +      +     + E        +  N   A  V I+V     G + G G 
Sbjct: 64  ALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGG 123

Query: 386 SAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439
           + V  + + +G  ++L    Q        + V+ +SGE +  + A+  ++ +++
Sbjct: 124 ATVKAIMEQSGAWVQL---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 = 65.6 bits (160), Expect = 1e-12
 Identities = 31/195 (15%), Positives = 62/195 (31%), Gaps = 51/195 (26%)

Query: 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP-ACAAIDDQLIQITGATLAVKKAL 191
           +L  +   G ++GKGG+ + +++ E+GA I +           +++  I G   A+    
Sbjct: 10  VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVH 69

Query: 192 VAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEF 251
             +   ++                                                    
Sbjct: 70  GFIAEKIRE------------------------------------------------MPQ 81

Query: 252 HSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGA--LISF 309
           + +  +              +   ++++    TA  IIGK GA V+++   SGA   +S 
Sbjct: 82  NVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQ 141

Query: 310 AAPLTKSGERVVTIS 324
                    RVVT+S
Sbjct: 142 KPDGINLQNRVVTVS 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 = 51.0 bits (122), Expect = 1e-07
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 5   SNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EG 62
           +     S  +      PD     +++ P    G +IG+ G+ + +I   +   +    + 
Sbjct: 84  AKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKP 143

Query: 63  GFPGSDHRVILVVGS 77
                 +RV+ V G 
Sbjct: 144 DGINLQNRVVTVSGE 158

>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 = 39.8 bits (93), Expect = 7e-04
 Identities = 18/111 (16%), Positives = 39/111 (35%), Gaps = 4/111 (3%)

Query: 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV-GGEQVLGCAAQNDVVIQIS 421
           G    + +L+ +   G + G G   + +++  TG  IKL    +   G     + V  I 
Sbjct: 3   GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGT---TERVCLIQ 59

Query: 422 GEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSV 472
           G  + +      +  ++R   ++           P   V     +++   V
Sbjct: 60  GTIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIV 110

>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 =  101 bits (254), Expect = 2e-25
 Identities = 34/179 (18%), Positives = 64/179 (35%), Gaps = 26/179 (14%)

Query: 23  DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH-CEGGFPGSDHRVILVVGSGSID 81
           +    ++  P   VG +IG+ G  I  + R     I       P S  R++++ G     
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITG----- 55

Query: 82  RRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCG-LLANTTKI 140
                                EA  +   R++    E    G  ++V     +    +  
Sbjct: 56  -------------------PPEAQFKAQGRIYGKLKEENFFGPKEEVKLETHIRVPASAA 96

Query: 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199
           G V+GKGG+ V  ++  + A++V+         D  +++I G   A + A   +   L 
Sbjct: 97  GRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILA 155

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens} Length = 163

 Score = 90.6 bits (225), Expect = 2e-21
 Identities = 33/169 (19%), Positives = 66/169 (39%), Gaps = 15/169 (8%)

Query: 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLT-KSGERVVTISALEYLD 330
           ++  +++         IIGK+G  ++ L   + A I  A P T  S  R+V I+      
Sbjct: 1   EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP--- 57

Query: 331 TRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSE 390
                   A   ++ +  E         G  +   +   I V A   G + G G   V+E
Sbjct: 58  ---EAQFKAQGRIYGKLKEEN-----FFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNE 109

Query: 391 MEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439
           ++++T  ++ +   +        + V+++I G +   Q A  ++   L 
Sbjct: 110 LQNLTAAEVVVPRDQT---PDENDQVIVKIIGHFYASQMAQRKIRDILA 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 = 48.2 bits (115), Expect = 8e-07
 Identities = 8/59 (13%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 21  PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSDHRVILVVGS 77
            +  +   +  P    G +IG+ G  ++ ++  T   +    +     +D  ++ ++G 
Sbjct: 81  EEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGH 139

>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 = 99.1 bits (247), Expect = 2e-24
 Identities = 33/170 (19%), Positives = 71/170 (41%), Gaps = 12/170 (7%)

Query: 270 RKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYL 329
           +   + +R+L  G     IIGK+G  V+ ++  SGA I+ +       ER++T++     
Sbjct: 1   KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAG---- 54

Query: 330 DTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVS 389
               + +  A  ++  +  E       +S       V + ++V A   G L G G   + 
Sbjct: 55  --PTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIK 112

Query: 390 EMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439
           E+ + TG  +++ G           +  I I+G  +++   + ++   + 
Sbjct: 113 EIRESTGAQVQVAGDM----LPNSTERAITIAGIPQSIIECVKQICVVML 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 = 94.8 bits (236), Expect = 5e-23
 Identities = 27/180 (15%), Positives = 67/180 (37%), Gaps = 25/180 (13%)

Query: 22  DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSID 81
           +  ++ RL+     VG +IG+ G  +  +R ++  RI+          R+I + G     
Sbjct: 2   NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP---- 55

Query: 82  RRIMFCENDVVVEGGEVSSTQEAVIRVFERMWE--VEAEVEGDGDGDDVAYCGLLANTTK 139
                            ++  +A   + +++ E    +               L+   ++
Sbjct: 56  ----------------TNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQ 99

Query: 140 IGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199
            G ++GKGG  +  +R  +GA++  +         ++ I I G   ++ + +  +   + 
Sbjct: 100 CGSLIGKGGCKIKEIRESTGAQVQ-VAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 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 = 53.2 bits (128), Expect = 1e-08
 Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 21  PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGF-PGSDHRVILVVGS 77
               V+ RLV P    G LIG+ G  I  IR  T  ++   G   P S  R I + G 
Sbjct: 85  SRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI 142

>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 = 45.9 bits (109), Expect = 5e-06
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 257 DADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA-PLTK 315
           +             +  V LR++        +IGK G  ++ ++ ++GA +  A   L  
Sbjct: 72  EDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN 131

Query: 316 SGERVVTIS 324
           S ER +TI+
Sbjct: 132 STERAITIA 140

>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 = 95.7 bits (238), Expect = 3e-23
 Identities = 35/176 (19%), Positives = 61/176 (34%), Gaps = 6/176 (3%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS-GSIDRR 83
               +  P   VG +IGR+G +I  I+ D   RI  +     +  R+  + G        
Sbjct: 3   HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHA 62

Query: 84  IMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVV 143
                + +               R   R           G    +     +  T K G++
Sbjct: 63  AEIITDLLRSVQAGNPGGPGPGGRGRGRGQ----GNWNMGPPGGLQEFNFIVPTGKTGLI 118

Query: 144 VGKGGRNVTRMRIESGAKIVMLP-PPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
           +GKGG  +  +  +SGA+I +   PP  A  + +L  I G    +  A   +   +
Sbjct: 119 IGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 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 = 88.4 bits (219), Expect = 1e-20
 Identities = 29/181 (16%), Positives = 59/181 (32%), Gaps = 23/181 (12%)

Query: 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTR 332
              + +    +    +IG+ G +++ +QN +G  I F      + ER+  I+        
Sbjct: 2   SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITG------P 55

Query: 333 HSPVQNAAVLVFA---------------RSVEVEGQQGFSSGENKGDAVAVSILVGADFV 377
               Q+AA ++                         QG  +    G     + +V     
Sbjct: 56  PDRAQHAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKT 115

Query: 378 GCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGR 437
           G + G G   +  +   +G  I+L         A  N  +  I G  + +  A   +  +
Sbjct: 116 GLIIGKGGETIKSISQQSGARIEL--QRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEK 173

Query: 438 L 438
           +
Sbjct: 174 I 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 = 68.7 bits (168), Expect = 9e-14
 Identities = 29/189 (15%), Positives = 54/189 (28%), Gaps = 47/189 (24%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            +G+V+G+ G  + +++ ++G +I   P        +++ QITG     + A   +T  L
Sbjct: 13  AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTT--PERIAQITGPPDRAQHAAEIITDLL 70

Query: 199 QHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADA 258
           +                                             + N           
Sbjct: 71  RS------------------------------------------VQAGNPGGPGPGGRGR 88

Query: 259 DRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALI---SFAAPLTK 315
            R     +            +        IIGK G  ++S+   SGA I       P   
Sbjct: 89  GRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 148

Query: 316 SGERVVTIS 324
              ++ TI 
Sbjct: 149 PNMKLFTIR 157

>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 = 49.9 bits (119), Expect = 2e-07
 Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 4   HSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63
                G  +   GP   P  +  F  + PT   G +IG+ G  I SI + +  RI  +  
Sbjct: 86  RGRGRGQGNWNMGP---PGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRN 142

Query: 64  FP---GSDHRVILVVGS 77
            P     + ++  + G+
Sbjct: 143 PPPNADPNMKLFTIRGT 159

>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 = 91.0 bits (226), Expect = 1e-21
 Identities = 23/176 (13%), Positives = 58/176 (32%), Gaps = 21/176 (11%)

Query: 26  SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSDHRVILVVGSGSIDRR 83
              ++ P    G +IG+ G  I  ++     ++    +G    +  + + ++G       
Sbjct: 3   VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPY---- 58

Query: 84  IMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVV 143
                        +V    E V+ +     +       +          +      +GVV
Sbjct: 59  -------------KVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVV 105

Query: 144 VGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199
           +G+ G  + +++ ++G +I            +++  I G     + A   +   LQ
Sbjct: 106 IGRSGEMIKKIQNDAGVRIQFKQDDGTG--PEKIAHIMGPPDRCEHAARIINDLLQ 159

>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 = 75.6 bits (186), Expect = 3e-16
 Identities = 28/173 (16%), Positives = 62/173 (35%), Gaps = 15/173 (8%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG--ERVVTISALEYLDTRH 333
             ++     A  +IGK G  ++ LQ  +G  +      +++   ++ + I          
Sbjct: 4   QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG------DP 57

Query: 334 SPVQNAAVLVFAR-SVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEME 392
             VQ A  +V        +G  G  +         + + V    VG + G     + +++
Sbjct: 58  YKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117

Query: 393 DVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG 445
           +  G  I+    +         + +  I G     ++A   +   L+ +L+SG
Sbjct: 118 NDAGVRIQFKQDD-----GTGPEKIAHIMGPPDRCEHAARIINDLLQ-SLRSG 164

>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 = 55.6 bits (134), Expect = 2e-09
 Identities = 14/57 (24%), Positives = 23/57 (40%)

Query: 21  PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
                   +  P   VG +IGRSG +I  I+ D   RI  +        ++  ++G 
Sbjct: 87  SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP 143

>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 = 49.8 bits (119), Expect = 2e-07
 Identities = 16/62 (25%), Positives = 34/62 (54%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
           K G+V+GKGG  + +++  +G K++++   +     D+ ++I G    V++A   V   L
Sbjct: 12  KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 71

Query: 199 QH 200
           + 
Sbjct: 72  RE 73

>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 = 47.5 bits (113), Expect = 2e-06
 Identities = 11/66 (16%), Positives = 26/66 (39%)

Query: 259 DRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGE 318
                  ++ G +    + +     +   +IG+ G +++ +QN +G  I F        E
Sbjct: 76  QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE 135

Query: 319 RVVTIS 324
           ++  I 
Sbjct: 136 KIAHIM 141

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 15/59 (25%), Positives = 31/59 (52%)

Query: 19 NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          +L   +++ ++  P  + G +IG+ G  I  IR ++   I  +    GS+ R+I + G+
Sbjct: 8  DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT 66

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDT 331
             +  ++      A  IIGK G  ++ +++ SGA I    PL  S +R++TI+      T
Sbjct: 12  PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-----T 66

Query: 332 RHSPVQNAAVLVFARSVEVEGQQ 354
           +   +QNA  L+     +  G+ 
Sbjct: 67  QDQ-IQNAQYLLQNSVKQYSGKF 88

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
             G ++GKGG+ + ++R ESGA I +  P   +  +D++I ITG    ++ A   +   +
Sbjct: 24  LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS--EDRIITITGTQDQIQNAQYLLQNSV 81

Query: 199 Q 199
           +
Sbjct: 82  K 82

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
             +++ ++  P  + G +IG+ G  I  IR ++   I  +    GS+ R+I + G+
Sbjct: 3  MGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT 59

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
             G ++GKGG+ + ++R ESGA I +  P   +  +D++I ITG    ++ A   +   +
Sbjct: 17  LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS--EDRIITITGTQDQIQNAQYLLQNSV 74

Query: 199 Q 199
           +
Sbjct: 75  K 75

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDT 331
             +  ++      A  IIGK G  ++ +++ SGA I    PL  S +R++TI+      T
Sbjct: 5   PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-----T 59

Query: 332 RHSPVQNAAVLVFARSVEVEGQQ 354
           +   +QNA  L+     +  G+ 
Sbjct: 60  QDQ-IQNAQYLLQNSVKQYSGKF 81

>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 = 53.0 bits (128), Expect = 3e-09
 Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          +  ++ RL+     VG +IG+ G  +  +R ++  RI+   G      R+I + G 
Sbjct: 2  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGP 55

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 4/67 (5%)

Query: 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALV 192
           LL +  ++G ++GK G +V +MR ESGA+I +          +++I + G T A+ KA  
Sbjct: 9   LLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC----PERIITLAGPTNAIFKAFA 64

Query: 193 AVTTCLQ 199
            +   L+
Sbjct: 65  MIIDKLE 71

>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 = 45.3 bits (108), Expect = 1e-06
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           + +R+L  G     IIGK+G  V+ ++  SGA I+ +       ER++T++
Sbjct: 5   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP--ERIITLA 53

>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 = 37.3 bits (87), Expect = 8e-04
 Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 370 ILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN 429
           +L+    VG + G    +V +M + +G  I +  G     C    + +I ++G    +  
Sbjct: 9   LLMHGKEVGSIIGKKGESVKKMREESGARINISEG----NC---PERIITLAGPTNAIFK 61

Query: 430 ALSEVVGRLRHN 441
           A + ++ +L  +
Sbjct: 62  AFAMIIDKLEED 73

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 17/53 (32%), Positives = 27/53 (50%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
           S  L  P  ++G +IGR G+ I+ IR+ +  +I       GS  R + + GS
Sbjct: 5  TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS 57

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            IG ++G+ G  +  +R  SGA+I +  P   +   D+ + ITG+  ++  A   +   L
Sbjct: 15  LIGCIIGRQGAKINEIRQMSGAQIKIANPVEGS--TDRQVTITGSAASISLAQYLINVRL 72

Query: 199 Q 199
            
Sbjct: 73  S 73

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} Length = 76

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 17/55 (30%), Positives = 28/55 (50%)

Query: 270 RKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           + Q  +  +         IIG++GA +  ++  SGA I  A P+  S +R VTI+
Sbjct: 1   KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55

>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 = 50.0 bits (120), Expect = 3e-08
 Identities = 16/53 (30%), Positives = 27/53 (50%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
           +  L  P  ++G +IGR G+ I+ IR+ +  +I       GS  R + + GS
Sbjct: 6  TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS 58

>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 = 46.9 bits (112), Expect = 4e-07
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            IG ++G+ G N+  +R  SGA+I +  P        + + ITG+  ++  A   +   L
Sbjct: 16  LIGCIIGRQGANINEIRQMSGAQIKIANP--VEGSSGRQVTITGSAASISLAQYLINARL 73

Query: 199 Q 199
            
Sbjct: 74  S 74

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS 347
           IIG++GA +  ++  SGA I  A P+  S  R VTI+      +  S +  A  L+ AR 
Sbjct: 20  IIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG-----SAAS-ISLAQYLINAR- 72

Query: 348 VEVEGQQGFS 357
           +  E   G S
Sbjct: 73  LSSEKGMGCS 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 = 48.9 bits (117), Expect = 9e-08
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGS 77
              +  P  +VG ++G+ G  +   +  T  RI         PG+ +R + + GS
Sbjct: 3  ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>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 = 44.6 bits (106), Expect = 3e-06
 Identities = 13/62 (20%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA-IDDQLIQITGATLAVKKALVAVTTC 197
            +G ++GKGG+ +   +  +GA+I +           ++ + ITG+  A + A   ++  
Sbjct: 13  LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQR 72

Query: 198 LQ 199
           + 
Sbjct: 73  VT 74

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 3/55 (5%)

Query: 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA---PLTKSGERVVTIS 324
           +  + +         I+GK G  +   Q  +GA I  +     L  +  R VTI+
Sbjct: 2   KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>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 = 1e-07
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
             V++     P  +VG +IGR G  IS I++++ C+I       G   R  ++ G+
Sbjct: 11 QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT 67

>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 = 43.2 bits (102), Expect = 1e-05
 Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
            +G ++G+GG  ++R++ ESG KI + P      + ++   +TG   +V+ A
Sbjct: 25  MVGFIIGRGGEQISRIQQESGCKIQIAPDS--GGLPERSCMLTGTPESVQSA 74

>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 = 41.3 bits (97), Expect = 6e-05
 Identities = 11/37 (29%), Positives = 16/37 (43%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           IIG+ G  +  +Q  SG  I  A       ER   ++
Sbjct: 29  IIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLT 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 = 39.7 bits (93), Expect = 2e-04
 Identities = 19/107 (17%), Positives = 39/107 (36%), Gaps = 15/107 (14%)

Query: 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA 411
           G  G S  + +   +     V    VG + G G   +S ++  +G  I++          
Sbjct: 1   GSSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDS-----G 55

Query: 412 AQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSG 458
              +    ++G  ++VQ+A   +           +I+ + R    SG
Sbjct: 56  GLPERSCMLTGTPESVQSAKRLL----------DQIVEKGRSGPSSG 92

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 16/61 (26%), Positives = 34/61 (55%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
           K G+V+GKGG  + +++  +G K++++   +     D+ ++I G    V++A   V   L
Sbjct: 24  KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 83

Query: 199 Q 199
           +
Sbjct: 84  R 84

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 8/58 (13%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSDHRVILVVGS 77
           +     ++ P    G +IG+ G  I  ++     ++    +G    +  + + ++G 
Sbjct: 11 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD 68

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Length = 85

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 2/61 (3%)

Query: 266 DKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA--APLTKSGERVVTI 323
           +  G +      ++     A  +IGK G  ++ LQ  +G  +          + ++ + I
Sbjct: 6   NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRI 65

Query: 324 S 324
            
Sbjct: 66  I 66

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH---CEGGFPGSDHRVILVVGS 77
              +  P  +VG ++G+ G  +   +  T  RI         PG+ +R + + GS
Sbjct: 3  ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 13/62 (20%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA-IDDQLIQITGATLAVKKALVAVTTC 197
            +G ++GKGG+ +   +  +GA+I +           ++ + ITG+  A + A   ++  
Sbjct: 13  LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQR 72

Query: 198 LQ 199
           + 
Sbjct: 73  VT 74

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 3/55 (5%)

Query: 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA---PLTKSGERVVTIS 324
           +  + M         I+GK G  +   Q  +GA I  +     L  +  R VTI+
Sbjct: 2   KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 49.0 bits (117), Expect = 2e-07
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
             +  P   VG +IGRSG +I  I+ D   RI  +        ++  ++G 
Sbjct: 12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGP 63

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            +GVV+G+ G  + +++ ++G +I            +++  I G     + A   +   L
Sbjct: 21  SVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTG--PEKIAHIMGPPDRCEHAARIINDLL 78

Query: 199 Q 199
           Q
Sbjct: 79  Q 79

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 106

 Score = 41.7 bits (98), Expect = 6e-05
 Identities = 10/49 (20%), Positives = 22/49 (44%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           + +     +   +IG+ G +++ +QN +G  I F        E++  I 
Sbjct: 13  IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61

>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 = 47.0 bits (112), Expect = 5e-07
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
           K G+V+GKGG  + +++  +G K+VM+         D+ ++ITG    V++A
Sbjct: 25  KAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 76

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 3/69 (4%)

Query: 11 SSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSD 68
          SS   G  + P +     ++ P    G +IG+ G  I  ++     ++    +G      
Sbjct: 2  SSGSSGHGDGPGNA-VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA 60

Query: 69 HRVILVVGS 77
           + + + G 
Sbjct: 61 DKPLRITGD 69

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 19/107 (17%), Positives = 39/107 (36%), Gaps = 13/107 (12%)

Query: 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA 411
           G  G S   +        I++ A   G + G G   + ++++  G  + ++         
Sbjct: 1   GSSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT-- 58

Query: 412 AQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSG 458
              D  ++I+G+   VQ A   V+          E++ +      SG
Sbjct: 59  -GADKPLRITGDPYKVQQAKEMVL----------ELIRDQGSGPSSG 94

>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 = 37.8 bits (88), Expect = 8e-04
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 2/54 (3%)

Query: 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA--APLTKSGERVVTIS 324
                ++     A  +IGK G  ++ LQ  +G  +      P     ++ + I+
Sbjct: 14  NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRIT 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 = 45.6 bits (108), Expect = 2e-06
 Identities = 15/52 (28%), Positives = 25/52 (48%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
            +G ++G+GG  +  +   SGAKI          +  +LI+I+G    V  A
Sbjct: 25  SVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAA 76

>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 = 41.3 bits (97), Expect = 6e-05
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 11 SSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSD 68
          SS   G L   +  V  +L  P   VG +IGR G  I SI + +  +I C  E       
Sbjct: 2  SSGSSGILT-ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL 60

Query: 69 HRVILVVGS 77
           R+I + G+
Sbjct: 61 SRLIKISGT 69

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 44.5 bits (105), Expect = 6e-06
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 137 TTKIGVVVGKGGRNVTRMRIESGAKI-VMLPPPACAAIDDQLIQITGATLAVKKALVAVT 195
           T K G+V+G+GG NV  +  ++GA + +    P     + +L  I G+   +  A   + 
Sbjct: 15  THKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIE 74

Query: 196 TCLQ 199
             ++
Sbjct: 75  EKIE 78

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Length = 107

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 3/55 (5%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGS 77
                PT   G +IGR G  + +I + T   +            + ++ ++ GS
Sbjct: 8  EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS 62

>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 = 44.7 bits (105), Expect = 3e-05
 Identities = 30/167 (17%), Positives = 58/167 (34%), Gaps = 24/167 (14%)

Query: 36  VGGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGSGSIDRRIMFCENDVV 92
           +  LIG+ G     I + TK +I      G    +  +        + D   ++   D+V
Sbjct: 45  IAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTK-------ETEDPLAVWKARDIV 97

Query: 93  VEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVT 152
           +  G   S + A      R+      +E     D +      A     G ++G+ GR   
Sbjct: 98  LAIGRGFSPERAF-----RLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQ 152

Query: 153 RMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199
            +   SGA +          +  + + I G  + ++ A  A+    +
Sbjct: 153 IIEEMSGASVS---------VYGKTVAIIGNPIQIEIAKTAIEKLAR 190

>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 = 43.1 bits (101), Expect = 6e-05
 Identities = 26/174 (14%), Positives = 55/174 (31%), Gaps = 19/174 (10%)

Query: 26  SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIM 85
              +      +G +IG  G + + I R T   I  +     +++ +++V         + 
Sbjct: 5   RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-----TENSMVIVEPEAEGIPPVN 59

Query: 86  FCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVG 145
             +   VV+   +    E   R+ E    +         GD   +          G ++G
Sbjct: 60  LMKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNH-----LKRIKGRIIG 114

Query: 146 KGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199
           +GGR    +   +   I          + +  + I G       A  A+    +
Sbjct: 115 EGGRARRTIEEMTDTYIN---------VGEYEVAIIGDYERAMAAKQAIEMLAE 159

>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 = 40.1 bits (94), Expect = 1e-04
 Identities = 12/69 (17%), Positives = 22/69 (31%), Gaps = 2/69 (2%)

Query: 9  GYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSD 68
          G S      +       S  +  P      +IG++G  +  +   T  +I      P   
Sbjct: 1  GSSGSSGDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDP 58

Query: 69 HRVILVVGS 77
             I + G+
Sbjct: 59 SNQIKITGT 67

>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 = 41.2 bits (96), Expect = 2e-04
 Identities = 25/178 (14%), Positives = 50/178 (28%), Gaps = 45/178 (25%)

Query: 28  RLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFC 87
           + +    ++G  IG  G+ I   R+                               I   
Sbjct: 7   QFIVREDLMGLAIGTHGANIQQARKVPGV-------------------------TAIDLD 41

Query: 88  ENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKG 147
           E+            Q+AV +    +              + A   +      +G V+GK 
Sbjct: 42  EDTCTFHI--YGEDQDAVKKARSFL--------------EFAEDVIQVPRNLVGKVIGKN 85

Query: 148 GRNVTRMRIESGAKIVMLPPPACAAIDDQL----IQITGATLAVKKALVAVTTCLQHL 201
           G+ +  +  +SG   V +       +  +         G   ++  A V +   L +L
Sbjct: 86  GKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLNYL 143

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	587
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.92
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.91
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.91
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.91
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.9
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.9
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.9
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	99.89
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.88
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.88
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.88
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.81
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.7
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.69
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.56
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.51
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.46
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.45
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.45
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.45
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.45
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.43
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.41
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.41
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.41
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.41
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.41
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.4
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.39
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.38
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.37
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.36
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.35
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.35
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.34
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.34
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.33
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.33
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.32
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.32
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.3
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.3
1we8_A	104	Tudor and KH domain containing protein; structural	99.3
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.29
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.29
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.27
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.26
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.26
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.25
1we8_A	104	Tudor and KH domain containing protein; structural	99.25
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.17
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.14
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.13
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.1
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.07
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.01
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	99.0
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.98
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.88
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.73
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.51
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.44
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.35
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.28
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.23
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.92
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.88
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.69
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.62
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.59
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.54
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.88
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.86
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.86
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.94
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.81
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	94.69
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.15
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.12
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.62
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.6
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	91.57
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.29
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	91.04

>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*

Probab=99.92  E-value=3.1e-25  Score=211.64  Aligned_cols=161  Identities=19%  Similarity=0.373  Sum_probs=126.4

Q ss_pred             CCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCC---CCCCCceEEEEecCCchhhhhhhccccccccCCCc
Q 007844           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG---FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV   98 (587)
Q Consensus        22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~---~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~   98 (587)
                      ++.++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|+|+|+|+.+++.+|..            
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~A~~------------   70 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHG------------   70 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHHHHH------------
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHHHHH------------
Confidence            678999999999999999999999999999999999999753   46788999999998877544322            


Q ss_pred             cHHHHHHHHHHHHHHhhhhc-----------cCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844           99 SSTQEAVIRVFERMWEVEAE-----------VEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~-----------~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                              .+.+.+.+....           .......+...+++|+||.+++|+||||+|++|++|+++|||+|+|.+.
T Consensus        71 --------~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~  142 (178)
T 2anr_A           71 --------FIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK  142 (178)
T ss_dssp             --------HHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCC
T ss_pred             --------HHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCC
Confidence                    222222111000           0000012235789999999999999999999999999999999999875


Q ss_pred             CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCC
Q 007844          168 PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLS  202 (587)
Q Consensus       168 p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~  202 (587)
                      +.++...+++|+|+|+.++|.+|+.+|.++|++++
T Consensus       143 ~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e~p  177 (178)
T 2anr_A          143 PDGINLQNRVVTVSGEPEQNRKAVELIIQKIQEDP  177 (178)
T ss_dssp             C----CCEEEEEEESSHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhCC
Confidence            44556788999999999999999999999998854

>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=99.91  E-value=2.7e-24  Score=202.18  Aligned_cols=154  Identities=19%  Similarity=0.304  Sum_probs=126.0

Q ss_pred             cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCC-CCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG-FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~-~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      .-+++|+||.+++|.||||+|++|++|+++|||+|+|.+. .+++.+|+|+|+|+.++                    +.
T Consensus         2 ~~~~~~~ip~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G~~e~--------------------v~   61 (163)
T 3krm_A            2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEA--------------------QF   61 (163)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECHHH--------------------HH
T ss_pred             ceEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCHHH--------------------HH
Confidence            3579999999999999999999999999999999999875 57889999999998766                    33


Q ss_pred             HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCC-CcEEEEe
Q 007844          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID-DQLIQIT  181 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~-dr~V~I~  181 (587)
                      .|...++..+.+....   .......++++|+||.+++|+||||+|++|++|+++|||+|.|..+ ..+... ++.|+|+
T Consensus        62 ~A~~~I~~~~~e~~~~---~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~-~~~~~~~~~~v~I~  137 (163)
T 3krm_A           62 KAQGRIYGKLKEENFF---GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD-QTPDENDQVIVKII  137 (163)
T ss_dssp             HHHHHHHHHHHHTTSS---CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTT-CCCCTTSEEEEEEE
T ss_pred             HHHHHHHHHHhccccc---ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCC-CCCCCCCceEEEEE
Confidence            4455555554433111   1123346788999999999999999999999999999999999875 223334 4589999


Q ss_pred             ecHHHHHHHHHHHHHHHhcC
Q 007844          182 GATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       182 G~~e~V~~A~~~I~~~L~e~  201 (587)
                      |++++|.+|..+|.+++++.
T Consensus       138 G~~~~v~~A~~~I~~~i~~~  157 (163)
T 3krm_A          138 GHFYASQMAQRKIRDILAQV  157 (163)
T ss_dssp             ECHHHHHHHHHHHHHHHHHH
T ss_pred             eCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999874

>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=99.91  E-value=2.7e-24  Score=201.60  Aligned_cols=155  Identities=18%  Similarity=0.344  Sum_probs=126.1

Q ss_pred             CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|++.  ++++|+|+|+|+.+++.                    
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v~--------------------   60 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIF--------------------   60 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHHH--------------------
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHHH--------------------
Confidence            46899999999999999999999999999999999999875  56899999999876632                    


Q ss_pred             HHHHHHHHHHHhhhhcc-C-CCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEE
Q 007844          103 EAVIRVFERMWEVEAEV-E-GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI  180 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~-~-~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I  180 (587)
                      .|...+.+.+.+..... . +.......++++|+||.+++|+||||+|++|++|+++|||+|+|.++ ..+...++.|+|
T Consensus        61 ~A~~~I~~~i~e~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~-~~~~~~~~~v~I  139 (160)
T 2jzx_A           61 KAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD-MLPNSTERAITI  139 (160)
T ss_dssp             HHHHHHHHHHHHHHTSCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC-CSTTCCEEEEEE
T ss_pred             HHHHHHHHHHHhhccccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC-CCCCCCceEEEE
Confidence            33333443333321110 0 00112336899999999999999999999999999999999999874 456678999999


Q ss_pred             eecHHHHHHHHHHHHHHHhc
Q 007844          181 TGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       181 ~G~~e~V~~A~~~I~~~L~e  200 (587)
                      +|++++|.+|+.+|.+++.+
T Consensus       140 ~G~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          140 AGIPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EECHHHHHHHHHHHHHHHHH
T ss_pred             EcCHHHHHHHHHHHHHHHhc
Confidence            99999999999999999876

>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=99.91  E-value=3.4e-24  Score=203.72  Aligned_cols=159  Identities=21%  Similarity=0.325  Sum_probs=123.3

Q ss_pred             CcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        23 ~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      +..+++|+||.+++|.||||+|++|++|+++|||+|+|.+..++..||+|+|+|+.+++.+                 |.
T Consensus         1 g~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~~-----------------A~   63 (174)
T 1j4w_A            1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH-----------------AA   63 (174)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHHH-----------------HH
T ss_pred             CCeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHHH-----------------HH
Confidence            4578999999999999999999999999999999999987666788999999999877543                 33


Q ss_pred             HHHHHHHHHHHhhhhccC--------------CCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-
Q 007844          103 EAVIRVFERMWEVEAEVE--------------GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-  167 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~~--------------~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-  167 (587)
                      +.+..++...........              ........++++|+||.+++|+||||+|++|++|+++|||+|+|.+. 
T Consensus        64 ~~I~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~  143 (174)
T 1j4w_A           64 EIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP  143 (174)
T ss_dssp             HHHHHHHHHHC-----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC
T ss_pred             HHHHHHHHhcccCCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC
Confidence            333333322210000000              00001224689999999999999999999999999999999999885 


Q ss_pred             CCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          168 PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       168 p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      +.+....+++|+|+|+.++|.+|+.+|.++|
T Consensus       144 ~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          144 PPNADPNMKLFTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             TTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCceEEEEECCHHHHHHHHHHHHHhC
Confidence            4455678899999999999999999998874

>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=99.90  E-value=4.9e-24  Score=200.43  Aligned_cols=154  Identities=14%  Similarity=0.215  Sum_probs=121.3

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCC--CCCCCceEEEEecCCchhhhhhhccccccccCCCccHHH
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG--FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~--~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~  102 (587)
                      ++++|+||.+++|.||||+|++||+|+++|||+|+|.+.  .++..+|+|+|+|+.+++.                    
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v~--------------------   61 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQ--------------------   61 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHHH--------------------
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHHH--------------------
Confidence            689999999999999999999999999999999999653  3467799999999876632                    


Q ss_pred             HHHHHHHHHHHhhhhcc-C--CCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEE
Q 007844          103 EAVIRVFERMWEVEAEV-E--GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ  179 (587)
Q Consensus       103 ~Al~~i~~~i~~~~~~~-~--~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~  179 (587)
                      .|...+...+.+..... .  .+......++++|+||..++|+||||+|++|++|+++|||+|.|.+.  .+...++.|+
T Consensus        62 ~A~~~I~~ii~e~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~--~~~~~~~~v~  139 (164)
T 2jvz_A           62 QACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD--DGTGPEKIAH  139 (164)
T ss_dssp             HHHHHHHHHTTCSSSCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCC--CTTSSEEEEE
T ss_pred             HHHHHHHHHHHhccCCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCC--CCCCCcEEEE
Confidence            33333433333221100 0  00011113568899999999999999999999999999999999873  3445689999


Q ss_pred             EeecHHHHHHHHHHHHHHHhc
Q 007844          180 ITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       180 I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      |+|+.++|.+|+.+|.+++++
T Consensus       140 I~G~~~~v~~A~~~I~~~i~~  160 (164)
T 2jvz_A          140 IMGPPDRCEHAARIINDLLQS  160 (164)
T ss_dssp             EESCHHHHHHHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHhh
Confidence            999999999999999999976

>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=99.90  E-value=3.3e-23  Score=194.76  Aligned_cols=154  Identities=21%  Similarity=0.314  Sum_probs=128.2

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC-CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~-~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~  352 (587)
                      .+++|+||.+++|.||||+|++|++|+++|||+|+|.+. .+++.+|.|+|+|+.      ..+..|..++...+.+...
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 EMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPP------EAQFKAQGRIYGKLKEENF   76 (163)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCEEEECCCSSTTCSEEEEEEEECH------HHHHHHHHHHHHHHHHTTS
T ss_pred             eEEEEEechhhcceeECCCcHHHHHHHHHHCCeEEEcCCCCCCCCceEEEEEcCH------HHHHHHHHHHHHHHhcccc
Confidence            478999999999999999999999999999999999975 567899999999973      4566777777777655421


Q ss_pred             cCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHH
Q 007844          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALS  432 (587)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~  432 (587)
                      .     +.......+.+|.||.+++|+|||++|++|++|++.|||+|+|++.. .|.  ..+++.|+|+|++++|++|+.
T Consensus        77 ~-----~~~~~~~~~~~i~vp~~~~g~iIGkgG~~I~~i~~~tga~I~i~~~~-~~~--~~~~~~v~I~G~~~~v~~A~~  148 (163)
T 3krm_A           77 F-----GPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQ-TPD--ENDQVIVKIIGHFYASQMAQR  148 (163)
T ss_dssp             S-----CSSCCCCEEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEECCTTC-CCC--TTSEEEEEEEECHHHHHHHHH
T ss_pred             c-----ccccCCceEEEEEcChhheeeEEcCCChHHHHHHHHhCCeEEECCCC-CCC--CCCceEEEEEeCHHHHHHHHH
Confidence            1     11123467889999999999999999999999999999999997643 232  344568999999999999999


Q ss_pred             HHHHHHhhc
Q 007844          433 EVVGRLRHN  441 (587)
Q Consensus       433 ~I~~~Lr~~  441 (587)
                      +|.+.|++.
T Consensus       149 ~I~~~i~~~  157 (163)
T 3krm_A          149 KIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999863

>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=99.90  E-value=1.4e-23  Score=200.21  Aligned_cols=162  Identities=21%  Similarity=0.338  Sum_probs=128.2

Q ss_pred             CcceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC---CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhh
Q 007844          271 KQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS  347 (587)
Q Consensus       271 ~~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~---~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v  347 (587)
                      ..+++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|.|+|+|+.      ..+.+|..+|.+.+
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~------~~v~~A~~~I~~~~   76 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTI------EALNAVHGFIAEKI   76 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECH------HHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCH------HHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999853   356789999999984      44566776776666


Q ss_pred             hcccccCC-------CCC--CCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEE
Q 007844          348 VEVEGQQG-------FSS--GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI  418 (587)
Q Consensus       348 ~e~~~~~g-------~~~--g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V  418 (587)
                      .+......       +.+  ........+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..+.   ....++.|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~~~~---~~~~~~~v  153 (178)
T 2anr_A           77 REMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDG---INLQNRVV  153 (178)
T ss_dssp             TCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCCC-------CCEEEE
T ss_pred             hccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCCCCC---CCCCceEE
Confidence            44311000       000  0011235789999999999999999999999999999999999875432   24578999


Q ss_pred             EEcCCHHHHHHHHHHHHHHHhhc
Q 007844          419 QISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       419 ~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      +|+|++++|++|+.+|.++|++.
T Consensus       154 ~I~G~~~~v~~A~~~I~~~i~e~  176 (178)
T 2anr_A          154 TVSGEPEQNRKAVELIIQKIQED  176 (178)
T ss_dssp             EEESSHHHHHHHHHHHHHHHHSC
T ss_pred             EEEcCHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999874

>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=99.89  E-value=2.2e-23  Score=195.32  Aligned_cols=156  Identities=21%  Similarity=0.402  Sum_probs=127.6

Q ss_pred             cceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc
Q 007844          272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE  351 (587)
Q Consensus       272 ~~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~  351 (587)
                      ..++++|+||.+++|.||||+|.+|++|+++|||+|+|.+.  +..+|.|+|+|+.      ..+.+|...+.+.+.+..
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~------~~v~~A~~~I~~~i~e~~   74 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPT------NAIFKAFAMIIDKLEEDI   74 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEH------HHHHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCH------HHHHHHHHHHHHHHHhhc
Confidence            35689999999999999999999999999999999999965  4678999999983      455677777776665432


Q ss_pred             ccCCCCCC-CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHH
Q 007844          352 GQQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNA  430 (587)
Q Consensus       352 ~~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A  430 (587)
                      . ...... .......+.+|.||.+++|+|||++|++|++|++.|||+|+|.+. ..|   ..+++.|+|+|++++|++|
T Consensus        75 ~-~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~i~~~tga~I~i~~~-~~~---~~~~~~v~I~G~~~~v~~A  149 (160)
T 2jzx_A           75 S-SSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD-MLP---NSTERAITIAGIPQSIIEC  149 (160)
T ss_dssp             T-SCCCSSSCCCCCSEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHSSEECCCCC-CST---TCCEEEEEEEECHHHHHHH
T ss_pred             c-ccCCCCccCCCCCEEEEEEEChhheeeEECCCCHHHHHHHHHhCCeEEECCC-CCC---CCCceEEEEEcCHHHHHHH
Confidence            1 111110 112346899999999999999999999999999999999999763 233   4678999999999999999


Q ss_pred             HHHHHHHHhh
Q 007844          431 LSEVVGRLRH  440 (587)
Q Consensus       431 ~~~I~~~Lr~  440 (587)
                      +.+|.+.|.+
T Consensus       150 ~~~I~~~i~e  159 (160)
T 2jzx_A          150 VKQICVVMLE  159 (160)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhc
Confidence            9999998876

>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=99.88  E-value=1.1e-22  Score=193.24  Aligned_cols=157  Identities=19%  Similarity=0.306  Sum_probs=122.7

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ  353 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~  353 (587)
                      .+++|+||.+++|.||||+|++|++|+++|||+|+|.+...+..+|.|+|+|+.      ..+..|..+|.+.+.+....
T Consensus         3 ~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~------~~v~~A~~~I~~~~~~~~~~   76 (174)
T 1j4w_A            3 HMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP------DRAQHAAEIITDLLRSVQAG   76 (174)
T ss_dssp             EEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH------HHHHHHHHHHHHHHHHHC--
T ss_pred             eEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCH------HHHHHHHHHHHHHHHhcccC
Confidence            578999999999999999999999999999999999876667789999999984      44556666665555432100


Q ss_pred             C-C--------CCCC---C---CCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEE
Q 007844          354 Q-G--------FSSG---E---NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI  418 (587)
Q Consensus       354 ~-g--------~~~g---~---~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V  418 (587)
                      . +        ...+   +   ......+.+|.||.+++|+||||+|++|++|++.|||+|+|.+..  +.+...+++.|
T Consensus        77 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~~~~~~~~v  154 (174)
T 1j4w_A           77 NPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKLF  154 (174)
T ss_dssp             ---------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTTSCTTEEEE
T ss_pred             CCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCCCCCCceEE
Confidence            0 0        0000   0   011346889999999999999999999999999999999998743  22345678999


Q ss_pred             EEcCCHHHHHHHHHHHHHHH
Q 007844          419 QISGEYKNVQNALSEVVGRL  438 (587)
Q Consensus       419 ~I~G~~~~V~~A~~~I~~~L  438 (587)
                      +|+|++++|++|+.+|.++|
T Consensus       155 ~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          155 TIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEECCHHHHHHHHHHHHHHC
T ss_pred             EEECCHHHHHHHHHHHHHhC
Confidence            99999999999999999865

>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=99.88  E-value=2.2e-22  Score=189.12  Aligned_cols=156  Identities=17%  Similarity=0.243  Sum_probs=125.3

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCC--CCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE  351 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~  351 (587)
                      ++++|+||.+++|.||||+|++||+|+++|||+|++.+.  .++..+|.|+|+|+.      ..+..|...|...+.+..
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~------~~v~~A~~~I~~ii~e~~   75 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDP------YKVQQACEMVMDILRERD   75 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECH------HHHHHHHHHHHHHTTCSS
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCH------HHHHHHHHHHHHHHHhcc
Confidence            478899999999999999999999999999999999754  345678999999973      455677777777765432


Q ss_pred             ccCCCCCCC--CCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007844          352 GQQGFSSGE--NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN  429 (587)
Q Consensus       352 ~~~g~~~g~--~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~  429 (587)
                      . .++.+..  ......+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+     ...++.|+|+|++++|+.
T Consensus        76 ~-~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~-----~~~~~~v~I~G~~~~v~~  149 (164)
T 2jvz_A           76 Q-GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEH  149 (164)
T ss_dssp             S-CCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCT-----TSSEEEEEEESCHHHHHH
T ss_pred             C-CCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCC-----CCCcEEEEEEcCHHHHHH
Confidence            1 1111110  0011356889999999999999999999999999999999987542     345799999999999999


Q ss_pred             HHHHHHHHHhhc
Q 007844          430 ALSEVVGRLRHN  441 (587)
Q Consensus       430 A~~~I~~~Lr~~  441 (587)
                      |+.+|.+.|++.
T Consensus       150 A~~~I~~~i~~~  161 (164)
T 2jvz_A          150 AARIINDLLQSL  161 (164)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhh
Confidence            999999998864

>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=6.1e-22  Score=206.36  Aligned_cols=225  Identities=17%  Similarity=0.104  Sum_probs=160.1

Q ss_pred             CCceEEEEEeecceeeeeeecCc--hHHHHHHhhhCCeEEecCCC---CCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGG--RNVTRMRIESGAKIVMLPPP---ACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG--~~Ik~I~~etGa~I~I~~~p---~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ...+|+.+-||..+++.||||+|  ++|++|+++|||+|+|....   ..+......|+|+|..++|++|..+|.+++- 
T Consensus        27 ~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~AR~~I~~l~P-  105 (376)
T 3n89_A           27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNCH-  105 (376)
T ss_dssp             TTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHHHHHHHHHSCE-
T ss_pred             CCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHHHHHHHHhcCC-
Confidence            45899999999999999999999  99999999999999997631   1122456789999999999999999887431 


Q ss_pred             CCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEe
Q 007844          201 LSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLF  280 (587)
Q Consensus       201 ~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~V  280 (587)
                                                                                               .++.+.+
T Consensus       106 -------------------------------------------------------------------------l~i~~el  112 (376)
T 3n89_A          106 -------------------------------------------------------------------------FTVFMAL  112 (376)
T ss_dssp             -------------------------------------------------------------------------EEEEEEC
T ss_pred             -------------------------------------------------------------------------ceEEEEc
Confidence                                                                                     1222233


Q ss_pred             ecccccccccccchhhHhhhhhcCceEEeeCCCC--CCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCCCCC
Q 007844          281 SGWTASGIIGKRGAIVRSLQNASGALISFAAPLT--KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSS  358 (587)
Q Consensus       281 P~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~--~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~  358 (587)
                      |...++.  ..-+..|.+ ++.++++|.|.....  +.....|+|+|.+   .....+.+|+..+.+.+.+...      
T Consensus       113 p~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~---~nv~~akeA~~~Ll~~l~~~e~------  180 (376)
T 3n89_A          113 SKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITARE---KNQHELIEAAKRLNEILFRESP------  180 (376)
T ss_dssp             TTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEG---GGHHHHHHHHHHHHHHHCC--C------
T ss_pred             cccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcCh---hhHHHHHHHHHHHHHHHHhhhc------
Confidence            3322221  111234444 577999999864311  1235679999984   2233556777777777644210      


Q ss_pred             CCCCCCceEEEEEeCcccccccccCCC--chhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHH
Q 007844          359 GENKGDAVAVSILVGADFVGCLTGSGS--SAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVG  436 (587)
Q Consensus       359 g~~~~~~~t~~l~VP~~~vG~IIGkgG--~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~  436 (587)
                        .....++.+|.|+.++|..|||++|  ..|++|+++|||+|.+++.++... ...+...|+|+|+.++|++|++.|.+
T Consensus       181 --~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d-~~~~~~~ItItGs~e~V~~Ark~I~~  257 (376)
T 3n89_A          181 --APENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNE-TRGNIYEIKVVGNIDNVLKARRYIMD  257 (376)
T ss_dssp             --CCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHH
T ss_pred             --ccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCccc-ccCCceEEEEEeCHHHHHHHHHHHHh
Confidence              1134689999999999999999999  566999999999999987543110 11346799999999999999999999


Q ss_pred             HHh
Q 007844          437 RLR  439 (587)
Q Consensus       437 ~Lr  439 (587)
                      .|=
T Consensus       258 lLP  260 (376)
T 3n89_A          258 LLP  260 (376)
T ss_dssp             TSE
T ss_pred             hCC
Confidence            776

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

Probab=99.81  E-value=1.4e-19  Score=188.62  Aligned_cols=297  Identities=10%  Similarity=0.096  Sum_probs=188.0

Q ss_pred             CCCCCCCcEEEEEEeccCccceeccCCC--hHHHHHHhHhCceEEEeCCC-----CCCCceEEEEecCCchhhhhhhccc
Q 007844           17 PLNLPDDVVSFRLVCPTPVVGGLIGRSG--SIISSIRRDTKCRIHCEGGF-----PGSDHRVILVVGSGSIDRRIMFCEN   89 (587)
Q Consensus        17 ~~~~~~~~v~~riLvP~~~vG~IIGk~G--~~Ik~IreeTga~I~V~~~~-----~~~~eRvI~I~G~~e~~~~a~~~~~   89 (587)
                      ........+++.+-||..+++.||||+|  ++|++|+++|||+|+|++..     +......|+|+|..++|++      
T Consensus        22 ~le~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE~------   95 (376)
T 3n89_A           22 MIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDR------   95 (376)
T ss_dssp             CCCCCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHHH------
T ss_pred             EEEecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHHH------
Confidence            3445577899999999999999999999  99999999999999998764     1134578999999998654      


Q ss_pred             cccccCCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCC
Q 007844           90 DVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPA  169 (587)
Q Consensus        90 ~~~~e~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~  169 (587)
                                 |..+|..    +              .++++.+-+|...++.  ..-+..|.+ ++..+++|.+...+.
T Consensus        96 -----------AR~~I~~----l--------------~Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~  143 (376)
T 3n89_A           96 -----------ARMLMRR----N--------------CHFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPE  143 (376)
T ss_dssp             -----------HHHHHHH----S--------------CEEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-
T ss_pred             -----------HHHHHHh----c--------------CCceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccc
Confidence                       3333332    1              1455555555543222  111335555 567999999865321


Q ss_pred             CCCCCCcEEEEeecHHHHHHHHHHHHHHHhcCCCCCCCCcccCCCccccccCCCCCCCCCCCCCcCCCCCCCCCCCCCCC
Q 007844          170 CAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNAS  249 (587)
Q Consensus       170 ~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~y~~  249 (587)
                      ........|+|+|...+|.+|..++..+++......                                            
T Consensus       144 ~~~~~sd~V~IrG~~~nv~~akeA~~~Ll~~l~~~e--------------------------------------------  179 (376)
T 3n89_A          144 KNGIVTTYLRITAREKNQHELIEAAKRLNEILFRES--------------------------------------------  179 (376)
T ss_dssp             ----CEEEEEEEEEGGGHHHHHHHHHHHHHHHCC----------------------------------------------
T ss_pred             ccCCCCCEEEEEcChhhHHHHHHHHHHHHHHHHhhh--------------------------------------------
Confidence            111125679999999877776666655554321000                                            


Q ss_pred             ccCCCCCCCCCCCCCCCccCCCcceEEEEEeecccccccccccc--hhhHhhhhhcCceEEeeCCCC----CCCccEEEE
Q 007844          250 EFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRG--AIVRSLQNASGALISFAAPLT----KSGERVVTI  323 (587)
Q Consensus       250 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vG~IIGk~G--~~Ik~I~~~tga~I~i~~~~~----~~~er~V~I  323 (587)
                                        ......++..|.|+..+|..|||++|  ..|++|+++||++|.|++...    ......|+|
T Consensus       180 ------------------~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d~~~~~~~ItI  241 (376)
T 3n89_A          180 ------------------PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKV  241 (376)
T ss_dssp             ------------------CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC---------CCEEEEEE
T ss_pred             ------------------cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCcccccCCceEEEE
Confidence                              00123468889999999999999998  566999999999999985421    123568999


Q ss_pred             EecCCcCCCCChHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844          324 SALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (587)
Q Consensus       324 sG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~  403 (587)
                      +|+.      ..+.+|...|.+.+                 .+...+.++.+..-.-...--..|-.+.++.++-|.|.+
T Consensus       242 tGs~------e~V~~Ark~I~~lL-----------------Pv~l~Fd~~~~d~~~~~~~~~~~~~~~~~~~~v~~~~~~  298 (376)
T 3n89_A          242 VGNI------DNVLKARRYIMDLL-----------------PISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTP  298 (376)
T ss_dssp             ESCH------HHHHHHHHHHHHTS-----------------EEEEEEEEEGGGBC--------CBEEEECTTSCEEEEEE
T ss_pred             EeCH------HHHHHHHHHHHhhC-----------------CEEEEEecCCcccccccccchhHHHHHHHhcCeEEEEee
Confidence            9995      45556665555543                 456667766654433334444456667889999999976


Q ss_pred             CCcccccCCCC---CcEEEEcC---CHHHHHHHHHHHHH
Q 007844          404 GEQVLGCAAQN---DVVIQISG---EYKNVQNALSEVVG  436 (587)
Q Consensus       404 ~~~~p~~~~~~---~r~V~I~G---~~~~V~~A~~~I~~  436 (587)
                      ..--|..-.++   -..|.|++   +..++..|...++.
T Consensus       299 ~~~~~~~~~~~~~~~~~~~~~s~e~n~~~~y~~~~~~l~  337 (376)
T 3n89_A          299 SVYEPADLLSGEVPLNCASLRSKEFNIKKLYTAYQKVLS  337 (376)
T ss_dssp             EEECCSSSSCCCEEEEEEEEEEEGGGHHHHHHHHHHHBC
T ss_pred             cCCCchhhcccccccceEEEEEEeccHHHHHHHHHHHhC
Confidence            43222100111   13455554   45566666655544

>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=99.70  E-value=2.7e-17  Score=151.04  Aligned_cols=137  Identities=16%  Similarity=0.157  Sum_probs=101.5

Q ss_pred             ceEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccc
Q 007844          273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (587)
Q Consensus       273 ~~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~  352 (587)
                      .++.+++||.+.+|.+||++|++|+.|++++|  |.+.....  +...+++.|.       +|+  ++..+.. +.+   
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~~--~~~~~i~~~~-------~p~--~v~~~~~-~l~---   65 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDE--DTCTFHIYGE-------DQD--AVKKARS-FLE---   65 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEET--TTTEEEEEES-------SHH--HHHHHHH-HHC---
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccCC--CchheeeccC-------CHH--HHHHHHH-hhh---
Confidence            45788999999999999999999999999999  44432211  1234666665       222  2222211 111   


Q ss_pred             cCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCC-eEEEcCCCcccccCCCCC--cEEEEcCCHHHHHH
Q 007844          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGT-DIKLVGGEQVLGCAAQND--VVIQISGEYKNVQN  429 (587)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa-~I~i~~~~~~p~~~~~~~--r~V~I~G~~~~V~~  429 (587)
                                  ....++.||.+++|++|||+|++|+.|++.||| +|+|.+.++..  ...++  +.|+|+|++++|+.
T Consensus        66 ------------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~--~~~~~~~~~vtI~G~~~~v~~  131 (144)
T 2qnd_A           66 ------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKN--VPQEEGMVPFVFVGTKDSIAN  131 (144)
T ss_dssp             ------------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTC--CCCCTTEEEEEEEEEHHHHHH
T ss_pred             ------------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCC--ccccCCeeEEEEEeCHHHHHH
Confidence                        124789999999999999999999999999997 99998755421  11233  35899999999999


Q ss_pred             HHHHHHHHHhh
Q 007844          430 ALSEVVGRLRH  440 (587)
Q Consensus       430 A~~~I~~~Lr~  440 (587)
                      |+.+|..+|..
T Consensus       132 Ak~li~~~l~~  142 (144)
T 2qnd_A          132 ATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHh
Confidence            99999999875

>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=99.69  E-value=5.1e-17  Score=149.26  Aligned_cols=136  Identities=14%  Similarity=0.140  Sum_probs=100.1

Q ss_pred             cEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHH
Q 007844           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQE  103 (587)
Q Consensus        24 ~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~  103 (587)
                      .++.+++||.+.+|++||++|++|++|++++|  |++-... ..+++.+...+.++.+                      
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~g--I~ii~~~-~~~~~~i~~~~~p~~v----------------------   57 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPG--VTAIDLD-EDTCTFHIYGEDQDAV----------------------   57 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTT--EEEEEEE-TTTTEEEEEESSHHHH----------------------
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHC--CeEeccC-CCchheeeccCCHHHH----------------------
Confidence            35789999999999999999999999999999  5443221 2244544444444332                      


Q ss_pred             HHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCC-eEEecCCC-CCCCCCCc--EEE
Q 007844          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGA-KIVMLPPP-ACAAIDDQ--LIQ  179 (587)
Q Consensus       104 Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa-~I~I~~~p-~~~~~~dr--~V~  179 (587)
                        ..+.. +..             ...+++.||.+++|++|||+|++|+.|++.||| +|.|.+.. ......++  .|+
T Consensus        58 --~~~~~-~l~-------------~~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~~~~~~~~~vt  121 (144)
T 2qnd_A           58 --KKARS-FLE-------------FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFV  121 (144)
T ss_dssp             --HHHHH-HHC-------------EEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCCCCCTTEEEEE
T ss_pred             --HHHHH-hhh-------------cceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCccccCCeeEEE
Confidence              11111 111             113789999999999999999999999999997 99998741 11122344  489


Q ss_pred             EeecHHHHHHHHHHHHHHHhc
Q 007844          180 ITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       180 I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      |+|+.++|++|..+|.++|..
T Consensus       122 I~G~~~~v~~Ak~li~~~l~~  142 (144)
T 2qnd_A          122 FVGTKDSIANATVLLDYHLNY  142 (144)
T ss_dssp             EEEEHHHHHHHHHHHHHHHHT
T ss_pred             EEeCHHHHHHHHHHHHHHHHh
Confidence            999999999999999999965

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

Probab=99.56  E-value=7.9e-15  Score=143.22  Aligned_cols=147  Identities=16%  Similarity=0.191  Sum_probs=99.6

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHH
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA  104 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~A  104 (587)
                      -+.++.||.+++|.|||++|++|+.|+++|||+|+++.     .++.|.|.++....+               ...++.|
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d---------------~~~i~kA   93 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETED---------------PLAVWKA   93 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCS---------------HHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCC---------------HHHHHHH
Confidence            35689999999999999999999999999999999963     246788987652100               0112222


Q ss_pred             HHHHHHHHHhhhhccCCCCCCCCceEEE-EEe-----ec------ceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCC
Q 007844          105 VIRVFERMWEVEAEVEGDGDGDDVAYCG-LLA-----NT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA  172 (587)
Q Consensus       105 l~~i~~~i~~~~~~~~~~~~~~~~vt~r-llV-----p~------~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~  172 (587)
                      ...|..-......+.... --.+...+. +-+     +.      ..+|+||||+|++|+.|++.|||+|.|.       
T Consensus        94 ~~~I~~i~rg~~~e~g~~-ll~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-------  165 (219)
T 2e3u_A           94 RDIVLAIGRGFSPERAFR-LLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-------  165 (219)
T ss_dssp             HHHHHHHHTTCCHHHHGG-GGSTTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-------
T ss_pred             HHHHHHHhccCCccccce-eccCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-------
Confidence            222222110000000000 000112222 222     22      2689999999999999999999999994       


Q ss_pred             CCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          173 IDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       173 ~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                        ++.|.|.|+.++|+.|..+|.+++.+.
T Consensus       166 --~~~v~i~G~~~~i~~A~~~i~~li~g~  192 (219)
T 2e3u_A          166 --GKTVAIIGNPIQIEIAKTAIEKLARGS  192 (219)
T ss_dssp             --TTEEEEEECHHHHHHHHHHHHHHHTTC
T ss_pred             --CeEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence              467999999999999999999999663

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

Probab=99.51  E-value=2.7e-14  Score=139.49  Aligned_cols=146  Identities=15%  Similarity=0.175  Sum_probs=104.9

Q ss_pred             EEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccC
Q 007844          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ  354 (587)
Q Consensus       275 ~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~  354 (587)
                      ...+.||.+.+|.|||++|.+|+.|+++||++|+++..     ++.|+|.++..-.+ ...++.|...|...+.....+.
T Consensus        35 i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~~-----~g~V~I~~~~~t~d-~~~i~kA~~~I~~i~rg~~~e~  108 (219)
T 2e3u_A           35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSE-----TGEVWITSTKETED-PLAVWKARDIVLAIGRGFSPER  108 (219)
T ss_dssp             EEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECTT-----TCEEEEEECTTCCS-HHHHHHHHHHHHHHHTTCCHHH
T ss_pred             EEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEcC-----CCEEEEecCCCCCC-HHHHHHHHHHHHHHhccCCccc
Confidence            56799999999999999999999999999999999832     46799998731111 1345566665555431111000


Q ss_pred             CCCCCCCCCCceEEEEEeC-----------cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC
Q 007844          355 GFSSGENKGDAVAVSILVG-----------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE  423 (587)
Q Consensus       355 g~~~g~~~~~~~t~~l~VP-----------~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~  423 (587)
                      +... . ........+.++           ...+|+||||+|++|+.|++.|||+|.|..            +.|+|.|+
T Consensus       109 g~~l-l-~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~~------------~~v~i~G~  174 (219)
T 2e3u_A          109 AFRL-L-NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYG------------KTVAIIGN  174 (219)
T ss_dssp             HGGG-G-STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEET------------TEEEEEEC
T ss_pred             ccee-c-cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEECC------------eEEEEEeC
Confidence            0000 0 011122223333           237999999999999999999999999953            56999999


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 007844          424 YKNVQNALSEVVGRLRH  440 (587)
Q Consensus       424 ~~~V~~A~~~I~~~Lr~  440 (587)
                      +++++.|+.+|...|..
T Consensus       175 ~~~i~~A~~~i~~li~g  191 (219)
T 2e3u_A          175 PIQIEIAKTAIEKLARG  191 (219)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcC
Confidence            99999999999999865

>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=99.46  E-value=5.1e-14  Score=113.95  Aligned_cols=71  Identities=18%  Similarity=0.421  Sum_probs=65.3

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ...++.+|+||.+++|+|||++|++|++|+++|||+|+|.+.       +..+|.|+|+|+++++.+|+.+|..+|++
T Consensus         2 ~~~~~~~i~ip~~~ig~iIGkgG~~Ik~I~~~tga~I~i~~~-------~~~er~v~I~G~~~~v~~A~~~I~~~l~e   72 (73)
T 2axy_A            2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG-------NCPERIITLAGPTNAIFKAFAMIIDKLEE   72 (73)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECSS-------CCSEEEEEEEECHHHHHHHHHHHHHHHHC
T ss_pred             CceEEEEEEEChhHeeeEECCCCHHHHHHHHHHCCEEEEecC-------CCCcEEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            356899999999999999999999999999999999999863       24689999999999999999999999986

>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=99.45  E-value=1.4e-13  Score=113.99  Aligned_cols=74  Identities=20%  Similarity=0.414  Sum_probs=66.4

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..     .+.+++.|+|+|++++|++|+.+|.+++++.
T Consensus         4 g~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~-----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            4 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT-----SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3568999999999999999999999999999999999997632     2467899999999999999999999999863

>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=99.45  E-value=8.4e-14  Score=112.71  Aligned_cols=70  Identities=30%  Similarity=0.458  Sum_probs=65.4

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.    +..+|+|+|+|++++|.+|+.+|.++|++
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            36899999999999999999999999999999999999873    45789999999999999999999999976

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=99.45  E-value=1.1e-13  Score=112.81  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=65.0

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ..+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+..  .+..++.|+|+|+++++++|+.+|.++|++
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCC--CCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            36889999999999999999999999999999999998754321  246789999999999999999999998764

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

Probab=99.45  E-value=7.6e-14  Score=113.86  Aligned_cols=72  Identities=19%  Similarity=0.409  Sum_probs=65.7

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+..     .+..++.|+|+|+++++++|+.+|.++|++
T Consensus         3 ~~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~-----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPV-----EGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCCC-----CCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            568899999999999999999999999999999999998631     356799999999999999999999999875

>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=99.43  E-value=1.3e-13  Score=114.20  Aligned_cols=73  Identities=16%  Similarity=0.387  Sum_probs=65.3

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+..     .+..++.|+|+|+++++++|+.+|.+++.+.
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 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCC-----TTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecCC-----CCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            568999999999999999999999999999999999998632     2567999999999999999999999988753

>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=99.41  E-value=1.4e-13  Score=113.99  Aligned_cols=70  Identities=21%  Similarity=0.347  Sum_probs=63.6

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|++.+        +++.|+|+|+++++++|+++|.++++.
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 GGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD--------KEPVFAVTGMPENVDRAREEIEAHITL   76 (83)
T ss_dssp             CCSEEEEEECCHHHHHHHHTTTTSSHHHHHHHTTCEEECCCSS--------SCCEEEEEECTTTHHHHHHHHHHHHHS
T ss_pred             CCceEEEEEeChHHeeeeECCCchHHHHHHHHhCCeEEecCCC--------CCCeEEEEcCHHHHHHHHHHHHHHHhc
Confidence            4678999999999999999999999999999999999998632        368999999999999999999997664

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

Probab=99.41  E-value=2.3e-13  Score=111.04  Aligned_cols=71  Identities=23%  Similarity=0.363  Sum_probs=66.8

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .++.+|+||.+++|+||||+|++|++|+++|||+|+|.+  .++...+|.|+|+|++++|.+|+.+|.+++.+
T Consensus         4 ~~~~~i~Ip~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~--~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~   74 (76)
T 2p2r_A            4 TTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN--PVEGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECC--CCTTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             ceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcC--CCCCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            688999999999999999999999999999999999987  35677899999999999999999999999975

>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=99.41  E-value=4.2e-13  Score=111.10  Aligned_cols=72  Identities=24%  Similarity=0.414  Sum_probs=66.9

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+  .++...+|+|+|+|++++|.+|+.+|.+++.+
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 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   76 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC--TTSCSSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcC--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3789999999999999999999999999999999999987  34567889999999999999999999999976

>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=99.41  E-value=3.2e-13  Score=111.85  Aligned_cols=73  Identities=22%  Similarity=0.336  Sum_probs=66.6

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ..++.+|+||.+.+|+||||+|++|++|+++|||+|+|.+  .+++..+|.|+|+|++++|.+|+.+|.+++.+.
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 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN--PVEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECC--CCTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEec--CCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4789999999999999999999999999999999999987  356678999999999999999999999999774

>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=99.41  E-value=3.3e-13  Score=109.99  Aligned_cols=73  Identities=18%  Similarity=0.311  Sum_probs=65.8

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .++++|+||.+.+|+||||+|++|++|+++|||+|+|.+. ..+++..+|.|+|+|++++|.+|+.+|.+++.+
T Consensus         2 ~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            2 KELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             CEEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            4688999999999999999999999999999999999875 234567889999999999999999999998864

>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=99.40  E-value=5.1e-13  Score=113.07  Aligned_cols=74  Identities=16%  Similarity=0.258  Sum_probs=67.1

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+     ...++.|+|+|++++|++|+.+|.++|++.
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 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT-----TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCCCC-----CCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999999987432     456899999999999999999999998874

>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=99.39  E-value=3.1e-13  Score=113.17  Aligned_cols=74  Identities=23%  Similarity=0.367  Sum_probs=66.1

Q ss_pred             eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+..  .+..++.|+|+|++++++.|+.+|.++|.+.
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 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS--TTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            5789999999999999999999999999999999998754321  2467899999999999999999999998864

>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=99.38  E-value=2.9e-13  Score=113.84  Aligned_cols=74  Identities=20%  Similarity=0.414  Sum_probs=67.0

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..     ...+++.|+|+|++++|++|+.+|.+++++.
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~~~-----~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e~   84 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECSCC-----SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecCCC-----CCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            4678999999999999999999999999999999999997632     2467899999999999999999999999874

>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=99.37  E-value=6e-13  Score=111.93  Aligned_cols=73  Identities=23%  Similarity=0.409  Sum_probs=67.7

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ...++++|+||.+.+|.||||+|++|++|+++|||+|+|.+  .++...+|+|+|+|++++|.+|+.+|.+++.+
T Consensus        11 ~~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~I~~--~~~~~~~~~v~I~G~~e~v~~A~~~I~~~i~e   83 (89)
T 1j5k_A           11 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ   83 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECS--CCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecC--CCCCCCccEEEEEcCHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999999987  34567899999999999999999999999987

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

Probab=99.36  E-value=1e-12  Score=114.34  Aligned_cols=74  Identities=15%  Similarity=0.230  Sum_probs=65.3

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+ |. .+..++.|+|+|++++|++|+.+|.++|++..
T Consensus         8 ~~~i~IP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~-~~-~~~~~r~V~I~G~~e~v~~A~~~I~~~i~e~~   81 (107)
T 2hh2_A            8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP-PN-GDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCC-TT-CCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccC-CC-CCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            7899999999999999999999999999999999987533 21 24568999999999999999999999988743

>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=99.35  E-value=1.5e-12  Score=124.16  Aligned_cols=145  Identities=15%  Similarity=0.136  Sum_probs=100.1

Q ss_pred             EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCchhhhhhhccccccccCCCccHHHHHH
Q 007844           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (587)
Q Consensus        26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al  105 (587)
                      .++++||.+.+|.|||++|++++.|++++|++|+++.     .++.+.|..+....+.            ..+..|.+.+
T Consensus         5 ~~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t~dp------------~~i~KA~dlI   67 (191)
T 1tua_A            5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEGIPP------------VNLMKAAEVV   67 (191)
T ss_dssp             CEEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCH------------HHHHHHHHHH
T ss_pred             ceEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCH------------HHHHHHHHHH
Confidence            3699999999999999999999999999999999963     4677888733221000            0012233333


Q ss_pred             HHHHHHHHhhhhccCCCCCCCCceEEEEE-ee----------cceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCC
Q 007844          106 IRVFERMWEVEAEVEGDGDGDDVAYCGLL-AN----------TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID  174 (587)
Q Consensus       106 ~~i~~~i~~~~~~~~~~~~~~~~vt~rll-Vp----------~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~  174 (587)
                      ..+..-. +  .+... .-.++++.+.++ ++          ....|+||||+|.+|+.|+..|||+|.|.         
T Consensus        68 ~ai~rgf-~--~e~A~-~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~---------  134 (191)
T 1tua_A           68 KAISLGF-P--PEKAF-RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG---------  134 (191)
T ss_dssp             HHHHHTC-C--HHHHG-GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC---------
T ss_pred             HHHHcCC-C--HHHhh-hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc---------
Confidence            2221100 0  00000 000013444433 33          23689999999999999999999999994         


Q ss_pred             CcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          175 DQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       175 dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ++.|.|.|+++++..|...|.+++..
T Consensus       135 ~~~v~i~G~~~~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          135 EYEVAIIGDYERAMAAKQAIEMLAEG  160 (191)
T ss_dssp             SSEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             CCEEEEEeChHHHHHHHHHHHHHHcC
Confidence            35899999999999999999999965

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

Probab=99.35  E-value=1.7e-12  Score=108.25  Aligned_cols=74  Identities=22%  Similarity=0.368  Sum_probs=65.4

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|+|.+....   ....+|.|+|+|+++++++|+.+|.+.+++
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 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQ---NTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             SSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCS---STTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            45788999999999999999999999999999999999874331   246789999999999999999999998764

>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=99.34  E-value=1.6e-12  Score=110.46  Aligned_cols=76  Identities=18%  Similarity=0.344  Sum_probs=67.6

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      +..++.+|.||.+++|+||||+|++||+|+++|||+|+|.+....   ....+|.|+|+|++++|++|+.+|.++|++.
T Consensus        12 p~~~~~~i~Ip~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   87 (94)
T 1x4m_A           12 PGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQ---NTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCC---SSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCC---CCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            567899999999999999999999999999999999999864331   1346899999999999999999999998864

>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=99.34  E-value=8.6e-13  Score=110.49  Aligned_cols=74  Identities=18%  Similarity=0.294  Sum_probs=67.0

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      .++++|+||.+.+|+||||+|++|++|+++|||+|.|.+. ...++..+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus         2 k~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (87)
T 1ec6_A            2 KELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYE   76 (87)
T ss_dssp             CSEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence            4678999999999999999999999999999999999874 2345678899999999999999999999999763

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

Probab=99.33  E-value=1.5e-12  Score=112.94  Aligned_cols=73  Identities=14%  Similarity=0.230  Sum_probs=64.3

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ..+.+|.||.+++++||||+|++||+|+++|||+|+|.+...     ...+|.|+|+|+++++++|+.+|.+.+++..
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~-----~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCS-----SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCC-----CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            347899999999999999999999999999999999986432     3568999999999999999999999998744

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

Probab=99.33  E-value=2.7e-12  Score=106.92  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=66.7

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ....+.+|.||.+.+|.||||+|++|++|+++|||+|.|..+.......+|.|+|+|++++|.+|+.+|.+++.+
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 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE   85 (85)
T ss_dssp             CSSEEEEEEECTTTHHHHHTTTTHHHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEECHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEEeChhheeeeECCCCHHHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHhcC
Confidence            446789999999999999999999999999999999999885222456899999999999999999999998864

>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=99.32  E-value=1.6e-12  Score=109.93  Aligned_cols=74  Identities=22%  Similarity=0.390  Sum_probs=67.5

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ...++.+|+||.+.+|+||||+|++|++|+++|||+|+|...  .+...+|.|+|+|+.++|.+|+.+|.+++.+.
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 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD--SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   85 (92)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC--CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEChHHcceeECCCchHHHHHHHHhCCEEEEcCC--CCCCCccEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            347899999999999999999999999999999999999874  34567899999999999999999999999873

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

Probab=99.32  E-value=1.5e-12  Score=113.25  Aligned_cols=72  Identities=22%  Similarity=0.331  Sum_probs=65.0

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      +++|+||.+++|+||||+|++||+|+++|||+|+|.+. .......+|+|+|+|+.++|.+|+.+|.+++.+.
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 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGP   80 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEESCHHHHHHHHHHHHHHSCSC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccCCCCCCCceEEEEECCHHHHHHHHHHHHHHHhcc
Confidence            78999999999999999999999999999999999885 2233457899999999999999999999999874

>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=99.30  E-value=2.1e-12  Score=109.71  Aligned_cols=77  Identities=26%  Similarity=0.430  Sum_probs=68.0

Q ss_pred             CCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ....++.+|+||.+.+|+||||+|++|++|+++|||+|.|.++.......+|+|+|+|++++|.+|+.+|.+++.+.
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 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRDQ   87 (94)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCCC
T ss_pred             CCCcEEEEEEEChhhcceEECCCCHHHHHHHHHHCCeEEecCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            34578999999999999999999999999999999999998751112447899999999999999999999999773

>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=99.30  E-value=3.9e-12  Score=108.16  Aligned_cols=76  Identities=14%  Similarity=0.242  Sum_probs=67.9

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ...++.+|.||.++++.|||++|++|++|+++|||+|+|++..+      .+++.|+|+|+++++++|+++|...++++.
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~g~------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~~   87 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEEYL   87 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCCCC------CCCcEEEEEcCHHHHHHHHHHHHHHHHHHH
Confidence            56789999999999999999999999999999999999976432      347899999999999999999999988866


Q ss_pred             cC
Q 007844          443 KS  444 (587)
Q Consensus       443 ~~  444 (587)
                      -+
T Consensus        88 ~~   89 (95)
T 2ctm_A           88 AD   89 (95)
T ss_dssp             TS
T ss_pred             HH
Confidence            43

>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=99.30  E-value=3.1e-12  Score=110.70  Aligned_cols=77  Identities=19%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ....+.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+.   ...+++.|+|+|+.+++++|+.+|.+++++..
T Consensus        12 ~ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~---~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~~   88 (104)
T 1we8_A           12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSEDE   88 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCC---CCCCcceEEEEcCHHHHHHHHHHHHHHHhhCh
Confidence            467899999999999999999999999999999999999875431   12358999999999999999999999997643

>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=99.29  E-value=4.4e-12  Score=120.85  Aligned_cols=145  Identities=19%  Similarity=0.229  Sum_probs=103.2

Q ss_pred             EEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHHhhhhcccccCC
Q 007844          276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG  355 (587)
Q Consensus       276 ~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~~~v~e~~~~~g  355 (587)
                      +++.||.+.+|.|||++|++++.|++.+|++|+++.     .++.|+|..+..- ......+.|...+..-......+..
T Consensus         6 ~~i~VP~~rvg~liGk~g~~~k~i~e~~g~~i~id~-----~~~~V~i~t~~~t-~dp~~i~KA~dlI~ai~rgf~~e~A   79 (191)
T 1tua_A            6 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDT-----ENSMVIVEPEAEG-IPPVNLMKAAEVVKAISLGFPPEKA   79 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTT-SCHHHHHHHHHHHHHHHHTCCHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCC-CCHHHHHHHHHHHHHHHcCCCHHHh
Confidence            578999999999999999999999999999999983     3678888854211 1113455665555333221110000


Q ss_pred             CCCCCCCCCceEEEEEeC----------cccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHH
Q 007844          356 FSSGENKGDAVAVSILVG----------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK  425 (587)
Q Consensus       356 ~~~g~~~~~~~t~~l~VP----------~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~  425 (587)
                      .  ..-.+...-..+.++          ....|+|||++|.+|+.|++.|||+|.|..            ..|.|.|+++
T Consensus        80 ~--~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~~------------~~v~i~G~~~  145 (191)
T 1tua_A           80 F--RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGE------------YEVAIIGDYE  145 (191)
T ss_dssp             G--GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEECS------------SEEEEEEEHH
T ss_pred             h--hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEcC------------CEEEEEeChH
Confidence            0  000112222334444          246899999999999999999999999953            4899999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 007844          426 NVQNALSEVVGRLRH  440 (587)
Q Consensus       426 ~V~~A~~~I~~~Lr~  440 (587)
                      +++.|...|...+..
T Consensus       146 ~i~~Ar~~i~~li~g  160 (191)
T 1tua_A          146 RAMAAKQAIEMLAEG  160 (191)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcC
Confidence            999999999998864

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.29  E-value=6.5e-12  Score=107.19  Aligned_cols=73  Identities=15%  Similarity=0.244  Sum_probs=65.2

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ...+.+|.||.++++.|||++|++|++|+++|||+|+|++..+    ....++.|+|+|+.+++++|+.+|...+++
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----GNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC----CCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            3478999999999999999999999999999999999987543    134679999999999999999999998875

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

Probab=99.27  E-value=4.1e-12  Score=102.11  Aligned_cols=67  Identities=19%  Similarity=0.308  Sum_probs=60.7

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHH
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGR  437 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~  437 (587)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++..       ..++.|+|+|+.+++++|+.+|...
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i   69 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHH
Confidence            457889999999999999999999999999999999998632       3568999999999999999999874

>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=99.26  E-value=3.5e-12  Score=105.57  Aligned_cols=70  Identities=17%  Similarity=0.237  Sum_probs=63.5

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ...++++|.||.+++|+||||+|++||+|+++|||+|+|.+.     .++++|+|+|+.++|++|+.+|.+++..
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            457899999999999999999999999999999999999762     2478999999999999999999998764

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

Probab=99.26  E-value=4.9e-12  Score=109.62  Aligned_cols=72  Identities=18%  Similarity=0.301  Sum_probs=64.2

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ..+++|+||.+.+++||||+|++||+|+++|||+|+|.++  .....+|+|+|+|+.++|.+|+.+|.+++.+.
T Consensus        10 ~~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~--~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           10 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD--DGTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             --CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSS--CSSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecC--CCCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            3468899999999999999999999999999999999873  34557899999999999999999999999873

>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=99.25  E-value=6.5e-12  Score=106.63  Aligned_cols=72  Identities=15%  Similarity=0.232  Sum_probs=64.7

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.+++|.|||++|++|++|+++|||+|+|++.+       ..++.|+|+|+++++++|+.+|...+++.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            4568999999999999999999999999999999999998632       23579999999999999999999988764

>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=99.25  E-value=8.5e-12  Score=107.97  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=66.2

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      .+++.+|+||.+.+|+||||+|++|++|+++|||+|.|.+........++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus        13 ap~~~~i~Ip~~~ig~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T 1we8_A           13 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             CEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChhheeeeECCCCHHHHHHHHHHCCEEEEecCCCCCCCCcceEEEEcCHHHHHHHHHHHHHHHhhC
Confidence            478899999999999999999999999999999999998741111236899999999999999999999999764

>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=99.17  E-value=2.8e-11  Score=104.60  Aligned_cols=72  Identities=21%  Similarity=0.273  Sum_probs=64.2

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++..       ...+.|+|+|+.+++++|+.+|...+++..
T Consensus        15 ap~~~~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           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKELQ   86 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhHH
Confidence            458999999999999999999999999999999999998633       235699999999999999999999887643

>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=99.15  E-value=5.6e-11  Score=101.39  Aligned_cols=72  Identities=17%  Similarity=0.178  Sum_probs=64.9

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..++.|.||...++.||||+|++|++|+++|||+|.|.++ ..+...++.|+|+|..++|.+|+.+|..++.+
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 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDK-DDGNQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCT-TTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCC-CCCCCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999874 22334678999999999999999999999876

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

Probab=99.14  E-value=3.8e-11  Score=96.41  Aligned_cols=67  Identities=19%  Similarity=0.318  Sum_probs=60.6

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      ..+..|.||..++|.|||++|++|++|+++|||+|.|.++    +..+|.|+|+|..++|.+|+.+|.+++
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 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD----SEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC----CSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCC----CCcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            5678999999999999999999999999999999999773    236789999999999999999998764

>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=99.13  E-value=4.2e-11  Score=101.62  Aligned_cols=72  Identities=21%  Similarity=0.269  Sum_probs=64.8

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      +..++.+|.||...+|.|||++|++|++|+++|||+|+|.+.    ...++.|+|+|+.++|.+|+.+|.+++.+.
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~----~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP----DDPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT----TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC----CCCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            347899999999999999999999999999999999999762    224689999999999999999999999774

>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=99.10  E-value=9.7e-11  Score=99.49  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=65.3

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ...++..|.||..+++.|||++|++|++|+++|||+|+|..+   ....++.|+|+|..++|.+|+.+|..++.+.
T Consensus        14 ~~~vt~~i~Ip~~~ig~IIG~gG~~Ir~I~e~tg~~I~i~~~---g~~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   86 (95)
T 2ctm_A           14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS---GAPDPNCVTVTGLPENVEEAIDHILNLEEEY   86 (95)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT---TCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cccEEEEEEECHHHccccCCCCcchHHHHHHHHCCeEEecCC---CCCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999763   2235789999999999999999999999773

>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=99.07  E-value=1.3e-10  Score=98.50  Aligned_cols=72  Identities=14%  Similarity=0.240  Sum_probs=65.2

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhh-CCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT-GTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T-Ga~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      .+.++.+|.||.++++.|||++|++|++|+++| ||+|.|++.       +...+.|+|+|+.++|++|+.+|...+.+.
T Consensus        14 ~~~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           14 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   86 (95)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC-------CCCcceEEEEcCHHHHHHHHHHHHHHHhhh
Confidence            567899999999999999999999999999999 999999763       345679999999999999999999988763

>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=99.01  E-value=3.4e-10  Score=97.75  Aligned_cols=69  Identities=17%  Similarity=0.240  Sum_probs=62.6

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      +++..|.||...++.|||++|++|++|+++|||+|.|.+.    +...+.|+|+|..++|.+|+.+|..++.+
T Consensus        16 p~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~----g~~~~~V~I~G~~e~v~~A~~~I~~i~~e   84 (104)
T 2ctk_A           16 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAP----ELQSDIIAITGLAANLDRAKAGLLERVKE   84 (104)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCT----TTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCC----CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            5788999999999999999999999999999999999773    22456999999999999999999999876

>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=99.00  E-value=5.5e-10  Score=96.00  Aligned_cols=68  Identities=12%  Similarity=0.193  Sum_probs=61.3

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHh-hCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ..++.+|.||.++|++|||++|++|++|+++ ++++|+|++          +++.|+|+|+++.|.+|+.+|...+++.
T Consensus        25 ~~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~----------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           25 SFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC----------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            4488999999999999999999999999996 599999975          2578999999999999999999988763

>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=98.98  E-value=6.1e-10  Score=95.73  Aligned_cols=67  Identities=18%  Similarity=0.274  Sum_probs=61.2

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhh-hCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIE-SGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e-tGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      .++.+|.||..++++|||++|++|++|+++ ++++|.|+.       .++.|+|+|+.+.|.+|..+|..++.+.
T Consensus        26 ~~t~~i~vp~~~h~~IIG~~G~~Ik~i~~~~~~v~I~fp~-------~~~~ItI~G~~~~V~~a~~~I~~~v~el   93 (102)
T 2ctf_A           26 FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-------GEDKITLEGPTEDVSVAQEQIEGMVKDL   93 (102)
T ss_dssp             CEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEeCHHHHhhhcCCCCccHHHHHHHcCCcEEEeCC-------CCCEEEEECCHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999997 599999854       4679999999999999999999999763

>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=98.88  E-value=1.9e-09  Score=91.39  Aligned_cols=72  Identities=17%  Similarity=0.183  Sum_probs=64.9

Q ss_pred             CCCceEEEEEeecceeeeeeecCchHHHHHHhhh-CCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIES-GAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~et-Ga~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .++.++..|.||..+++.|||++|++|++|+++| ||+|.|...    +...+.|+|+|..++|.+|+.+|.+++.+
T Consensus        13 ~~~~vt~~i~Ip~~~i~~iIG~gGk~Ir~I~eetggv~I~i~~~----g~~~~~V~I~G~~~~v~~A~~~I~~iv~e   85 (95)
T 2ctj_A           13 LANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE----GSGSDTVVIRGPSSDVEKAKKQLLHLAEE   85 (95)
T ss_dssp             CCSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT----TTTCCEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             HhhcEEEEEEECHHHHhhhCCCCchhHHHHHHHcCCCEEEeCCC----CCCcceEEEEcCHHHHHHHHHHHHHHHhh
Confidence            3457889999999999999999999999999999 999999762    34567899999999999999999999976

>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=4e-09  Score=88.03  Aligned_cols=73  Identities=19%  Similarity=0.192  Sum_probs=62.3

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCe-EEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (587)
                      ...+..+|.||.+++|.+||++|++|++|++.|||+ |.|.+          ++..|+|.| +.+++++|+.+|...-..
T Consensus        12 ~~~~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           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE----------DTGTFRIYGESADAVKKARGFLEFVEDF   81 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET----------TTTEEEEEESSHHHHHHHHHHHSCCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc----------CCCEEEEEECCHHHHHHHHHHHHhhheE
Confidence            356889999999999999999999999999999998 99953          358999999 899999999999875444


Q ss_pred             cccCc
Q 007844          441 NLKSG  445 (587)
Q Consensus       441 ~~~~~  445 (587)
                      +.++.
T Consensus        82 ~~vp~   86 (91)
T 2cpq_A           82 IQVPS   86 (91)
T ss_dssp             CCCCS
T ss_pred             EecCh
Confidence            44443

>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=98.51  E-value=7.5e-08  Score=80.33  Aligned_cols=67  Identities=22%  Similarity=0.254  Sum_probs=58.5

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCe-EEecCCCCCCCCCCcEEEEee-cHHHHHHHHHHHHHHHh
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQ  199 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~-I~I~~~p~~~~~~dr~V~I~G-~~e~V~~A~~~I~~~L~  199 (587)
                      ...+...|.||.+.+|.+||++|++|++|+++|||+ |.|..       ++..|+|.| +.+++.+|+.+|..+-.
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-------ddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-------CCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            346888999999999999999999999999999998 99964       458999999 69999999988765443

>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=98.44  E-value=3.7e-07  Score=81.75  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=63.0

Q ss_pred             CceEEEEEeCcc------cccccccCCCchhHHHHHhhCCeEEEcCCCcc-----------cccCCCCCcEEEEcC-CHH
Q 007844          364 DAVAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGCAAQNDVVIQISG-EYK  425 (587)
Q Consensus       364 ~~~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~-----------p~~~~~~~r~V~I~G-~~~  425 (587)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|..+.-.           +.....++-.|.|++ +.+
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            457889999988      88999999999999999999999999763210           000123467888888 578


Q ss_pred             HHHHHHHHHHHHHhhcc
Q 007844          426 NVQNALSEVVGRLRHNL  442 (587)
Q Consensus       426 ~V~~A~~~I~~~Lr~~~  442 (587)
                      .+++|+.+|...|..++
T Consensus        85 ~~~~A~~~I~~ll~~~~  101 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQGI  101 (131)
T ss_dssp             HHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHhccC
Confidence            99999999999987744

>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=98.35  E-value=6.9e-07  Score=80.02  Aligned_cols=73  Identities=18%  Similarity=0.215  Sum_probs=61.7

Q ss_pred             ceEEEEEeecc------eeeeeeecCchHHHHHHhhhCCeEEecCCC--------------CCCCCCCcEEEEeec-HHH
Q 007844          128 VAYCGLLANTT------KIGVVVGKGGRNVTRMRIESGAKIVMLPPP--------------ACAAIDDQLIQITGA-TLA  186 (587)
Q Consensus       128 ~vt~rllVp~~------~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p--------------~~~~~~dr~V~I~G~-~e~  186 (587)
                      .++.+|.||.+      .+|.|||++|.+||+|+++|||+|.|....              ......+-.|.|++. .++
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            68899999988      888999999999999999999999997530              001234668889996 999


Q ss_pred             HHHHHHHHHHHHhc
Q 007844          187 VKKALVAVTTCLQH  200 (587)
Q Consensus       187 V~~A~~~I~~~L~e  200 (587)
                      +.+|+.+|..+|.+
T Consensus        86 ~~~A~~~I~~ll~~   99 (131)
T 1k1g_A           86 VKKAVEQIRNILKQ   99 (131)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999976

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

Probab=98.28  E-value=2.8e-06  Score=74.59  Aligned_cols=77  Identities=22%  Similarity=0.230  Sum_probs=58.2

Q ss_pred             CceEEEEEeCcc-------cccccccCCCchhHHHHHhhCCeEEEcCCCc-----ccccCCCCCcEEEEc-CCHHHHHHH
Q 007844          364 DAVAVSILVGAD-------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ-----VLGCAAQNDVVIQIS-GEYKNVQNA  430 (587)
Q Consensus       364 ~~~t~~l~VP~~-------~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~-----~p~~~~~~~r~V~I~-G~~~~V~~A  430 (587)
                      ...+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|..+.-     ...-...++-.|.|+ .+.+++++|
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            357788888764       8999999999999999999999999964311     000011234567776 568899999


Q ss_pred             HHHHHHHHhh
Q 007844          431 LSEVVGRLRH  440 (587)
Q Consensus       431 ~~~I~~~Lr~  440 (587)
                      +.+|...|..
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999998885

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

Probab=98.23  E-value=1.6e-06  Score=76.13  Aligned_cols=73  Identities=21%  Similarity=0.189  Sum_probs=58.4

Q ss_pred             ceEEEEEeecc-------eeeeeeecCchHHHHHHhhhCCeEEecCCC--------CCCCCCCcEEEEeec-HHHHHHHH
Q 007844          128 VAYCGLLANTT-------KIGVVVGKGGRNVTRMRIESGAKIVMLPPP--------ACAAIDDQLIQITGA-TLAVKKAL  191 (587)
Q Consensus       128 ~vt~rllVp~~-------~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p--------~~~~~~dr~V~I~G~-~e~V~~A~  191 (587)
                      .++.+|.||-.       .+|.|||++|.+||+|+++|||+|.|..+.        ......+-.|.|.+. .+++.+|+
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            57788988875       788999999999999999999999997320        001123456778766 99999999


Q ss_pred             HHHHHHHhc
Q 007844          192 VAVTTCLQH  200 (587)
Q Consensus       192 ~~I~~~L~e  200 (587)
                      .+|.++|.+
T Consensus        91 ~~Ie~Ll~~   99 (119)
T 2yqr_A           91 KLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhhc
Confidence            999999975

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

Probab=97.92  E-value=8.8e-06  Score=73.29  Aligned_cols=74  Identities=23%  Similarity=0.324  Sum_probs=55.2

Q ss_pred             eEEEEEeCcc------cccccccCCCchhHHHHHhhCCeEEEcCCCcc------------cccC-CCCCcEEEEcCC-HH
Q 007844          366 VAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV------------LGCA-AQNDVVIQISGE-YK  425 (587)
Q Consensus       366 ~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~------------p~~~-~~~~r~V~I~G~-~~  425 (587)
                      ++.+|.||-+      ++|.|||++|.++|+|+++|||+|.|-.+.-.            |.+. ..+.--|.|++. ++
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      59999999999999999999999999865410            1111 223347778874 32


Q ss_pred             -----HHHHHHHHHHHHHh
Q 007844          426 -----NVQNALSEVVGRLR  439 (587)
Q Consensus       426 -----~V~~A~~~I~~~Lr  439 (587)
                           .+++|+.+|...|.
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                 78999999988776

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

Probab=97.88  E-value=8.1e-06  Score=73.54  Aligned_cols=72  Identities=21%  Similarity=0.265  Sum_probs=56.1

Q ss_pred             eEEEEEeecce------eeeeeecCchHHHHHHhhhCCeEEecCCCCC----------------CCCCCcEEEEeec-HH
Q 007844          129 AYCGLLANTTK------IGVVVGKGGRNVTRMRIESGAKIVMLPPPAC----------------AAIDDQLIQITGA-TL  185 (587)
Q Consensus       129 vt~rllVp~~~------vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~----------------~~~~dr~V~I~G~-~e  185 (587)
                      ++.++.||.+.      +|.|||++|.++|+|+++|||+|.|..+-..                ....+=-|.|++. .+
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            56788999765      8999999999999999999999999864100                0112237889985 32


Q ss_pred             -----HHHHHHHHHHHHHhc
Q 007844          186 -----AVKKALVAVTTCLQH  200 (587)
Q Consensus       186 -----~V~~A~~~I~~~L~e  200 (587)
                           .+.+|+.+|..+|..
T Consensus        82 ~~~~~~l~~A~~~I~~lL~p  101 (140)
T 2bl5_A           82 NRAELKLKRAVEEVKKLLVP  101 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             hhHHHHHHHHHHHHHHHCCC
Confidence                 799999999999864

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

Probab=97.69  E-value=4.2e-05  Score=85.41  Aligned_cols=92  Identities=15%  Similarity=0.192  Sum_probs=68.6

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..+++..+.+...+...+...-.+....|-||.+.++.|||+||++||+|+++|||+|.|..        +..|
T Consensus       537 ~~A~~g~~~I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d--------~G~V  608 (630)
T 3u1k_A          537 QQASVAKKEILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD--------EETF  608 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS--------SSEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC--------CcEE
Confidence            44666666666665544332211122233667888999999999999999999999999999999954        5789


Q ss_pred             EEeec-HHHHHHHHHHHHHHH
Q 007844          179 QITGA-TLAVKKALVAVTTCL  198 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L  198 (587)
                      .|.|. .+++.+|+.+|..++
T Consensus       609 ~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          609 SVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             EEEESSHHHHHHHHHHTTC--
T ss_pred             EEEeCCHHHHHHHHHHHHHHh
Confidence            99998 789999999987654

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

Probab=97.62  E-value=5.3e-05  Score=84.58  Aligned_cols=65  Identities=14%  Similarity=0.162  Sum_probs=55.6

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHH
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRL  438 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~L  438 (587)
                      ......++.||.++++.|||+||++||+|+++|||+|.|.+           +-.|.|.|+ .+.+++|+++|.+.+
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            35678889999999999999999999999999999999953           578999987 578999999987654

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

Probab=97.59  E-value=0.00013  Score=64.49  Aligned_cols=67  Identities=12%  Similarity=0.071  Sum_probs=59.7

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr  439 (587)
                      ...+.|.++.++.|+|++|+.|+.|+..|+|.|+|..-+      .++.-.|+|.|++..-..|+.+|.....
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~------s~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWG------PERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCC------TTSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccC------CCCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            456889999999999999999999999999999998753      2468999999999999999999987655

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

Probab=97.54  E-value=4e-05  Score=69.41  Aligned_cols=103  Identities=17%  Similarity=0.234  Sum_probs=72.1

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHH
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQE  103 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~  103 (587)
                      -.+.++|+...+|+.||++|++|+.|+++.|-+|+|-....+           ++. +.++             ++||. 
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d-----------~~~fI~na-------------LsPA~-   90 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSD-----------LERIVKNL-------------FPGVK-   90 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSS-----------HHHHHHHH-------------STTSC-
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCC-----------HHHHHHHh-------------cCCce-
Confidence            356789999999999999999999999999999998543211           110 0000             11110 


Q ss_pred             HHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEec
Q 007844          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (587)
Q Consensus       104 Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~  165 (587)
                              +.......    . +....+.+.||..+.+..|||+|.+++-..+-||.+|.|.
T Consensus        91 --------V~~V~i~~----~-~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~  139 (144)
T 2cxc_A           91 --------IESINVRE----R-NGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVE  139 (144)
T ss_dssp             --------EEEEEEEE----E-TTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEE
T ss_pred             --------EEEEEEee----c-CCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCce
Confidence                    00000000    0 1256788999999999999999999999999999887764

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

Probab=97.00  E-value=0.0011  Score=58.64  Aligned_cols=68  Identities=13%  Similarity=0.029  Sum_probs=59.6

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .+.+.|.+..++.|+|++|+.|+.|+..|+|.|++...  . .+..--|+|.|++..=.+|+.+|..+..-
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~--~-s~g~tEVtIfG~~~~Q~rak~MI~sLA~~  124 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVW--G-PERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC--C-TTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc--C-CCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            35678899999999999999999999999999999884  2 23567799999999999999999988754

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

Probab=96.88  E-value=0.00047  Score=77.89  Aligned_cols=94  Identities=17%  Similarity=0.242  Sum_probs=25.2

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..+++..+.+.....-.+-....+....|-||.+.++.|||+||.+||+|.++||++|.|..        |..|
T Consensus       540 ~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d--------dG~v  611 (726)
T 4aid_A          540 AQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND--------DGVV  611 (726)
T ss_dssp             HHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC-------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC--------CceE
Confidence            44666666666665543322211111223456678899999999999999999999999999999954        4567


Q ss_pred             EEeec-HHHHHHHHHHHHHHHhc
Q 007844          179 QITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .|.+. .+++.+|+.+|..++.+
T Consensus       612 ~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          612 KVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             --CCSCHHHHHHHHHC-------
T ss_pred             EEEeCCHHHHHHHHHHHHHHhhh
Confidence            77776 89999999999988864

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

Probab=96.86  E-value=0.00066  Score=61.41  Aligned_cols=103  Identities=20%  Similarity=0.210  Sum_probs=72.7

Q ss_pred             eEEEEEeecccccccccccchhhHhhhhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhccc
Q 007844          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVE  351 (587)
Q Consensus       274 ~~~~i~VP~~~vG~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~  351 (587)
                      ..+.++|+...+|..||++|.+|+.|.++.|-+|.|-.-..+                   +. .-+...+  .++....
T Consensus        36 dr~i~vVk~g~vGa~IG~~G~ri~~i~~elgekIdIV~~s~d-------------------~~-~fI~naLsPA~V~~V~   95 (144)
T 2cxc_A           36 NRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSD-------------------LE-RIVKNLFPGVKIESIN   95 (144)
T ss_dssp             TEEEEEECTTCHHHHHCGGGHHHHHHHHHHSSEEEEEECCSS-------------------HH-HHHHHHSTTSCEEEEE
T ss_pred             CEEEEEEeCCCccccCccCchHHHHHHHHhCCeeEEEEcCCC-------------------HH-HHHHHhcCCceEEEEE
Confidence            366788999999999999999999999999999877643211                   00 0010000  0111100


Q ss_pred             ccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcC
Q 007844          352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (587)
Q Consensus       352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~  403 (587)
                      ..       ..+......+.||.++.+..|||+|.+++-..+.||.+|.|.+
T Consensus        96 i~-------~~~~~~~~~V~V~~~q~slAIGk~G~NvrLa~~Ltg~~idI~~  140 (144)
T 2cxc_A           96 VR-------ERNGVKQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFGVEK  140 (144)
T ss_dssp             EE-------EETTEEEEEEEECTTTHHHHHCGGGHHHHHHHHHHHHHHCEEE
T ss_pred             Ee-------ecCCcEEEEEEEChHHhhhccCCCCHHHHHHHHHhCCeeCceE
Confidence            00       0023467889999999999999999999999999999887743

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

Probab=96.86  E-value=0.0006  Score=77.04  Aligned_cols=97  Identities=12%  Similarity=0.154  Sum_probs=22.3

Q ss_pred             hHHHHHHHHHhhhhcccccCCCCCCCCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCC
Q 007844          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (587)
Q Consensus       335 ~a~~Av~~i~~~v~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~  414 (587)
                      .+.++...|++.+.+..... .. ..........++.||.++++.|||+||.+||+|+++|||+|.|.+           
T Consensus       541 ~A~~g~~~I~~~m~~al~~~-r~-~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d-----------  607 (726)
T 4aid_A          541 QAKEGRAHILGEMNKAMDAP-RA-DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-----------  607 (726)
T ss_dssp             HHHHHHHHHHHHHHTTCSSC-CS-SCCSSCCC------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhh-hh-hhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-----------
Confidence            34445555665554432111 00 011233456788999999999999999999999999999998843           


Q ss_pred             CcEEEEcCC-HHHHHHHHHHHHHHHhhcccC
Q 007844          415 DVVIQISGE-YKNVQNALSEVVGRLRHNLKS  444 (587)
Q Consensus       415 ~r~V~I~G~-~~~V~~A~~~I~~~Lr~~~~~  444 (587)
                      +..|.|.+. .+++++|+.+|...+.+..+.
T Consensus       608 dG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG  638 (726)
T 4aid_A          608 DGVVKVSASDGAKIKAAIDWIKSITDEAEVG  638 (726)
T ss_dssp             ------CCSCHHHHHHHHHC-----------
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhhhhcCC
Confidence            455677666 778999999999887765433

>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=95.94  E-value=0.004  Score=61.15  Aligned_cols=95  Identities=14%  Similarity=0.121  Sum_probs=63.4

Q ss_pred             CccceeccCCChHHHHH-HhHhCceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSI-RRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEAVIRVFER  111 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~I-reeTga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~  111 (587)
                      +-+|+.||++|++|+.| ++-.|-+|+|-....+           ++. +.+|             ++||.         
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-----------p~~fi~na-------------lsPA~---------  172 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-----------PARFVANA-------------LSPAK---------  172 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-----------HHHHHHHH-------------TTTSC---------
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC-----------HHHHHHhc-------------cCCcc---------
Confidence            55899999999999999 6666888887543211           100 0000             11110         


Q ss_pred             HHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          112 MWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       112 i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                      +......+      ...-.+.+.||..+.+.-|||+|.+++.-..-||.+|.|...
T Consensus       173 V~~V~i~~------~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          173 VVSVSVID------QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             CSEEEEEE------TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             eEEEEEEc------CCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            00000000      012468899999999999999999999999999999999763

>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=95.81  E-value=0.0051  Score=63.74  Aligned_cols=95  Identities=14%  Similarity=0.158  Sum_probs=65.0

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEAVIRVFER  111 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~  111 (587)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+           ++. +.+|             ++||.         
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-----------p~~fi~na-------------lsPA~---------  295 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-----------PARFVANA-------------LSPAK---------  295 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-----------HHHHHHHH-------------TTTSC---------
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCC-----------HHHHHHHh-------------cCCcc---------
Confidence            568999999999999999999 888887543211           000 0000             11110         


Q ss_pred             HHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC
Q 007844          112 MWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (587)
Q Consensus       112 i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~  167 (587)
                      +..... .     ......+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus       296 V~~V~~-~-----~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          296 VVSVSV-I-----DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             CSEEEE-E-----ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             eeEEEE-E-----cCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            000000 0     0114468899999999999999999999999999999999763

>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=94.69  E-value=0.037  Score=54.32  Aligned_cols=96  Identities=21%  Similarity=0.195  Sum_probs=65.3

Q ss_pred             ccccccccccchhhHhh-hhhcCceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhcccccCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSL-QNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG  359 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I-~~~tga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~~~~g~~~g  359 (587)
                      +-+|.-||++|.+|+.| ++-.|-+|.|-.-..+                   ++ .-+...+  .++.....       
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-------------------p~-~fi~nalsPA~V~~V~i-------  178 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-------------------PA-RFVANALSPAKVVSVSV-------  178 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-------------------HH-HHHHHHTTTSCCSEEEE-------
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC-------------------HH-HHHHhccCCcceEEEEE-------
Confidence            56899999999999999 6667888877643211                   11 0111100  00100000       


Q ss_pred             CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (587)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~  406 (587)
                       ......++.+.||.++.+.-|||+|.+++.-.+.||.+|.|...++
T Consensus       179 -~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          179 -IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             -EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             -EcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence             0012347889999999999999999999999999999999987554

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.15  E-value=0.031  Score=57.65  Aligned_cols=94  Identities=22%  Similarity=0.288  Sum_probs=63.3

Q ss_pred             CccceeccCCChHHHHHHhHh-CceEEEeCCCCCCCceEEEEecCCch-hhhhhhccccccccCCCccHHHHHHHHHHHH
Q 007844           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEAVIRVFER  111 (587)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~~~~eRvI~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~  111 (587)
                      +-+|+.||.+|+.|+.+.++. |-+|+|-....+           ++. +.+|             ++||     +    
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~d-----------~~~fi~na-------------l~Pa-----~----  291 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDD-----------PKQLIANA-------------LAPA-----T----  291 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSS-----------HHHHHHHH-------------TCSS-----C----
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCCC-----------HHHHHHHh-------------cCcc-----E----
Confidence            568999999999999999999 667776433111           000 0000             0111     0    


Q ss_pred             HHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecC
Q 007844          112 MWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (587)
Q Consensus       112 i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~  166 (587)
                      +......      ....-.+.+.||..+.+.-|||+|.+++.-..-||.+|.|..
T Consensus       292 v~~v~~~------d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          292 VIEVEIL------DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             CSEEEEE------ETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             EEEEEEE------cCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            0000000      011446889999999999999999999999999999999965

>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=94.12  E-value=0.054  Score=56.12  Aligned_cols=96  Identities=20%  Similarity=0.180  Sum_probs=66.4

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhcccccCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG  359 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~~~~g~~~g  359 (587)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-..+                   ++ .-+...+  .++.....       
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-------------------p~-~fi~nalsPA~V~~V~~-------  301 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-------------------PA-RFVANALSPAKVVSVSV-------  301 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-------------------HH-HHHHHHTTTSCCSEEEE-------
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCC-------------------HH-HHHHHhcCCcceeEEEE-------
Confidence            568999999999999999998 877776532111                   11 0111100  01100000       


Q ss_pred             CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (587)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~  406 (587)
                       ..+....+.+.||..+.+..|||+|.+++-..+.||.+|.|....+
T Consensus       302 -~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  347 (366)
T 1k0r_A          302 -IDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  347 (366)
T ss_dssp             -EETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEESSC
T ss_pred             -EcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEHHH
Confidence             0012457899999999999999999999999999999999987554

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

Probab=93.62  E-value=0.022  Score=64.59  Aligned_cols=93  Identities=20%  Similarity=0.242  Sum_probs=9.8

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++...++..+..........-..-.+....+-||.+.++.+||++|.+|+.|.+++|+.|.|..        +..|
T Consensus       530 ~~A~~~~~~I~~~m~~al~~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk~I~~I~~~~G~~IdI~~--------dg~v  601 (723)
T 3cdi_A          530 NQAKGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIED--------DGTV  601 (723)
T ss_dssp             HHHHHHHHHHHHHHHHHCC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhhhcchhccccCceEEEEEECHHHhcccccccceeeeeeehhhCceEEecC--------CccE
Confidence            34555666666555443322211111122455667889999999999999999999999999998843        4567


Q ss_pred             EEeec-HHHHHHHHHHHHHHHh
Q 007844          179 QITGA-TLAVKKALVAVTTCLQ  199 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~  199 (587)
                      .|.+. .+.+.+|..+|..++.
T Consensus       602 ~I~~~~~~~~~~a~~~i~~i~~  623 (723)
T 3cdi_A          602 KIAATDGEKAKHAIRRIEEITA  623 (723)
T ss_dssp             ----------------------
T ss_pred             EEecCCHHHHHHHHHHHHHHhh
Confidence            77665 6777888777776654

>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=92.60  E-value=0.018  Score=65.61  Aligned_cols=91  Identities=19%  Similarity=0.245  Sum_probs=34.3

Q ss_pred             cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEE
Q 007844           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (587)
Q Consensus        99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V  178 (587)
                      ..|.++..+++..+....... ..-..-.+....+-||.+.++.+||++|.+|++|.+++|+.|.|..        +..|
T Consensus       569 ~~A~~~~~~I~~~m~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~--------dG~v  639 (757)
T 1e3p_A          569 KQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED--------DGTI  639 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSC-CCCCTTSCBCCCC------------------CTTCCCCCSCC----------------
T ss_pred             HHHHHHHHHHHHHHHHHhccc-ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC--------CceE
Confidence            446666666666655433322 2111122344457799999999999999999999999999998843        4667


Q ss_pred             EEeec-HHHHHHHHHHHHHHH
Q 007844          179 QITGA-TLAVKKALVAVTTCL  198 (587)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L  198 (587)
                      .|+.. .+...+|...|..+.
T Consensus       640 ~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          640 YIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             CCCBSSHHHHCC---------
T ss_pred             EEecCCHHHHHHHHHHHHHhc
Confidence            77766 677777776666544

>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=91.57  E-value=0.025  Score=64.35  Aligned_cols=64  Identities=17%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHH
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRL  438 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~L  438 (587)
                      ......+.||.++++.+||++|.+||+|++.||+.|.|..           +..|.|+.. .+..++|+.+|....
T Consensus       596 ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------dG~v~Is~~~~~~~~~a~~~i~~i~  660 (757)
T 1e3p_A          596 APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAADGPAAEAARATINGIA  660 (757)
T ss_dssp             SCBCCCC------------------CTTCCCCCSCC-------------------CCCBSSHHHHCC---------
T ss_pred             CceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------CceEEEecCCHHHHHHHHHHHHHhc
Confidence            3445568899999999999999999999999999998853           355666654 456666766665543

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

Probab=91.29  E-value=0.063  Score=60.83  Aligned_cols=66  Identities=18%  Similarity=0.296  Sum_probs=0.0

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHHhh
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRH  440 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~Lr~  440 (587)
                      ......+.||.++++.+||++|.+|++|.++||+.|.|..           +..|.|.+. .+.+++|+.+|...+.+
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            4456778999999999999999999999999999997743           355666654 45677787777665544

>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=91.04  E-value=0.24  Score=51.02  Aligned_cols=94  Identities=18%  Similarity=0.180  Sum_probs=63.7

Q ss_pred             ccccccccccchhhHhhhhhc-CceEEeeCCCCCCCccEEEEEecCCcCCCCChHHHHHHHHH--hhhhcccccCCCCCC
Q 007844          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG  359 (587)
Q Consensus       283 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~er~V~IsG~~~p~~~~~~a~~Av~~i~--~~v~e~~~~~g~~~g  359 (587)
                      +-+|..||.+|.+|+.|.++. |-+|.+-.-..                   .++ .-+...+  .++.....       
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~-------------------d~~-~fi~nal~Pa~v~~v~~-------  297 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSD-------------------DPK-QLIANALAPATVIEVEI-------  297 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS-------------------SHH-HHHHHHTCSSCCSEEEE-------
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCC-------------------CHH-HHHHHhcCccEEEEEEE-------
Confidence            568999999999999999998 66666543211                   111 0111000  01100000       


Q ss_pred             CCCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCC
Q 007844          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (587)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~  404 (587)
                       ..+...++.+.||..+.+.-|||+|.+++.-.+.||.+|.|...
T Consensus       298 -~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          298 -LDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             -EETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             -EcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence             00234578899999999999999999999999999999999753

---

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	587
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	3e-09
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	5e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	1e-04
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-04
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	5e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	8e-08
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	2e-05
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	8e-05
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	9e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-05
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-05
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-08
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	1e-06
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-04
d1j4wa1	74	d.51.1.1 (A:1-74) Far upstream binding element, FB	2e-04
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-08
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	2e-06
d1x4ma1	81	d.51.1.1 (A:8-88) Far upstream binding element, FB	3e-04
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	4e-08
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	2e-06
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	3e-05
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	7e-04
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	1e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	9e-07
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	2e-06
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	0.002
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	1e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	4e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	6e-05
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	0.004
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	4e-07
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	8e-06
d1we8a_	104	d.51.1.1 (A:) Tudor and KH domain containing prote	1e-05
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	8e-06
d2ctla1	84	d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [T	2e-04
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	2e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	5e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.001
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	3e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	4e-04
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	9e-04
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	0.001
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	1e-04
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.003
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.004
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	4e-04
d1e3ha4	54	d.52.3.1 (A:579-632) Polynucleotide phosphorylase/	0.001
d2ctma1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
d2cpqa1	78	d.51.1.1 (A:212-289) Fragile X mental retardation	0.003

>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 = 51.4 bits (123), Expect = 3e-09
 Identities = 16/53 (30%), Positives = 27/53 (50%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
           +  L  P  ++G +IGR G+ I+ IR+ +  +I       GS  R + + GS
Sbjct: 2  TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS 54

>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 = 44.8 bits (106), Expect = 5e-07
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            IG ++G+ G N+  +R  SGA+I +  P   +    + + ITG+  ++  A   +    
Sbjct: 12  LIGCIIGRQGANINEIRQMSGAQIKIANPVEGS--SGRQVTITGSAASISLAQYLIN--- 66

Query: 199 QHLS 202
             LS
Sbjct: 67  ARLS 70

>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 = 38.3 bits (89), Expect = 1e-04
 Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 370 ILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN 429
           + +  + +GC+ G   + ++E+  ++G  IK+            +   + I+G   ++  
Sbjct: 6   LTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN-----PVEGSSGRQVTITGSAASISL 60

Query: 430 ALSEVVGRL 438
           A   +  RL
Sbjct: 61  AQYLINARL 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 = 37.9 bits (88), Expect = 2e-04
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTR 332
           +    +         IIG++GA +  ++  SGA I  A P+  S  R VTI+      + 
Sbjct: 1   QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITG-----SA 55

Query: 333 HSPVQNAAVLVFAR 346
            S +  A  L+ AR
Sbjct: 56  AS-ISLAQYLINAR 68

>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 = 51.0 bits (122), Expect = 5e-09
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          V++     P  +VG +IGR G  IS I++++ C+I       G   R  ++ G+
Sbjct: 7  VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGT 60

>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 = 47.5 bits (113), Expect = 8e-08
 Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            +G ++G+GG  ++R++ ESG KI +   P    + ++   +TG   +V+ A   +   +
Sbjct: 18  MVGFIIGRGGEQISRIQQESGCKIQI--APDSGGLPERSCMLTGTPESVQSAKRLLDQIV 75

Query: 199 Q 199
           +
Sbjct: 76  E 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 = 41.0 bits (96), Expect = 2e-05
 Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 15/93 (16%)

Query: 360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419
           + +   +     V    VG + G G   +S ++  +G  I++             +    
Sbjct: 2   QQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAP-----DSGGLPERSCM 56

Query: 420 ISGEYKNVQNALSEVVGRLRHNLKSGEILNEAR 452
           ++G  ++VQ+A   +           +I+ + R
Sbjct: 57  LTGTPESVQSAKRLLD----------QIVEKGR 79

>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 = 39.0 bits (91), Expect = 8e-05
 Identities = 11/55 (20%), Positives = 19/55 (34%)

Query: 270 RKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           ++  +             IIG+ G  +  +Q  SG  I  A       ER   ++
Sbjct: 4   QRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLT 58

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          +  ++ RL+     VG +IG+ G  +  +R ++  RI+          R+I + G 
Sbjct: 1  NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGP 54

>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 = 47.1 bits (112), Expect = 9e-08
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 4/67 (5%)

Query: 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALV 192
           LL +  ++G ++GK G +V +MR ESGA+I +          +++I + G T A+ KA  
Sbjct: 8   LLMHGKEVGSIIGKKGESVKKMREESGARINISEGNC----PERIITLAGPTNAIFKAFA 63

Query: 193 AVTTCLQ 199
            +   L+
Sbjct: 64  MIIDKLE 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 = 41.3 bits (97), Expect = 1e-05
 Identities = 13/74 (17%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425
           + + +L+    VG + G    +V +M + +G  I +  G          + +I ++G   
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-------CPERIITLAGPTN 56

Query: 426 NVQNALSEVVGRLR 439
            +  A + ++ +L 
Sbjct: 57  AIFKAFAMIIDKLE 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 = 40.5 bits (95), Expect = 2e-05
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           + +R+L  G     IIGK+G  V+ ++  SGA I+ +       ER++T++
Sbjct: 4   LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLA 52

>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 = 49.5 bits (118), Expect = 2e-08
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
             +  P   VG +IGR+G +I  I+ D   RI  +     +  R+  + G 
Sbjct: 4  MIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55

>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 = 43.7 bits (103), Expect = 1e-06
 Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            +G+V+G+ G  + +++ ++G +I   P        +++ QITG     + A   +T  L
Sbjct: 13  AVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTT--PERIAQITGPPDRAQHAAEIITDLL 70

Query: 199 Q 199
           +
Sbjct: 71  R 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 = 37.9 bits (88), Expect = 2e-04
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
           + + +    VG + G     + ++++  G  I+              + + QI+G     
Sbjct: 5   IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQ-----FKPDDGTTPERIAQITGPPDRA 59

Query: 428 QNALSEVVGRLR 439
           Q+A   +   LR
Sbjct: 60  QHAAEIITDLLR 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 = 37.5 bits (87), Expect = 2e-04
 Identities = 11/37 (29%), Positives = 21/37 (56%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           +IG+ G +++ +QN +G  I F      + ER+  I+
Sbjct: 17  VIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQIT 53

>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 = 49.2 bits (117), Expect = 3e-08
 Identities = 22/77 (28%), Positives = 41/77 (53%)

Query: 123 GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182
           GDG   A   ++   +K G+V+GKGG  + +++  +G K+VM+         D+ ++ITG
Sbjct: 2   GDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITG 61

Query: 183 ATLAVKKALVAVTTCLQ 199
               V++A   V   ++
Sbjct: 62  DPYKVQQAKEMVLELIR 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 = 43.4 bits (102), Expect = 2e-06
 Identities = 8/55 (14%), Positives = 20/55 (36%), Gaps = 2/55 (3%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSDHRVILVVGS 77
              ++ P    G +IG+ G  I  ++     ++    +G       + + + G 
Sbjct: 8  AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD 62

>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 = 37.6 bits (87), Expect = 3e-04
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425
               I++ A   G + G G   + ++++  G  + ++            D  ++I+G+  
Sbjct: 8   AVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGP---QNTGADKPLRITGDPY 64

Query: 426 NVQNALSEVVGRLR 439
            VQ A   V+  +R
Sbjct: 65  KVQQAKEMVLELIR 78

>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 = 48.3 bits (115), Expect = 4e-08
 Identities = 14/54 (25%), Positives = 29/54 (53%)

Query: 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          +++ ++  P  + G +IG+ G  I  IR ++   I  +    GS+ R+I + G+
Sbjct: 3  IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT 56

>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 = 43.7 bits (103), Expect = 2e-06
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
             G ++GKGG+ + ++R ESGA I +  P   +  +D++I ITG    ++ A   +   +
Sbjct: 14  LAGSIIGKGGQRIKQIRHESGASIKIDEPLEGS--EDRIITITGTQDQIQNAQYLLQNSV 71

Query: 199 QHLS 202
           +  S
Sbjct: 72  KQYS 75

>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 = 40.2 bits (94), Expect = 3e-05
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422
           G  +   + +  D  G + G G   + ++   +G  IK+             D +I I+G
Sbjct: 1   GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE-----PLEGSEDRIITITG 55

Query: 423 EYKNVQNALSEVVGRLR 439
               +QNA   +   ++
Sbjct: 56  TQDQIQNAQYLLQNSVK 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 = 36.4 bits (84), Expect = 7e-04
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           +  ++      A  IIGK G  ++ +++ SGA I    PL  S +R++TI+
Sbjct: 4   ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT 54

>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 = 47.1 bits (112), Expect = 1e-07
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGS 77
            +  P  +VG ++G+ G  +   +  T  RI         PG+ +R + + GS
Sbjct: 5  VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58

>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 = 44.4 bits (105), Expect = 9e-07
 Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLP-PPACAAIDDQLIQITGATLAVKKAL 191
            +G ++GKGG+ +   +  +GA+I +           ++ + ITG+  A + A 
Sbjct: 13  LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQ 66

>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 = 43.7 bits (103), Expect = 2e-06
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
           V + V  + VG + G G   + E +++TG  I++    +        +  + I+G     
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEF--LPGTRNRRVTITGSPAAT 62

Query: 428 QNALSEVVGRL 438
           Q A   +  R+
Sbjct: 63  QAAQYLISQRV 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 = 34.8 bits (80), Expect = 0.002
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA---PLTKSGERVVTIS 324
           + M         I+GK G  +   Q  +GA I  +     L  +  R VTI+
Sbjct: 5   VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTIT 56

>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 = 46.8 bits (111), Expect = 1e-07
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 3/54 (5%)

Query: 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI---HCEGGFPGSDHRVILVVGS 77
          F  + PT   G +IG+ G  I SI + +  RI            + ++  + G+
Sbjct: 3  FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGT 56

>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 = 45.7 bits (108), Expect = 4e-07
 Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVM-LPPPACAAIDDQLIQITGATLAVKKAL 191
           K G+++GKGG  +  +  +SGA+I +   PP  A  + +L  I G    +  A 
Sbjct: 11  KTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYAR 64

>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 = 39.1 bits (91), Expect = 6e-05
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 2/67 (2%)

Query: 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNV 427
            + +V     G + G G   +  +   +G  I+L         A  N  +  I G  + +
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQ--RNPPPNADPNMKLFTIRGTPQQI 60

Query: 428 QNALSEV 434
             A   +
Sbjct: 61  DYARQLI 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 = 34.1 bits (78), Expect = 0.004
 Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 3/52 (5%)

Query: 276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFA---APLTKSGERVVTIS 324
              +        IIGK G  ++S+   SGA I       P      ++ TI 
Sbjct: 3   FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIR 54

>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 = 46.5 bits (110), Expect = 4e-07
 Identities = 15/61 (24%), Positives = 27/61 (44%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
            +G ++G+GG  +  +   SGAKI          +  +LI+I+G    V  A   +   +
Sbjct: 25  SVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKV 84

Query: 199 Q 199
            
Sbjct: 85  S 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 = 42.7 bits (100), Expect = 8e-06
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 11 SSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC--EGGFPGSD 68
          SS   G L   +  V  +L  P   VG +IGR G  I SI + +  +I C  E       
Sbjct: 2  SSGSSGILT-ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL 60

Query: 69 HRVILVVGS 77
           R+I + G+
Sbjct: 61 SRLIKISGT 69

>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 = 42.3 bits (99), Expect = 1e-05
 Identities = 20/107 (18%), Positives = 39/107 (36%), Gaps = 3/107 (2%)

Query: 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA 411
           G  G S    +   V   + V    VG + G G   +  +   +G  I     ++     
Sbjct: 1   GSSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGT 57

Query: 412 AQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSG 458
                +I+ISG  K V  A   ++ ++  + +  + +  +     SG
Sbjct: 58  LLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKRIAHSASGPSSG 104

>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 = 42.1 bits (99), Expect = 8e-06
 Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 1/66 (1%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198
               ++G+ G  +T++R+E    I   P           I ITG     + A  A+   +
Sbjct: 20  YHPKIIGRKGAVITQIRLEHDVNIQF-PDKDDGNQPQDQITITGYEKNTEAARDAILRIV 78

Query: 199 QHLSTM 204
             L  M
Sbjct: 79  GELEQM 84

>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 = 38.3 bits (89), Expect = 2e-04
 Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 1/54 (1%)

Query: 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC-EGGFPGSDHRVILVVGS 77
              +         +IGR G++I+ IR +    I   +          I + G 
Sbjct: 10 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGY 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 = 40.8 bits (96), Expect = 2e-05
 Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 2/56 (3%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
              S  +  P      +IG++G  +  +   T  +I      P      I + G+
Sbjct: 7  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR--PDDPSNQIKITGT 60

>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 = 39.7 bits (93), Expect = 5e-05
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
               V+GK G  +  + +++  KI +  P          I+ITG    ++KA
Sbjct: 20  HHRFVIGKNGEKLQDLELKTATKIQIPRPDD----PSNQIKITGTKEGIEKA 67

>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 = 35.8 bits (83), Expect = 0.001
 Identities = 11/69 (15%), Positives = 28/69 (40%), Gaps = 7/69 (10%)

Query: 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425
            + ++ +  +    + G     + ++E  T T I++   +            I+I+G  +
Sbjct: 10  ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKE 62

Query: 426 NVQNALSEV 434
            ++ A  EV
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 = 35.5 bits (82), Expect = 0.002
 Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           +IGK G  ++ L+  +   I    P        + I+
Sbjct: 24  VIGKNGEKLQDLELKTATKIQI--PRPDDPSNQIKIT 58

>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 = 41.0 bits (96), Expect = 3e-05
 Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 22/96 (22%)

Query: 25  VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRI 84
           V+  +  P  +   +IG+ GS I  +  + +  IH     P     +I + G        
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA--PELQSDIIAITGL------- 60

Query: 85  MFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVE 120
                         ++   A   + ER+ E++AE E
Sbjct: 61  -------------AANLDRAKAGLLERVKELQAEQE 83

>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 = 37.5 bits (87), Expect = 4e-04
 Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 4/56 (7%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194
               V+G+ G  + +M  E    I +  P         +I ITG    + +A   +
Sbjct: 20  LHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL----QSDIIAITGLAANLDRAKAGL 71

>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 = 36.7 bits (85), Expect = 9e-04
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425
           V + + V  D    + G   S + +M D    +I +   E           +I I+G   
Sbjct: 10  VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAA 62

Query: 426 NVQNALSEVVGRLR 439
           N+  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 = 35.9 bits (83), Expect = 0.001
 Identities = 11/67 (16%), Positives = 28/67 (41%), Gaps = 8/67 (11%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS 347
           +IG++G+ +R + +     I    P  +    ++ I+         + +  A   +  R 
Sbjct: 24  VIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITG-----LAAN-LDRAKAGLLERV 75

Query: 348 VEVEGQQ 354
            E++ +Q
Sbjct: 76  KELQAEQ 82

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
               ++GK G N+ R++ +    + + P          LI+I G    V++A
Sbjct: 15  FHRHLIGKSGANINRIKDQYKVSVRIPPDSE----KSNLIRIEGDPQGVQQA 62

>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 = 34.7 bits (80), Expect = 0.003
 Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 2/56 (3%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGS 77
          + +    +         LIG+SG+ I+ I+   K  +            +I + G 
Sbjct: 2  NRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP--DSEKSNLIRIEGD 55

>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 = 33.9 bits (78), Expect = 0.004
 Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS 324
           +IGK GA +  +++     +    P       ++ I 
Sbjct: 19  LIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIE 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 = 37.4 bits (87), Expect = 4e-04
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 136 NTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194
           N  ++  V+GK G  +  ++ E   +IV+          + LI + G    V  A  A+
Sbjct: 8   NPARVPRVIGKKGSMIKLLKSELDVQIVV--------GQNGLIWVNGDRRKVSIAEEAI 58

>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 = 35.0 bits (81), Expect = 0.001
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 8/45 (17%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA 183
           KIG V+G   + + +++ ++GA+I +         DD  I I  A
Sbjct: 13  KIGEVIGPKRQMINQIQEDTGAEITI--------EDDGTIYIGAA 49

>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 = 35.6 bits (82), Expect = 0.002
 Identities = 10/38 (26%), Positives = 15/38 (39%)

Query: 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59
          + +VS  +     V   +IG  G  I  I  + K  I 
Sbjct: 7  EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIR 44

>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 = 0.003
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 7/53 (13%)

Query: 139 KIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATL-AVKKA 190
            +G+ +G  G N+ + R   G   + L             +I G +  AVKKA
Sbjct: 18  LMGLAIGTHGSNIQQARKVPGVTAIELDEDTG------TFRIYGESADAVKKA 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	587
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.53
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.52
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.5
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.5
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.49
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.48
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.48
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.47
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.47
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.46
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.45
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.44
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.41
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.4
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.36
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.27
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.2
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.15
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.13
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.13
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.11
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.99
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.98
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.95
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.82
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.7
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.62
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.53
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.51
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.41
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.4
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.38
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.27
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.23
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.81
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.67
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.25
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.22
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.36
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.19
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	94.15
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.07
d1wh9a_	92	Ribosomal protein S3 N-terminal domain {Mouse (Mus	82.27
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	80.48

>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=99.55  E-value=4e-15  Score=119.23  Aligned_cols=73  Identities=19%  Similarity=0.398  Sum_probs=66.6

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ..+|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..+     ..+++.|+|+|++++|++|+.+|.++|++|
T Consensus         2 p~~t~~i~VP~~~vg~iIG~~G~~I~~I~~~sga~I~i~~~~~-----~~~~r~i~I~G~~~~v~~A~~~I~~~i~e~   74 (75)
T d1zzka1           2 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTTS-----CSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccCCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            3578999999999999999999999999999999999976433     467899999999999999999999999986

>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=99.53  E-value=4.7e-15  Score=117.18  Aligned_cols=69  Identities=17%  Similarity=0.413  Sum_probs=63.1

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~L  438 (587)
                      +.|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..+     +.++|.|+|+|++++|++|+.+|..+|
T Consensus         1 q~T~~i~VP~~~vg~iIGk~G~~I~~I~~~tga~I~i~~~~~-----~~~~r~v~I~G~~~~v~~A~~~I~~~i   69 (70)
T d1wvna1           1 QTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-----GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             CEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT-----TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             CeEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCC-----CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            368899999999999999999999999999999999976443     466899999999999999999999987

>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=99.52  E-value=5.6e-15  Score=117.07  Aligned_cols=70  Identities=30%  Similarity=0.458  Sum_probs=64.9

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..++++|+||.+++|+||||+|++|++|+++|||+|+|.+.    ...||+|+|+|++++|.+|+.+|.++|+|
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            37899999999999999999999999999999999999773    44689999999999999999999999975

>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=99.50  E-value=7.8e-15  Score=116.20  Aligned_cols=70  Identities=19%  Similarity=0.425  Sum_probs=64.0

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ..++.+|+||.+++|+|||++|++|++|++.|||+|+|++.       ...+|.|+|+|++++|.+|+.+|.++|++
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            35799999999999999999999999999999999999763       34579999999999999999999999875

>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=99.50  E-value=1e-14  Score=118.63  Aligned_cols=75  Identities=19%  Similarity=0.333  Sum_probs=68.0

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      +..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+..+.+   ...+|.|+|+|++++|.+|+.+|.++|++
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            4679999999999999999999999999999999999998755433   45789999999999999999999999875

>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=99.49  E-value=1.3e-14  Score=114.87  Aligned_cols=70  Identities=17%  Similarity=0.304  Sum_probs=62.3

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~L  438 (587)
                      +.+|.||++++|+|||++|++|++|++.|||+|+|++..+ +. ....+|.|+|+|++++|++|+.+|.++|
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-PN-ADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-TT-SCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-CC-CCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            5689999999999999999999999999999999987544 22 4567899999999999999999999875

>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=99.49  E-value=1.7e-14  Score=115.23  Aligned_cols=71  Identities=23%  Similarity=0.382  Sum_probs=63.8

Q ss_pred             eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 007844          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (587)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~L  438 (587)
                      .+.+|.||++++|+|||++|++|++|++.|||+|+|.+..+..  ...++|.|+|+|++++|++|+.+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCC--CCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            4678999999999999999999999999999999998865532  3467899999999999999999999876

>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=99.48  E-value=1.4e-14  Score=115.69  Aligned_cols=71  Identities=17%  Similarity=0.290  Sum_probs=64.9

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|+|.+.++     ...++.|+|+|++++|++|+.+|.+.|++
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            367899999999999999999999999999999999987543     45689999999999999999999999875

>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=99.48  E-value=1.7e-14  Score=117.26  Aligned_cols=76  Identities=26%  Similarity=0.443  Sum_probs=69.3

Q ss_pred             CCCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       125 ~~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      +...++.+|+||..++|+||||+|++|++|+++|||+|.|.+...++...+|+|+|+|++++|.+|..+|.++|++
T Consensus         4 ~~~~~~~~i~Vp~~~~g~iIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   79 (81)
T d1x4ma1           4 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELIRD   79 (81)
T ss_dssp             CCCCEEEEEEECHHHHHHHSCSSSSHHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEECTTTHHHHHHHHHHHHCC
T ss_pred             CCccEEEEEEECHHHcCeeECCCCchHHHHHHHhCCeEEEccCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            3458999999999999999999999999999999999999875345567899999999999999999999999976

>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=99.47  E-value=3.2e-14  Score=113.84  Aligned_cols=72  Identities=24%  Similarity=0.417  Sum_probs=66.7

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      .+|.+|.||.+++|+||||+|++|++|+++|||+|+|..  ..+...+|+|+|+|++++|.+|+.+|.++|+++
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 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECC--TTSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEcc--CCCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999999987  345678999999999999999999999999873

>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=99.47  E-value=2.8e-14  Score=112.64  Aligned_cols=68  Identities=24%  Similarity=0.379  Sum_probs=63.3

Q ss_pred             eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      .|.+|+||.+++|+||||+|++|++|+++|||+|.|.+  ..+...+|+|+|+|++++|.+|+.+|.++|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIAN--PVEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECC--CCTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcC--CCCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            57899999999999999999999999999999999987  355678899999999999999999999886

>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=99.47  E-value=2.4e-14  Score=113.37  Aligned_cols=69  Identities=25%  Similarity=0.419  Sum_probs=62.6

Q ss_pred             EEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       130 t~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      +.+|+||++.+|+||||+|++|++|+++|||+|+|.+. .......+|+|+|+|++++|.+|..+|.++|
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 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            46799999999999999999999999999999999875 3445678899999999999999999999875

>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=99.46  E-value=3.6e-14  Score=113.24  Aligned_cols=70  Identities=19%  Similarity=0.342  Sum_probs=64.0

Q ss_pred             eEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       129 vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~-p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      .+++|+||++++|+||||+|++|++|+++|||+|+|.+. ...+...+|+|+|+|++++|.+|..+|.++|
T Consensus         3 ~~i~i~VP~~~vg~iIGk~G~~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i   73 (74)
T d1dtja_           3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRV   73 (74)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEESHHHHHHHHHHHHHHC
T ss_pred             EEEEEEeCHHHcceeECCCChhHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEeCHHHHHHHHHHHHHHc
Confidence            467999999999999999999999999999999999876 3455678999999999999999999999876

>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=99.45  E-value=5e-14  Score=113.90  Aligned_cols=74  Identities=16%  Similarity=0.258  Sum_probs=67.5

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.+++|+|||++|.+|++|++.|||+|+|++.++     +.+++.|+|+|++++|++|+.+|.+.|++.
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 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG-----GLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSCCT-----TCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCCCC-----CCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            46789999999999999999999999999999999999987443     567899999999999999999999998863

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=6.3e-14  Score=113.80  Aligned_cols=74  Identities=15%  Similarity=0.248  Sum_probs=67.0

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ...++.++.||.++|++|||++|++|++|++.|||+|+|++.++      .+.+.|+|+|++++|++|+.+|...+++|+
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~~~------~~~~~v~I~G~~~~V~~A~~~I~~i~~e~~   80 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA------PDPNCVTVTGLPENVEEAIDHILNLEEEYL   80 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCTTC------SCTTEEEEESCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCccC------CCCCEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999987543      346789999999999999999999999876

>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=99.44  E-value=5e-14  Score=112.40  Aligned_cols=71  Identities=20%  Similarity=0.375  Sum_probs=65.5

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..+++|.||.+++|+||||+|++|++|+++|||+|+|...  .+...+|+|+|+|++++|.+|..+|.++|++
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 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD--DGTTPERIAQITGPPDRAQHAAEIITDLLRS   72 (74)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECC--TTSCSEEEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCHHHCCeeECCCCcHHHHHHHHcCCEEEeccC--CCCCCeeEEEEEeCHHHHHHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999999874  3456789999999999999999999999975

>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=99.41  E-value=1.8e-13  Score=116.42  Aligned_cols=78  Identities=19%  Similarity=0.262  Sum_probs=68.9

Q ss_pred             CCCCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          361 NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       361 ~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      .....++.+|.||.+++|+|||++|.+|++|++.|||+|.|++..+.   ....+|+|+|+|++++|++|+.+|.++|++
T Consensus        10 ~~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e   86 (104)
T d1we8a_          10 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSE   86 (104)
T ss_dssp             SSSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhC
Confidence            34567899999999999999999999999999999999999876542   245679999999999999999999999985


Q ss_pred             c
Q 007844          441 N  441 (587)
Q Consensus       441 ~  441 (587)
                      .
T Consensus        87 ~   87 (104)
T d1we8a_          87 D   87 (104)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.40  E-value=1.7e-13  Score=110.66  Aligned_cols=73  Identities=22%  Similarity=0.396  Sum_probs=67.4

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ..++.+|+||..++|+|||++|.+|++|+++|||+|.|.+.  .++..+|+|+|+|++++|.+|+.+|.++|.+.
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 SVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD--SGGLPERSCMLTGTPESVQSAKRLLDQIVEKG   78 (79)
T ss_dssp             CCEEEEEEEEHHHHHHHHCSSSHHHHHHHHHSCCEEEECSC--CTTCSEEEEEEEECHHHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEEEEChHhhcceECCCchhHHHHHHHhCCEEEEcCC--CCCCCceEEEEEeCHHHHHHHHHHHHHHHHcc
Confidence            47899999999999999999999999999999999999873  45668899999999999999999999999863

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=3.7e-13  Score=109.94  Aligned_cols=73  Identities=15%  Similarity=0.231  Sum_probs=65.8

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ..+.+|.||..++++|||++|++|++|++.|||+|+|++...    ....++.|+|+|+.++|++|+.+|...+++.
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----GNQPQDQITITGYEKNTEAARDAILRIVGEL   81 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT----CSSCSSEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCCCC----CCCCcceEEEECCHHHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999999999999999987544    3567889999999999999999999988763

>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=99.36  E-value=4e-13  Score=114.26  Aligned_cols=76  Identities=21%  Similarity=0.304  Sum_probs=67.8

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ..+++.+|+||..++|+||||+|.+|++|+++|||+|.|.+........+|+|+|+|++++|.+|+.+|.++|.+.
T Consensus        12 ~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          12 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCCCCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            3478899999999999999999999999999999999998752334557899999999999999999999999764

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=4.8e-13  Score=108.51  Aligned_cols=72  Identities=15%  Similarity=0.218  Sum_probs=65.4

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ....+.+|.||..++|+|||++|++|++|+++|||+|+|++.       ++.++.|+|+|++++|++|+.+|.+.+.+.
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~-------~~~~~~v~I~G~~~~v~~A~~~I~~iv~e~   78 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-------DDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT-------TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECCC-------CCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999999999999999763       346789999999999999999999988763

>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=99.33  E-value=8.7e-13  Score=104.15  Aligned_cols=67  Identities=19%  Similarity=0.312  Sum_probs=60.9

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHH
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGR  437 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~  437 (587)
                      ...+.+|.||.+++++|||++|++|++|+++|||+|+|++.       .++++.|+|+|++++|++|+.+|.+.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~i   69 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPD-------SEKSNLIRIEGDPQGVQQAKRELLEL   69 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCC-------CSSSEEEEEEESSHHHHHHHHHHHHT
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCCC-------CCCCCEEEEECCHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999999763       34678999999999999999999874

>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=99.31  E-value=9.6e-13  Score=106.94  Aligned_cols=72  Identities=14%  Similarity=0.237  Sum_probs=64.2

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHh-hCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...++.+|.||.++||+|||++|++|++|+++ ++++|++++.       +..++.|+|+|++++|++|+.+|.+.+++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~~-------~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVE-------GSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCCT-------TTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeCC-------CCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            35678999999999999999999999999977 5999999763       346799999999999999999999998863

>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=99.29  E-value=2e-12  Score=105.51  Aligned_cols=72  Identities=17%  Similarity=0.178  Sum_probs=66.2

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      ..+++|.||..++++|||++|++|++|+++|||+|.|++. ......+++|+|+|+.++|.+|..+|.+++.+
T Consensus         9 ~~~~~i~Vp~~~~~~iIG~~G~~i~~I~~~t~~~I~~~~~-~~~~~~~~~i~I~G~~e~v~~A~~~I~~~i~e   80 (84)
T d2ctla1           9 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDK-DDGNQPQDQITITGYEKNTEAARDAILRIVGE   80 (84)
T ss_dssp             TCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCT-TTCSSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEECHHHHhhhcCCCchhHHHHHHHhCCEEEECCC-CCCCCCcceEEEECCHHHHHHHHHHHHHHHHh
Confidence            5788999999999999999999999999999999999874 44567789999999999999999999999976

>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=99.27  E-value=2.1e-12  Score=107.01  Aligned_cols=71  Identities=20%  Similarity=0.268  Sum_probs=64.8

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ..++.+|.||.++|++|||++|++|++|++.|||+|.|++.       +..++.|+|+|+.++|++|+.+|...+.++
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            46899999999999999999999999999999999999763       345789999999999999999999988763

>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=99.22  E-value=4.9e-12  Score=102.38  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=64.7

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ++.++..+.||..++++|||++|++|++|+++|||+|+|.+.   ....++.|+|+|++++|.+|+.+|.++++++
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~~---~~~~~~~v~I~G~~~~V~~A~~~I~~i~~e~   79 (81)
T d2ctma1           7 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS---GAPDPNCVTVTGLPENVEEAIDHILNLEEEY   79 (81)
T ss_dssp             TTCCCEEEECCTTTHHHHHCSSSCHHHHHHHHHTCEEECCCT---TCSCTTEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             hcCEEEEEEECHHHHhhccCCCCccHHHHHHHhCCEEEeCCc---cCCCCCEEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            347788999999999999999999999999999999999763   2234578999999999999999999999874

>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=99.22  E-value=4.9e-12  Score=102.39  Aligned_cols=71  Identities=20%  Similarity=0.246  Sum_probs=65.2

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      +..++.+|.||..++++|||++|++|++|+++|||+|.|.+    ....++.|+|+|+.++|.+|..+|.+++.+
T Consensus         7 ~~~~t~~i~Ip~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~----~~~~~~~v~I~G~~~~v~~A~~~I~~iv~e   77 (81)
T d2ctea1           7 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR----PDDPSNQIKITGTKEGIEKARHEVLLISAE   77 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC----TTSSCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC----CCCCCCEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            34689999999999999999999999999999999999966    345778999999999999999999999976

>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=99.20  E-value=7.4e-12  Score=101.59  Aligned_cols=72  Identities=17%  Similarity=0.197  Sum_probs=64.6

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhh-hCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE-SGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~e-tGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      ++.++..|.||..++|+||||+|++|++|+++ ++++|.+..    .+..++.|+|+|+.++|.+|..+|.+++++.
T Consensus         7 ~~~~t~~i~Vp~~~~~~iIGk~G~~I~~I~~~~~~~~I~~~~----~~~~~~~v~I~G~~~~v~~A~~~I~~~v~e~   79 (82)
T d2ctja1           7 ANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPV----EGSGSDTVVIRGPSSDVEKAKKQLLHLAEEK   79 (82)
T ss_dssp             CSSCCEEEECCHHHHHHHHCSSSHHHHHHHHHHTSCEEECCC----TTTTCCEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEECHHHHhhcCCCCCccHHHHHHHcCCcEEEEeC----CCCCCceEEEeCCHHHHHHHHHHHHHHHhhh
Confidence            34788999999999999999999999999988 599999965    3557799999999999999999999999874

>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=99.18  E-value=1e-11  Score=97.90  Aligned_cols=68  Identities=19%  Similarity=0.314  Sum_probs=61.3

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L  198 (587)
                      ...+.+|.||..++++|||++|++|++|+++|||+|+|.+    ....++.|+|+|++++|.+|..+|.++.
T Consensus         3 ~~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~----~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP----DSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC----CCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC----CCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            3677899999999999999999999999999999999976    3456789999999999999999998764

>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=99.15  E-value=3.3e-11  Score=99.32  Aligned_cols=69  Identities=12%  Similarity=0.192  Sum_probs=62.5

Q ss_pred             CCceEEEEEeCcccccccccCCCchhHHHHHh-hCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007844          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (587)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (587)
                      ...+|.+|.||..+|++|||++|++|++|+++ +|++|.+++          ++..|+|+|++++|++|+.+|.+.+++.
T Consensus        18 ~~~~t~~v~VP~~~h~~iIG~~G~~I~~i~~~~~~v~I~~~~----------~~~~v~i~G~~~~ve~Ak~~I~~iv~el   87 (90)
T d2ctfa1          18 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE----------GEDKITLEGPTEDVSVAQEQIEGMVKDL   87 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS----------SSCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC----------CCceEEEeCCHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999 589999964          2567999999999999999999998874

>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=99.13  E-value=2.4e-11  Score=100.53  Aligned_cols=69  Identities=16%  Similarity=0.205  Sum_probs=64.1

Q ss_pred             ceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       128 ~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .++..+.||..+++.|||++|++|++|+++|||+|.|.+    .+..++.|+|+|+.++|.+|..+|.+++.+
T Consensus         9 ~vt~~i~Vp~~~~~~iIG~~G~~i~~I~~~tg~~I~~p~----~~~~~~~v~I~G~~~~V~~A~~~I~~~v~e   77 (91)
T d2ctka1           9 PVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPA----PELQSDIIAITGLAANLDRAKAGLLERVKE   77 (91)
T ss_dssp             CEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCC----TTTTCCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CEEEEEEECHHHHhHhcCCCchhHHHHHHHhCCEEEECC----CCCCcceEEEECCHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999966    355678999999999999999999999976

>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=99.13  E-value=1.4e-11  Score=98.56  Aligned_cols=64  Identities=19%  Similarity=0.231  Sum_probs=57.5

Q ss_pred             CceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHH
Q 007844          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVG  436 (587)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G-~~~~V~~A~~~I~~  436 (587)
                      ...+.+|.||.+++|+|||++|++|++|++.|||+|.+.+         ++++.|+|.| ++++|++|+.+|..
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 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELD---------EDTGTFRIYGESADAVKKARGFLEF   70 (78)
T ss_dssp             CSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEE---------TTTTEEEEEESSHHHHHHHHHHHSC
T ss_pred             CCceEEEEECHHHHHHHcCCChHHHHHHHHhcCcEEEEec---------CCCceEEEEECCHHHHHHHHHHHHH
Confidence            5678999999999999999999999999999999998864         3457899999 69999999999953

>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=99.11  E-value=4.6e-11  Score=96.94  Aligned_cols=64  Identities=13%  Similarity=0.101  Sum_probs=57.9

Q ss_pred             EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007844          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (587)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (587)
                      ..+.||.+++|.|||++|++|++|+++|||+|+|.+           +..|+|+|++++++.|+.+|...+++..
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            468899999999999999999999999999999953           4679999999999999999988887644

>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=98.99  E-value=3.3e-10  Score=93.17  Aligned_cols=68  Identities=16%  Similarity=0.255  Sum_probs=62.1

Q ss_pred             CCceEEEEEeecceeeeeeecCchHHHHHHhhh-CCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIES-GAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       126 ~~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~et-Ga~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .+.++..+.||..++++|||++|++|++|++++ |++|.+..       .+..|+|+|+.++|++|..+|.+++.+
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 NSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTE-------GEDKITLEGPTEDVSVAQEQIEGMVKD   86 (90)
T ss_dssp             CCCEEEEEECCSTTHHHHHTTTTCHHHHHHHHCSSSEEEECS-------SSCEEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEcCHHHHhhcCCCCchhHHHHHHHcCCcEEeeCC-------CCceEEEeCCHHHHHHHHHHHHHHHHH
Confidence            347899999999999999999999999999995 89999965       357899999999999999999999976

>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=98.98  E-value=2e-10  Score=93.03  Aligned_cols=62  Identities=24%  Similarity=0.253  Sum_probs=57.1

Q ss_pred             EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcC
Q 007844          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e~  201 (587)
                      -+.||.+.+|.||||+|++|++|+++|||+|.|.+        +..|+|+|++++|.+|..+|..++++.
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            47899999999999999999999999999999954        467999999999999999999998773

>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=98.95  E-value=2e-10  Score=91.74  Aligned_cols=64  Identities=23%  Similarity=0.291  Sum_probs=57.4

Q ss_pred             CceEEEEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEee-cHHHHHHHHHHHHH
Q 007844          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTT  196 (587)
Q Consensus       127 ~~vt~rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G-~~e~V~~A~~~I~~  196 (587)
                      +.++.++.||.+.+|+|||++|++|++|+++|||+|.+...      .++.|+|.| +.++|.+|..+|..
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            36788999999999999999999999999999999998652      568899999 59999999999853

>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=98.82  E-value=6e-10  Score=90.01  Aligned_cols=72  Identities=15%  Similarity=0.002  Sum_probs=56.3

Q ss_pred             EEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcccC
Q 007844          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKS  444 (587)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~~~~~  444 (587)
                      +++.||.+.+|.|||++|++||+|+++|||+|+|...+.     ....+.....|.+.++++|+.+|.+..|.|...
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g-----~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~Pe   76 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENS-----MVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPE   76 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTT-----EEEEEESSTTSCHHHHHHHHHHHHHHHHTCCHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCC-----eEEEecCCccccHHHHHHHHHHHHHHhCCCChH
Confidence            358999999999999999999999999999999964221     001122224678999999999999988776533

>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=3.8e-10  Score=87.96  Aligned_cols=61  Identities=11%  Similarity=0.004  Sum_probs=47.4

Q ss_pred             EEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHHhh
Q 007844          369 SILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRH  440 (587)
Q Consensus       369 ~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~Lr~  440 (587)
                      .+.||.+.+|.|||++|++||+|+++|||+|.|.+           +..|+|+|. .++++.|..+|....++
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            57899999999999999999999999999999943           357999996 67899999999776554

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.62  E-value=3.8e-08  Score=79.43  Aligned_cols=64  Identities=13%  Similarity=0.022  Sum_probs=56.3

Q ss_pred             EEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHHhhccc
Q 007844          369 SILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRHNLK  443 (587)
Q Consensus       369 ~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I~~~Lr~~~~  443 (587)
                      .+.||.+.++.|||++|++|+.|++.|||+|.|.+           +-.|.|.|. .+.+..|+.+|....++-.+
T Consensus         4 vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           4 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            57899999999999999999999999999999953           357999995 78999999999988776443

>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=98.53  E-value=4.4e-08  Score=78.80  Aligned_cols=63  Identities=14%  Similarity=0.219  Sum_probs=53.3

Q ss_pred             EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEe-----ecHHHHHHHHHHHHHHHhcC
Q 007844          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT-----GATLAVKKALVAVTTCLQHL  201 (587)
Q Consensus       132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~-----G~~e~V~~A~~~I~~~L~e~  201 (587)
                      .+-||.+.+|.||||+|++|++|+++|||+|+|..+       +..+.+.     |...++.+|..+|.++.+.+
T Consensus         6 ~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d-------~g~v~i~~~~~~~~~~a~~~a~~iI~aI~rGf   73 (84)
T d1tuaa1           6 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTE-------NSMVIVEPEAEGIPPVNLMKAAEVVKAISLGF   73 (84)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETT-------TTEEEEEESSTTSCHHHHHHHHHHHHHHHHTC
T ss_pred             EEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcC-------CCeEEEecCCccccHHHHHHHHHHHHHHhCCC
Confidence            478999999999999999999999999999999762       3445554     56889999999999887764

>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=98.51  E-value=2.2e-09  Score=83.48  Aligned_cols=61  Identities=16%  Similarity=0.138  Sum_probs=47.4

Q ss_pred             EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      .+-||.+.+|.||||+|++|++|+++|||+|.|..        +..|+|+|. .+++.+|..+|..+.++
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            36789999999999999999999999999999954        356899996 78999999999877655

>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=98.41  E-value=1e-08  Score=75.30  Aligned_cols=48  Identities=23%  Similarity=0.383  Sum_probs=15.8

Q ss_pred             EEEEEeccCccceeccCCChHHHHHHhHhCceEEEeCCCCCCCceEEEEecCCc
Q 007844           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGS   79 (587)
Q Consensus        26 ~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~~~~eRvI~I~G~~e   79 (587)
                      ..+|.||.+++|.|||++|++||+|+++|||+|++.+      |..|.|+|...
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            4568899999999999999999999999999999964      46788888653

>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=98.40  E-value=1.7e-07  Score=75.50  Aligned_cols=61  Identities=13%  Similarity=0.120  Sum_probs=54.9

Q ss_pred             EEEeecceeeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007844          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (587)
Q Consensus       132 rllVp~~~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~-~e~V~~A~~~I~~~L~e  200 (587)
                      -+-||.+.++.|||++|++|+.|+++|||+|.|..        +-.|.|.|. .+.+.+|+.+|..+.++
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 IVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR--------NGRIHLECPNEDLEAIAVMAIKIIDEE   65 (87)
T ss_dssp             EEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET--------TTEEEEECSCHHHHHHHHHHHHHHHHC
T ss_pred             EEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC--------CcEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            36799999999999999999999999999999965        246899996 89999999999998876

>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=98.38  E-value=1.4e-08  Score=74.53  Aligned_cols=46  Identities=20%  Similarity=0.412  Sum_probs=14.4

Q ss_pred             EEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC
Q 007844          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE  423 (587)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~  423 (587)
                      ..+|.||.+++|.|||++|++||+|+++|||+|.|.+           +..|+|.|.
T Consensus         4 ~~~i~Ip~~kig~vIG~GG~~Ik~I~~~tga~I~i~d-----------dg~v~I~a~   49 (54)
T d1e3ha4           4 IITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------DGTIYIGAA   49 (54)
T ss_dssp             CC---------------------CHHHHSCCCC-------------------CCCCB
T ss_pred             EEEEEeCHHHeeEEECCccHHHHHHHHHHCCEEEEeC-----------CeEEEEEec
Confidence            4468899999999999999999999999999998853           567777775

>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=98.27  E-value=3.7e-07  Score=76.04  Aligned_cols=52  Identities=19%  Similarity=0.199  Sum_probs=47.0

Q ss_pred             eeeeeecCchHHHHHHhhhCCeEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007844          140 IGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (587)
Q Consensus       140 vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~~~~~~dr~V~I~G~~e~V~~A~~~I~~~L~e  200 (587)
                      .|.|||++|.+|+.|++.|||+|.|..         ..|.|.|+++++..|..+|..++.+
T Consensus        24 ~GrIIG~gGktik~Ie~~Tg~~I~I~d---------~~v~iig~~e~i~~A~~~Ie~li~~   75 (104)
T d1tuaa2          24 KGRIIGEGGRARRTIEEMTDTYINVGE---------YEVAIIGDYERAMAAKQAIEMLAEG   75 (104)
T ss_dssp             HHHHHCGGGHHHHHHHHHHTCEEEECS---------SEEEEEEEHHHHHHHHHHHHHHHTT
T ss_pred             hcceeCCCcHHHHHHHHHHCCeEEEeC---------CeEEEEECchhHHHHHHHHHHHHcC
Confidence            488999999999999999999999943         4577889999999999999999975

>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=98.23  E-value=3.5e-07  Score=76.13  Aligned_cols=53  Identities=23%  Similarity=0.304  Sum_probs=47.6

Q ss_pred             cccccccCCCchhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007844          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (587)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~~~~V~~A~~~I~~~Lr~  440 (587)
                      ..|+|||++|.+|+.|++.|||+|.|..            ..|.|.|++++++.|+.+|...+.+
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            5799999999999999999999999942            3588889999999999999998865

>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=97.81  E-value=1.7e-05  Score=67.78  Aligned_cols=73  Identities=18%  Similarity=0.250  Sum_probs=58.6

Q ss_pred             ceEEEEEeecce------eeeeeecCchHHHHHHhhhCCeEEecCC-------------CCCC-CCCCcEEEEeec-HHH
Q 007844          128 VAYCGLLANTTK------IGVVVGKGGRNVTRMRIESGAKIVMLPP-------------PACA-AIDDQLIQITGA-TLA  186 (587)
Q Consensus       128 ~vt~rllVp~~~------vG~IIGkgG~~Ik~I~~etGa~I~I~~~-------------p~~~-~~~dr~V~I~G~-~e~  186 (587)
                      .++.+++||-+.      +|.|||.+|+++|+|+++|||+|.|...             ...+ ...+=-|.|+++ .+.
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            467889999875      8999999999999999999999999753             0000 122336778888 889


Q ss_pred             HHHHHHHHHHHHhc
Q 007844          187 VKKALVAVTTCLQH  200 (587)
Q Consensus       187 V~~A~~~I~~~L~e  200 (587)
                      +.+|+.+|..+|..
T Consensus        82 ~~~A~~~i~~ll~~   95 (122)
T d1k1ga_          82 VKKAVEQIRNILKQ   95 (122)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999999975

>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=97.67  E-value=5.1e-05  Score=64.76  Aligned_cols=77  Identities=18%  Similarity=0.343  Sum_probs=57.1

Q ss_pred             eEEEEEeCcc------cccccccCCCchhHHHHHhhCCeEEEcCCCc----------ccccC-CCCCcEEEEcCC-HHHH
Q 007844          366 VAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ----------VLGCA-AQNDVVIQISGE-YKNV  427 (587)
Q Consensus       366 ~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~----------~p~~~-~~~~r~V~I~G~-~~~V  427 (587)
                      ++.+|.||-+      ++|.|||++|+++|+|+++|||+|.|-.+.-          .+.+. .+..--|.|+++ ++.+
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            5778888875      5999999999999999999999999965321          11111 123345666665 5589


Q ss_pred             HHHHHHHHHHHhhcc
Q 007844          428 QNALSEVVGRLRHNL  442 (587)
Q Consensus       428 ~~A~~~I~~~Lr~~~  442 (587)
                      ..|+.+|...|...+
T Consensus        83 ~~A~~~i~~ll~~~~   97 (122)
T d1k1ga_          83 KKAVEQIRNILKQGI   97 (122)
T ss_dssp             HHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999999987633

>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=97.25  E-value=0.00014  Score=62.66  Aligned_cols=74  Identities=23%  Similarity=0.310  Sum_probs=53.6

Q ss_pred             eEEEEEeCc------ccccccccCCCchhHHHHHhhCCeEEEcCCCcc------------ccc-CCCCCcEEEEcCCH--
Q 007844          366 VAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV------------LGC-AAQNDVVIQISGEY--  424 (587)
Q Consensus       366 ~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~~------------p~~-~~~~~r~V~I~G~~--  424 (587)
                      ++.+|.||-      +++|.|||++|.++|+|+++|||+|.|-.+.-.            |.+ ...++--|.|++..  
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            456777774      589999999999999999999999999875421            111 12345566676652  


Q ss_pred             ----HHHHHHHHHHHHHHh
Q 007844          425 ----KNVQNALSEVVGRLR  439 (587)
Q Consensus       425 ----~~V~~A~~~I~~~Lr  439 (587)
                          ..+.+|..+|...|.
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                357788888887664

>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=97.22  E-value=0.00014  Score=62.81  Aligned_cols=72  Identities=22%  Similarity=0.257  Sum_probs=55.3

Q ss_pred             eEEEEEeecc------eeeeeeecCchHHHHHHhhhCCeEEecCCCC----------------CCCCCCcEEEEeecH--
Q 007844          129 AYCGLLANTT------KIGVVVGKGGRNVTRMRIESGAKIVMLPPPA----------------CAAIDDQLIQITGAT--  184 (587)
Q Consensus       129 vt~rllVp~~------~vG~IIGkgG~~Ik~I~~etGa~I~I~~~p~----------------~~~~~dr~V~I~G~~--  184 (587)
                      ++-+++||.+      .+|.|||.+|.++|+|+++|||+|.|-..-.                .....+=-|.|++..  
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            4667888854      7899999999999999999999999987510                011245567788762  


Q ss_pred             ----HHHHHHHHHHHHHHhc
Q 007844          185 ----LAVKKALVAVTTCLQH  200 (587)
Q Consensus       185 ----e~V~~A~~~I~~~L~e  200 (587)
                          ..+.+|+.+|..+|..
T Consensus        82 ~~a~~kl~~A~~~I~~lL~p  101 (134)
T d2bl5a1          82 NRAELKLKRAVEEVKKLLVP  101 (134)
T ss_dssp             HHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHHcCC
Confidence                3588999999999854

>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=94.36  E-value=0.01  Score=44.38  Aligned_cols=41  Identities=27%  Similarity=0.292  Sum_probs=36.5

Q ss_pred             CCcEEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC
Q 007844           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG   62 (587)
Q Consensus        22 ~~~v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~   62 (587)
                      ++.-.+.+.||.+..+..|||+|.|||-..+-||.+|+|..
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            34457889999999999999999999999999999999853

>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=94.19  E-value=0.014  Score=43.83  Aligned_cols=41  Identities=20%  Similarity=0.187  Sum_probs=37.0

Q ss_pred             eEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCCc
Q 007844          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (587)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~~  406 (587)
                      -...+.||.++.+.-|||+|.+++-..+.||.+|.|...++
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~~~   67 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMN   67 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEECCC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEccc
Confidence            46889999999999999999999999999999999976443

>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=94.15  E-value=0.013  Score=43.80  Aligned_cols=41  Identities=20%  Similarity=0.183  Sum_probs=37.3

Q ss_pred             ceEEEEEeCcccccccccCCCchhHHHHHhhCCeEEEcCCC
Q 007844          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (587)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~i~~~~  405 (587)
                      .....+.||.++....|||+|.+++-..+.||.+|.|....
T Consensus        25 ~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          25 ARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             CcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            34788999999999999999999999999999999997644

>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=94.07  E-value=0.017  Score=43.37  Aligned_cols=38  Identities=18%  Similarity=0.232  Sum_probs=35.0

Q ss_pred             EEEEEEeccCccceeccCCChHHHHHHhHhCceEEEeC
Q 007844           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG   62 (587)
Q Consensus        25 v~~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~   62 (587)
                      -.+.+.||.+..+..|||+|.|||-..+-||.+|+|..
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s   64 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP   64 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEE
Confidence            35779999999999999999999999999999999964

>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=82.27  E-value=0.25  Score=38.95  Aligned_cols=34  Identities=12%  Similarity=0.196  Sum_probs=28.8

Q ss_pred             EEEEeccCccceeccCCChHHHHHHhHhCceEEE
Q 007844           27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC   60 (587)
Q Consensus        27 ~riLvP~~~vG~IIGk~G~~Ik~IreeTga~I~V   60 (587)
                      .+|.+....-|.|||++|++|++|+++-.-++.+
T Consensus        37 i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~   70 (92)
T d1wh9a_          37 TEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF   70 (92)
T ss_dssp             EEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCC
T ss_pred             EEEEEEeCCCceeeccCchhHHHHHHHHHHHHCC
Confidence            5688899999999999999999999887654443

>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=80.48  E-value=1.4  Score=33.87  Aligned_cols=55  Identities=15%  Similarity=0.068  Sum_probs=43.7

Q ss_pred             EEEeCcccccccccCCCc-hhHHHHHhhCCeEEEcCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHH
Q 007844          369 SILVGADFVGCLTGSGSS-AVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEV  434 (587)
Q Consensus       369 ~l~VP~~~vG~IIGkgG~-~Ik~I~~~TGa~I~i~~~~~~p~~~~~~~r~V~I~G~-~~~V~~A~~~I  434 (587)
                      -+.|+..++.+|||++++ .++.|.+.+++.|-|-.           +-.|=|.|. ++....+...|
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----------NGrIWi~~~~~~~~i~i~~aI   60 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----------NGKIWVKCEELSNTLACYRTI   60 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----------TTEEEEECSSHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----------CcEEEEECCCHHHHHHHHHHH
Confidence            467999999999999998 89999999999999954           556888884 55555544444