Citrus Sinensis ID: 007293

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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-------590-------600-------61
Protein Sequence
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEEEEEcccEEEEEccccHHHHHHHHHcccEEEEcccccccccEEEEEEccccccHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEccccEEEEEccccHHHHHHHHHHccEEEEEcccccccccccEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccccccHHHHHHHHccccEEEcccccccccEEEEEEEcccccccccHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHHccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccEEEccccEEEcccccccccHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEcccccccccEEEEEEcccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEcccEEEEEcccccEHHHHHHHcccEEEEcccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEcccccEHHHHHHHcccEEEEccccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEEccccEEEEEcccccHHHHHHHHcccEEEEEcccccccccccccEEEEEEccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccEEEc
Coil and Loop (DISEMBL)
mmhhsnpygysskrrgplnlpddvvsfrlvcptpvvggligrsgsIISSIRRdtkcrihceggfpgsdHRVILVVGsgsidrrimFCENDVvveggevsstQEAVIRVFERMWEVEAevegdgdgddvaycGLLANTTKIGVvvgkggrnvtRMRIESgakivmlpppacaaiddQLIQITGATLAVKKALVAVTTCLQHlstmekspicfnrpiekvfysnssdphreffphlslvppltgnpsdnasefhsssadadrdhpgldkkgrKQEVALRMLFSgwtasgiigkrGAIVRSLQNASGALIsfaapltksgerVVTISALEyldtrhspvqNAAVLVFARSVevegqqgfssgenkgdAVAVSILVGADFvgcltgsgssavsemedvtgtdiklvggeqvlgcaaqnDVVIQISGEYKNVQNALSEVVGRLRhnlksgeilnearprspsgrvggpalhklhqsvalspefeqETIAVQGVdqfvlplnrsqtlqtegrrhatpttdgkpgsrmfeGSLELEKSLVHllptdmvdevgprscsdgmttasgednmltegvsqlglsdniigpstlqlpktgeEDIEYLIQKVKKAQPHLLIM
Flexible Loop (DISEMBL)
mmhhsnpygysskrrgplNLPDDVVSFRLVCPTpvvggligrsgsiissiRRDTKCRIHCeggfpgsdhrvILVVGSGSIDRRIMFCENDVvveggevsstqeaVIRVFERMWEVEAEvegdgdgdDVAYCGLLanttkigvvvgkggrnvTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLstmekspicfnRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSssadadrdhpgldKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISfaapltksgeRVVTISALEYLDTRHSPVQNAAVLVFARSVEVEgqqgfssgenkGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLksgeilnearprspSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNrsqtlqtegrrhatpttdgkpgsrMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVkkaqphllim
Low Complexity Region (SEG)
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVggligrsgsiissirrDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWeveaevegdgdgddvaYCGLLAnttkigvvvgkggrnvtrMRIESGAKIVMLPPPACAAIDDQLIQITGatlavkkalvavttCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
Disordered region (IsUnstruct)
*******************LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYS****************************************************VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG**********GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN***************************************ETIAVQGVDQFVLPL***************************************L********************************************************IEYLIQK***********
Disordered Region (DISOPRED)
************************VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVE*****STQEAVIRVF********************YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP**AAIDDQLIQITGATLAVKKALVAVTTCLQHLSTM***********EKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHS****************RKQEVALRMLFSGWTASGIIGKRGAIVRS**N****************E*VVTISALEYLDTRHSPVQNAAVLVFA**********************VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR**************************************************************************************************************************************DNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
Disordered Region (DISEMBL)
************KRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSD******************LDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNE*********VGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQ*****************PGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
Disordered Region (DISPRO)
*********************DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTM************KVFYSNSSDPHREFFPHLSLVPPLTG****************************KQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG******KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG***NEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMHHSNPYGYSSKRRGPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRSPSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEGSLELEKSLVHLLPTDMVDEVGPRSCSDGMTTASGEDNMLTEGVSQLGLSDNIIGPSTLQLPKTGEEDIEYLIQKVKKAQPHLLIM
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	609	2.2.26 [Sep-21-2011]
P58223	606	KH domain-containing prot	no	no	0.653	0.656	0.262	1e-30
Q5RB68	556	Insulin-like growth facto	no	no	0.541	0.593	0.224	2e-06
Q5SF07	592	Insulin-like growth facto	yes	no	0.607	0.625	0.218	8e-06
Q9UNW9	492	RNA-binding protein Nova-	yes	no	0.321	0.398	0.213	9e-06
Q32PX7	639	Far upstream element-bind	yes	no	0.269	0.256	0.245	1e-05
Q91WJ8	651	Far upstream element-bind	no	no	0.238	0.222	0.252	1e-05
Q96AE4	644	Far upstream element-bind	no	no	0.269	0.254	0.244	1e-05
Q756R8	316	Heterogeneous nuclear rnp	yes	no	0.359	0.693	0.221	3e-05
Q08CK7	598	Insulin-like growth facto	no	no	0.599	0.610	0.199	3e-05
O42254	576	Insulin-like growth facto	no	no	0.604	0.638	0.198	6e-05

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

 Score =  135 bits (339), 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|Q5SF07|IF2B2_MOUSE Insulin-like growth factor 2 mRNA-binding protein 2 OS=Mus musculus GN=Igf2bp2 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 8e-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|Q9UNW9|NOVA2_HUMAN RNA-binding protein Nova-2 OS=Homo sapiens GN=NOVA2 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 9e-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|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 = 52.0 bits (123), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/217 (24%), Positives = 92/217 (42%), Gaps = 53/217 (24%)

Query: 4   HSNPYGYSSKRRGPL---NLPD------------------------DVVSFRLVCPTPVV 36
           +SN YGY  ++R PL   + PD                         V++     P  +V
Sbjct: 54  NSNDYGYGGQKR-PLEDGDQPDAKKVAPQNDSFGTQLPPMHQQQSRSVMTEEYKVPDGMV 112

Query: 37  GGLIGRSGSIISSIRRDTKCRIHC---EGGFPGSDHRVILVVGSGSIDRRIMFCENDVVV 93
           G +IGR G  IS I++++ C+I      GG P    R  ++ G+                
Sbjct: 113 GFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPE-------------- 155

Query: 94  EGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTR 153
               V S +  + ++ E+         GDG G+ V    ++   +K G+V+GKGG  + +
Sbjct: 156 ---SVQSAKRLLDQIVEKGRPAPGFHHGDGPGNAVQE--IMIPASKAGLVIGKGGETIKQ 210

Query: 154 MRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKA 190
           ++  +G K+VM+         D+ ++ITG    V++A
Sbjct: 211 LQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 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|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|Q08CK7|IF2B1_DANRE Insulin-like growth factor 2 mRNA-binding protein 1 OS=Danio rerio GN=igf2bp1 PE=1 SV=1

 Score = 50.8 bits (120), 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|O42254|IF2B1_CHICK Insulin-like growth factor 2 mRNA-binding protein 1 OS=Gallus gallus GN=IGF2BP1 PE=1 SV=1

 Score = 49.7 bits (117), Expect = 6e-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	609
255583245	688	nucleic acid binding protein, putative [	0.899	0.796	0.456	1e-128
356496890	602	PREDICTED: KH domain-containing protein	0.711	0.719	0.448	4e-93
225464083	648	PREDICTED: KH domain-containing protein	0.850	0.799	0.393	1e-92
356529691	611	PREDICTED: poly(rC)-binding protein 3-li	0.691	0.689	0.443	7e-92
297821485	633	KH domain-containing protein [Arabidopsi	0.729	0.701	0.430	3e-91
30681758	632	RNA-binding KH domain-containing protein	0.712	0.686	0.421	2e-87
4314357	649	putative RNA-binding protein [Arabidopsi	0.857	0.804	0.382	2e-87
224097168	404	predicted protein [Populus trichocarpa]	0.630	0.950	0.460	1e-86
357485457	596	Poly(rC)-binding protein [Medicago trunc	0.706	0.721	0.411	2e-83
356546743	663	PREDICTED: poly(rC)-binding protein 3-li	0.678	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 = 4e-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 (890), 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 =  344 bits (883), Expect = 7e-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 (878), 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|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 =  330 bits (845), 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|4314357|gb|AAD15568.1| putative RNA-binding protein [Arabidopsis thaliana]

 Score =  329 bits (844), Expect = 2e-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|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 =  317 bits (811), 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	609
TAIR|locus:2066020	632	AT2G22600 "AT2G22600" [Arabido	0.733	0.707	0.352	8.7e-65
TAIR|locus:2017612	621	AT1G51580 "AT1G51580" [Arabido	0.311	0.305	0.350	2.8e-23
TAIR|locus:2161413	644	AT5G46190 "AT5G46190" [Arabido	0.770	0.728	0.231	9.6e-20
TAIR|locus:2168367	652	RCF3 "AT5G53060" [Arabidopsis	0.481	0.449	0.241	1.5e-13
TAIR|locus:2035807	479	AT1G14170 "AT1G14170" [Arabido	0.367	0.467	0.251	9.1e-13
TAIR|locus:2150956	548	AT5G15270 "AT5G15270" [Arabido	0.325	0.361	0.268	1.1e-12
TAIR|locus:2084908	577	FLK "AT3G04610" [Arabidopsis t	0.334	0.353	0.248	2.9e-08
TAIR|locus:2120755	495	PEP "AT4G26000" [Arabidopsis t	0.277	0.341	0.239	3.5e-06
TAIR|locus:2831364	606	AT4G18375 "AT4G18375" [Arabido	0.239	0.240	0.254	2.9e-05
ZFIN|ZDB-GENE-050706-149	222	zgc:110045 "zgc:110045" [Danio	0.323	0.887	0.248	3.2e-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 = 2.8e-23, Sum P(3) = 2.8e-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 = 9.6e-20, P = 9.6e-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 = 1.5e-13, P = 1.5e-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 = 9.1e-13, Sum P(2) = 9.1e-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 = 1.1e-12, P = 1.1e-12
 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 = 2.9e-08, P = 2.9e-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 = 3.5e-06, P = 3.5e-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 = 2.9e-05, Sum P(2) = 2.9e-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 = 3.2e-05, P = 3.2e-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

Your Input: fgenesh2_kg.4__179__AT2G22600.1 annotation not avaliable (633 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	609
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	4e-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	5e-07
pfam00013	59	pfam00013, KH_1, KH domain	2e-06
smart00322	68	smart00322, KH, K homology RNA-binding domain	1e-05
cd02396	65	cd02396, PCBP_like_KH, K homology RNA-binding doma	2e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-05
pfam13014	42	pfam13014, KH_3, KH domain	2e-05
pfam13014	42	pfam13014, KH_3, KH domain	3e-05
smart00322	68	smart00322, KH, K homology RNA-binding domain	3e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	9e-05
cd00105	64	cd00105, KH-I, K homology RNA-binding domain, type	2e-04
pfam00013	59	pfam00013, KH_1, KH domain	8e-04
smart00322	68	smart00322, KH, K homology RNA-binding domain	0.004

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

 Score = 61.3 bits (150), Expect = 4e-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 = 47.5 bits (114), 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 = 46.4 bits (111), 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 = 46.4 bits (111), Expect = 5e-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 = 44.9 bits (107), 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 = 43.1 bits (102), Expect = 1e-05
 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 = 2e-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 = 2e-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 = 41.0 bits (97), Expect = 3e-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 = 41.9 bits (99), Expect = 3e-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 = 40.2 bits (95), Expect = 9e-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 = 39.5 bits (93), 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 = 37.5 bits (88), Expect = 8e-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 = 0.004
 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	609
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	100.0
KOG1676	600	consensus K-homology type RNA binding proteins [RN	100.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	100.0
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.98
KOG1676	600	consensus K-homology type RNA binding proteins [RN	99.96
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	99.95
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.94
KOG2191	402	consensus RNA-binding protein NOVA1/PASILLA and re	99.89
KOG2190	485	consensus PolyC-binding proteins alphaCP-1 and rel	99.84
KOG2192	390	consensus PolyC-binding hnRNP-K protein HRB57A/hnR	99.59
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.47
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	99.45
PRK13763	180	putative RNA-processing protein; Provisional	99.44
PRK13763	180	putative RNA-processing protein; Provisional	99.39
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.31
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	99.29
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.24
KOG2279	608	consensus Kinase anchor protein AKAP149, contains	99.21
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	99.16
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	99.13
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	99.1
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	99.05
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	98.99
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	98.98
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.96
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	98.91
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.91
PF13014	43	KH_3: KH domain	98.8
KOG2208	753	consensus Vigilin [Lipid transport and metabolism]	98.76
smart00322	69	KH K homology RNA-binding domain.	98.76
PF13014	43	KH_3: KH domain	98.74
smart00322	69	KH K homology RNA-binding domain.	98.61
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.51
COG1094	194	Predicted RNA-binding protein (contains KH domains	98.5
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	98.0
KOG2113	394	consensus Predicted RNA binding protein, contains	97.94
PRK08406	140	transcription elongation factor NusA-like protein;	97.81
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.67
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.48
KOG2113	394	consensus Predicted RNA binding protein, contains	97.43
PRK08406	140	transcription elongation factor NusA-like protein;	97.41
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	97.25
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.13
KOG0119	554	consensus Splicing factor 1/branch point binding p	97.11
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.05
TIGR01952	141	nusA_arch NusA family KH domain protein, archaeal.	96.93
KOG0119	554	consensus Splicing factor 1/branch point binding p	96.77
COG0195	190	NusA Transcription elongation factor [Transcriptio	96.66
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.62
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.54
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.47
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.46
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.31
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.28
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	96.21
KOG1588	259	consensus RNA-binding protein Sam68 and related KH	96.09
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	96.04
TIGR01953	341	NusA transcription termination factor NusA. This m	96.02
KOG2814	345	consensus Transcription coactivator complex, P50 c	96.0
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.9
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.87
KOG2814	345	consensus Transcription coactivator complex, P50 c	95.85
COG0195	190	NusA Transcription elongation factor [Transcriptio	95.84
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.8
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.6
cd02134	61	NusA_KH NusA_K homology RNA-binding domain (KH). N	95.58
COG5176	269	MSL5 Splicing factor (branch point binding protein	95.57
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.43
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.36
PRK00468	75	hypothetical protein; Provisional	95.15
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.01
TIGR01953	341	NusA transcription termination factor NusA. This m	94.83
PRK02821	77	hypothetical protein; Provisional	94.53
PRK12704	520	phosphodiesterase; Provisional	94.25
PRK12328	374	nusA transcription elongation factor NusA; Provisi	94.23
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.17
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.96
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.91
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.78
PRK01064	78	hypothetical protein; Provisional	93.78
PRK00468	75	hypothetical protein; Provisional	93.74
COG1837	76	Predicted RNA-binding protein (contains KH domain)	93.67
PRK00106	535	hypothetical protein; Provisional	93.62
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.52
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	93.39
PRK02821	77	hypothetical protein; Provisional	93.35
COG5176	269	MSL5 Splicing factor (branch point binding protein	93.3
PF14611	210	SLS: Mitochondrial inner-membrane-bound regulator	93.24
PRK09202	470	nusA transcription elongation factor NusA; Validat	93.19
PRK01064	78	hypothetical protein; Provisional	93.1
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	93.03
PRK00106	535	hypothetical protein; Provisional	92.86
PRK12704	520	phosphodiesterase; Provisional	92.85
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	92.63
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	90.4
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	90.1
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	88.83
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	88.38
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	87.89
PRK12705	508	hypothetical protein; Provisional	86.49
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	86.4
KOG3273	252	consensus Predicted RNA-binding protein Pno1p inte	86.21
PF13083	73	KH_4: KH domain; PDB: 3GKU_B.	84.85
cd02409	68	KH-II KH-II (K homology RNA-binding domain, type I	84.21
PF13184	69	KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW	84.19
KOG4369	2131	consensus RTK signaling protein MASK/UNC-44 [Signa	84.15
PF07650	78	KH_2: KH domain syndrome, contains KH motifs.; Int	80.72

>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=1.2e-42  Score=377.84  Aligned_cols=367  Identities=28%  Similarity=0.461  Sum_probs=291.9

Q ss_pred             CCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcch
Q 007293           21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSS  100 (609)
Q Consensus        21 ~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~  100 (609)
                      ++...+||+||+.+.+|.||||+|..|++||++|.++|+|.+..+++.|||++|+|...+               ...++
T Consensus        39 p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~~~~~  103 (485)
T KOG2190|consen   39 PDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------LNLSP  103 (485)
T ss_pred             CCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------ccCCc
Confidence            344445999999999999999999999999999999999999999999999999997322               14788


Q ss_pred             HHHHHHHHHHHHhhhhhccC-----CC-CCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCC
Q 007293          101 TQEAVIRVFERMWEVEAEVE-----GD-GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID  174 (609)
Q Consensus       101 A~~Al~~v~~~i~~~~~~~~-----~~-~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~  174 (609)
                      +++|++++++.+.....+++     .. .....++++|||||.+++|+||||+|+.||+|+++|||+|+|.++ ..+..+
T Consensus       104 ~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~st  182 (485)
T KOG2190|consen  104 ATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNST  182 (485)
T ss_pred             hHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCccc
Confidence            99999999999987533211     11 112226899999999999999999999999999999999999997 667779


Q ss_pred             CceEEEeccHHHHHHHHHHHHHHHhccCCCCCC---CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcc
Q 007293          175 DQLIQITGATLAVKKALVAVTTCLQHLSTMEKS---PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEF  251 (609)
Q Consensus       175 dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~---~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~  251 (609)
                      +|.|+|.|.+++|.+|+..|..+|+++..+.-.   ...+|+|..              ..+...+|.......+|++  
T Consensus       183 er~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~--------------~~~~~~~~s~~~~~~~~~~--  246 (485)
T KOG2190|consen  183 ERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSA--------------SQGGPVLPSTAQTSPDAHP--  246 (485)
T ss_pred             ceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcc--------------cccCccccccccCCccccc--
Confidence            999999999999999999999999996533111   112222200              0000111211111100100  


Q ss_pred             CCCCCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccC
Q 007293          252 HSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDT  331 (609)
Q Consensus       252 ~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~  331 (609)
                                   +.......++.+++.+|...++.|||++|..|+.|+.++|+.|.+.+...+   |.|+++..+.+++
T Consensus       247 -------------~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~~  310 (485)
T KOG2190|consen  247 -------------FGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPED  310 (485)
T ss_pred             -------------ccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCccc
Confidence                         001223466788999999999999999999999999999999999977544   9999999999999


Q ss_pred             CCChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccC
Q 007293          332 RHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCA  411 (609)
Q Consensus       332 ~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~  411 (609)
                      ..+++++|+.+++.++.+.....      . ...++.+|+||++++||||||+|.+|.+|++.|||.|+|...++.   .
T Consensus       311 ~~s~a~~a~~~~~~~~~~~~~~~------~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~  380 (485)
T KOG2190|consen  311 RYSMAQEALLLVQPRISENAGDD------L-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---S  380 (485)
T ss_pred             ccccchhhhhhcccccccccccc------c-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---C
Confidence            99999999999999886643211      1 467899999999999999999999999999999999999987763   2


Q ss_pred             CCCCcEEEEcCCHHHHHHHHHHHHHHhhhcccCc
Q 007293          412 AQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSG  445 (609)
Q Consensus       412 ~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~  445 (609)
                      ..++++++|+|...+...|+++|..++...-...
T Consensus       381 ~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~  414 (485)
T KOG2190|consen  381 GVREALVQITGMLREDLLAQYLIRARLSAPKSSM  414 (485)
T ss_pred             CcceeEEEecchhHHHHhhhhhcccccccCccCC
Confidence            4679999999999999999999988777654433

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

Probab=100.00  E-value=7.3e-43  Score=373.24  Aligned_cols=340  Identities=22%  Similarity=0.302  Sum_probs=266.8

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      ..++-+.-||..+||.||||+|+.|..|..++||+|.+.....+..+|-|.++|..++++                 .|.
T Consensus        52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~-----------------~aK  114 (600)
T KOG1676|consen   52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVE-----------------VAK  114 (600)
T ss_pred             cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHH-----------------HHH
Confidence            556778899999999999999999999999999999987776677899999999998853                 355


Q ss_pred             HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec
Q 007293          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG  182 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G  182 (609)
                      ..+..+..+...... . ........++.+++||++.+|+||||+|++||.|++++||++.+..+.......++.+.|+|
T Consensus       115 ~li~evv~r~~~~~~-~-~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG  192 (600)
T KOG1676|consen  115 QLIGEVVSRGRPPGG-F-PDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG  192 (600)
T ss_pred             HhhhhhhhccCCCCC-c-cccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence            555555554431100 0 01223457899999999999999999999999999999999999997333445889999999


Q ss_pred             cHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007293          183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH  262 (609)
Q Consensus       183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~  262 (609)
                      ++++|+.|..+|.++|++...   ....                                ....|+.             
T Consensus       193 dp~~ve~a~~lV~dil~e~~~---~~~g--------------------------------~~~~~g~-------------  224 (600)
T KOG1676|consen  193 DPDKVEQAKQLVADILREEDD---EVPG--------------------------------SGGHAGV-------------  224 (600)
T ss_pred             CHHHHHHHHHHHHHHHHhccc---CCCc--------------------------------cccccCc-------------
Confidence            999999999999999986211   0000                                0000110             


Q ss_pred             CCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC-CCCCCccEEEEcccccccCCCChHHHHHH
Q 007293          263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV  341 (609)
Q Consensus       263 p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~s~er~vtIsG~e~p~~~~~~a~~A~~  341 (609)
                            ......+++|.||...||.||||+|++||+|+.+||++|+|..+ .+.+.||.+.|.|+.      ..+..|..
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                  01123388999999999999999999999999999999999865 448899999999995      55667777


Q ss_pred             HHHhhhhhcccccCCCCCCC-CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEE
Q 007293          342 LVFARSVEVEGQQGFSSGEN-KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI  420 (609)
Q Consensus       342 ~i~~~i~e~~~~~g~~~g~~-~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I  420 (609)
                      +|.+.|.+.....+...+.. ........+.||+++||.||||+|++||.|.++|||++.+.+.   +.+...++++|+|
T Consensus       293 lI~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~I  369 (600)
T KOG1676|consen  293 LINEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVI  369 (600)
T ss_pred             HHHHHHHHHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEE
Confidence            77777765433322221111 1122378999999999999999999999999999999999875   4446788999999


Q ss_pred             cCCHHHHHHHHHHHHHHhhhcccC
Q 007293          421 SGEYKNVQNALSEVVGRLRHNLKS  444 (609)
Q Consensus       421 ~G~~~~V~~A~~~I~~~Lr~~~~~  444 (609)
                      +|++.+|+.|+.||..++.+....
T Consensus       370 rG~~~QIdhAk~LIr~kvg~~~~n  393 (600)
T KOG1676|consen  370 RGDKRQIDHAKQLIRDKVGDIAPN  393 (600)
T ss_pred             ecCcccchHHHHHHHHHhcccCCC
Confidence            999999999999999999985433

>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=5.9e-42  Score=349.83  Aligned_cols=370  Identities=21%  Similarity=0.319  Sum_probs=273.3

Q ss_pred             CCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcC-CCCCCCceEEEEccCcchhhhhhhccccccccCCCc
Q 007293           20 LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV   98 (609)
Q Consensus        20 ~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~   98 (609)
                      ....+..+|+|||..++|.||||.|++||.|...|.|+|+|.. ...|..||+|+|.|++|.                 .
T Consensus       194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-----------------~  256 (584)
T KOG2193|consen  194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-----------------T  256 (584)
T ss_pred             ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-----------------h
Confidence            3457889999999999999999999999999999999999975 456889999999999987                 3


Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCce
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQL  177 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~  177 (609)
                      +.|+..++.|..+   ...+.    +-..++.+++|..+..||+||||.|++||+|+.+||++|.|++. .......||.
T Consensus       257 s~Ac~~ILeimqk---EA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERT  329 (584)
T KOG2193|consen  257 SKACKMILEIMQK---EAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERT  329 (584)
T ss_pred             HHHHHHHHHHHHH---hhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccce
Confidence            4455555544433   22111    22247899999999999999999999999999999999999986 3344567999


Q ss_pred             EEEeccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCC
Q 007293          178 IQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSAD  257 (609)
Q Consensus       178 V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~  257 (609)
                      |++.|+.++|.+|..+|+.+|++....+-.......++...    ...+.-+++|..+.++         ++.+.|....
T Consensus       330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~----l~~~~l~~f~ssS~~~---------~Ph~~Ps~v~  396 (584)
T KOG2193|consen  330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPG----LNLPALGLFPSSSAVS---------PPHFPPSPVT  396 (584)
T ss_pred             EEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcc----cCccccCCCCcccccC---------CCCCCCCccc
Confidence            99999999999999999999998643331111000000000    0000011111111100         0001111100


Q ss_pred             CCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC-CCCCCccEEEEcccccccCCCChH
Q 007293          258 ADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPV  336 (609)
Q Consensus       258 ~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~s~er~vtIsG~e~p~~~~~~a  336 (609)
                      ....-+.+  ....+...++|+||...+|.|||++|.+||.|.+.+||.|+|..+ .++..+|.|+|+|..      .+.
T Consensus       397 ~a~p~~~~--hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp------eaq  468 (584)
T KOG2193|consen  397 FASPYPLF--HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP------EAQ  468 (584)
T ss_pred             cCCCchhh--hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh------HHH
Confidence            00000111  112245578999999999999999999999999999999999865 677889999999983      333


Q ss_pred             HHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCc
Q 007293          337 QNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDV  416 (609)
Q Consensus       337 ~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er  416 (609)
                      -.|.-++|.++.|..+-     .....-...+.+.||...+|+||||||.+++++++.|+|.+.|+++. .|.  .++..
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            47777888888775321     12234567889999999999999999999999999999999998755 453  56778


Q ss_pred             EEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          417 VIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       417 ~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      +|.|.|..-+.+.|+..|.+++.++-
T Consensus       541 ivriiGhfyatq~aQrki~~iv~qvk  566 (584)
T KOG2193|consen  541 IVRIIGHFYATQNAQRKIAHIVNQVK  566 (584)
T ss_pred             eeeeechhhcchHHHHHHHHHHHHHH
Confidence            99999999999999999999998764

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

Probab=99.98  E-value=8.9e-31  Score=254.53  Aligned_cols=329  Identities=17%  Similarity=0.305  Sum_probs=208.0

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchH
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSST  101 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A  101 (609)
                      -..+.+|||+.++.+|+||||+|++||+|+.++++.|.|.++  ..++||++|+.+.+-+                    
T Consensus        45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~ti--------------------  102 (390)
T KOG2192|consen   45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIETI--------------------  102 (390)
T ss_pred             hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHHH--------------------
Confidence            466899999999999999999999999999999999999987  5689999999765431                    


Q ss_pred             HHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEe
Q 007293          102 QEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT  181 (609)
Q Consensus       102 ~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~  181 (609)
                      -+-|++|+.++-+.-       ...++..+||||+.+++|.|||++|++||+|++++.|+++|... -|+.++||+|.|.
T Consensus       103 ~~ilk~iip~lee~f-------~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv~l~~  174 (390)
T KOG2192|consen  103 GEILKKIIPTLEEGF-------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRVVLIG  174 (390)
T ss_pred             HHHHHHHhhhhhhCC-------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceEEEec
Confidence            223444444432221       12347899999999999999999999999999999999999985 7889999999999


Q ss_pred             ccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCC------CCCCcCCCc-CCCCCCCCCCCCCCCccCCC
Q 007293          182 GATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSD------PHREFFPHL-SLVPPLTGNPSDNASEFHSS  254 (609)
Q Consensus       182 G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~------~~~~~~p~~-~~~P~~~~~~~~Ya~~~~p~  254 (609)
                      |.+..|..++..|.+.|.+.+.+...     +|+...++.....      +..+ -|.. ..+|+.++..          
T Consensus       175 g~~k~v~~~i~~il~~i~e~pikgsa-----~py~p~fyd~t~dyggf~M~f~d-~pg~pgpapqrggqg----------  238 (390)
T KOG2192|consen  175 GKPKRVVECIKIILDLISESPIKGSA-----QPYDPNFYDETYDYGGFTMMFDD-RPGRPGPAPQRGGQG----------  238 (390)
T ss_pred             CCcchHHHHHHHHHHHhhcCCcCCcC-----CcCCccccCcccccCCceeecCC-CCCCCCCCCCCCCCC----------
Confidence            99999999999999999987654432     2332222211100      0000 0000 1111111000          


Q ss_pred             CCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCC
Q 007293          255 SADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHS  334 (609)
Q Consensus       255 ~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~  334 (609)
                                  +.+-..+.-  +.+.  .    -|+-|..-.       -.+.|.......         .  +.+..+
T Consensus       239 ------------pp~~~~sdl--may~--r----~GrpG~ryd-------g~vdFs~detw~---------s--aidtw~  280 (390)
T KOG2192|consen  239 ------------PPPPRGSDL--MAYD--R----RGRPGDRYD-------GMVDFSADETWP---------S--AIDTWS  280 (390)
T ss_pred             ------------CCCCCcccc--ceec--c----CCCCCcccc-------ccccccccccCC---------C--cCCCcC
Confidence                        000000000  0000  0    011111100       001111110000         0  000000


Q ss_pred             hHHHHHHHHHhhhhhcc----cccCCCC-CCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccc
Q 007293          335 PVQNAAVLVFARSVEVE----GQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLG  409 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~----~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~  409 (609)
                      +..=+  +.++--....    ...+..+ |.-....+|+.+.||++.-|.||||+|+.|++|++++||.|+|....+   
T Consensus       281 ~Sewq--maYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikideple---  355 (390)
T KOG2192|consen  281 PSEWQ--MAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLE---  355 (390)
T ss_pred             ccccc--cccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCC---
Confidence            00000  0000000000    0000000 111246789999999999999999999999999999999999976433   


Q ss_pred             cCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          410 CAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       410 ~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                        ++.+|+++|+|+.++++.|++++...++.+
T Consensus       356 --GsedrIitItGTqdQIqnAQYLlQn~Vkq~  385 (390)
T KOG2192|consen  356 --GSEDRIITITGTQDQIQNAQYLLQNSVKQY  385 (390)
T ss_pred             --CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence              678999999999999999999999988854

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

Probab=99.96  E-value=3.7e-29  Score=268.27  Aligned_cols=245  Identities=20%  Similarity=0.307  Sum_probs=197.2

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCC
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK  206 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~  206 (609)
                      ..++.+.-||..++|+||||+|+.|..|+.+|||+|+|...  ......|.|.++|.+++|+.|+.+|.+++....    
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            46788899999999999999999999999999999998774  235588999999999999999999999986521    


Q ss_pred             CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007293          207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS  286 (609)
Q Consensus       207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg  286 (609)
                      .+.                    .+++                                  .....+++.++.||.+++|
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             cccccccchhhhhhhccCeeEEEecC--CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc---ccCCCCCCC
Q 007293          287 GIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG---QQGFSSGEN  361 (609)
Q Consensus       287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~--~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~---~~g~~~g~~  361 (609)
                      .||||+|++||.|++.+||++.+..+  ......+.+.|+|..      ..++.|..++++.+.+..-   ..+...+..
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  223367889999984      5566777788887764311   111111222


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      .....+.+|.||...||.||||+|++||+|+.+|||+|+|.+.++ |   ...+|.+.|.|+.++|+.|.++|.++|++.
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            345569999999999999999999999999999999999998766 3   477999999999999999999999999864

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

Probab=99.95  E-value=1.6e-28  Score=251.53  Aligned_cols=239  Identities=17%  Similarity=0.292  Sum_probs=194.1

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCCC
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS  207 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~  207 (609)
                      +..+|+|||..++|.||||.|++||.|...|-|+|.|... ...+..|+.|+|-|.++...+|+.+|.+++......+  
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 4568899999999999999999999999997642111  


Q ss_pred             CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeccccccc
Q 007293          208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG  287 (609)
Q Consensus       208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~  287 (609)
                                                                                   ....++.++++..+.+||+
T Consensus       275 -------------------------------------------------------------k~~~e~pLk~lAHN~lvGR  293 (584)
T KOG2193|consen  275 -------------------------------------------------------------KVAEEIPLKILAHNNLVGR  293 (584)
T ss_pred             -------------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence                                                                         1225678899999999999


Q ss_pred             ccccccchhhhhhhccCeeEEEecC---CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhc------------cc
Q 007293          288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV------------EG  352 (609)
Q Consensus       288 IIGk~G~~Ik~I~~~tGa~I~i~~~---~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~------------~~  352 (609)
                      +|||.|.+||+|+++||++|.|...   ..-..||.|++.|+-      ..+..|-..|..++.+.            .+
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      33334444454444322            11


Q ss_pred             ccCCC-------------------CC----CC-------CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293          353 QQGFS-------------------SG----EN-------KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (609)
Q Consensus       353 ~~g~~-------------------~g----~~-------~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~  402 (609)
                      .+++.                   +.    +.       .......+|.||...+|.|||++|.+||.|.+.+||.|+|.
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            11110                   00    00       12445788999999999999999999999999999999998


Q ss_pred             CCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       403 ~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..+-    .+..+|+|+|+|.+++..+|+..|..+|.+
T Consensus       448 ppE~----pdvseRMViItGppeaqfKAQgrifgKikE  481 (584)
T KOG2193|consen  448 PPEI----PDVSERMVIITGPPEAQFKAQGRIFGKIKE  481 (584)
T ss_pred             CCCC----CCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence            7653    357899999999999999999999999997

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

Probab=99.94  E-value=3.5e-26  Score=228.82  Aligned_cols=242  Identities=19%  Similarity=0.293  Sum_probs=172.3

Q ss_pred             CCCCCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEc---CCCCCCCceEEEEccCcchhhhhhhccccccc
Q 007293           17 PLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGSGSIDRRIMFCENDVVV   93 (609)
Q Consensus        17 ~~~~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~---~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~   93 (609)
                      .+...++.+++|||||+..+|.||||+|++|.+|+++|||+|+++   +.+|++.||||+|.|+.+++.           
T Consensus        31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~-----------   99 (402)
T KOG2191|consen   31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN-----------   99 (402)
T ss_pred             ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH-----------
Confidence            344445569999999999999999999999999999999999996   578999999999999876521           


Q ss_pred             cCCCcchHHHHHHHHHHHHhhhhhccCC------CCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293           94 EGGEVSSTQEAVIRVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus        94 e~~~~~~A~~Al~~v~~~i~~~~~~~~~------~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                               .-+..|.++|.+.....++      ....++.-.++++||++.+|.||||+|.+||.|++++||.|+|++.
T Consensus       100 ---------av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq  170 (402)
T KOG2191|consen  100 ---------AVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ  170 (402)
T ss_pred             ---------HHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc
Confidence                     1122333444433222222      1123444669999999999999999999999999999999999954


Q ss_pred             -CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCC
Q 007293          168 -PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSD  246 (609)
Q Consensus       168 -p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~  246 (609)
                       |..-...||+|+++|++++..+|+.+|.++|.+++.....   .+.++.....                      ....
T Consensus       171 kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~sc---ln~sya~vsG----------------------pvaN  225 (402)
T KOG2191|consen  171 KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSC---LNISYANVSG----------------------PVAN  225 (402)
T ss_pred             CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccce---eccchhcccC----------------------cccc
Confidence             5555678999999999999999999999999997654321   1111111000                      0011


Q ss_pred             CCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC
Q 007293          247 NASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP  312 (609)
Q Consensus       247 Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~  312 (609)
                      |++...|+....         .........-.-++....|..-|.+|.++-.|-.-+|+.+.+.+.
T Consensus       226 snPtGspya~~~---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~  282 (402)
T KOG2191|consen  226 SNPTGSPYAYQA---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA  282 (402)
T ss_pred             cCCCCCCCCCCC---------ccccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence            111111111111         111222233456888899999999999999999999998888753

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

Probab=99.89  E-value=2.3e-22  Score=201.58  Aligned_cols=250  Identities=21%  Similarity=0.296  Sum_probs=195.3

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCC
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK  206 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~  206 (609)
                      .+.+++|||+..+|.||||+|++|.++|.+|||+|++++. ...|+++||+|.|+|+.+++......|.++|++.+....
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            4899999999999999999999999999999999999987 788999999999999999999999999999998543221


Q ss_pred             CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007293          207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS  286 (609)
Q Consensus       207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg  286 (609)
                      .+....+                        |                             ......-.++++||+..+|
T Consensus       118 k~v~~~~------------------------p-----------------------------qt~~r~kqikivvPNstag  144 (402)
T KOG2191|consen  118 KPVDILQ------------------------P-----------------------------QTPDRIKQIKIVVPNSTAG  144 (402)
T ss_pred             CCccccC------------------------C-----------------------------CCccccceeEEeccCCccc
Confidence            1100000                        0                             0001112478999999999


Q ss_pred             cccccccchhhhhhhccCeeEEEecCCC---CCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc---------cc
Q 007293          287 GIIGKRGAIVRSLQNASGALISFAAPLT---KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG---------QQ  354 (609)
Q Consensus       287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~---~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~---------~~  354 (609)
                      .||||+|.+||.|++++||+|+|.+.++   .-.+|+||++|..      +....|+.+|++++.++.-         ..
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            9999999999999999999999995332   3368999999984      5667899999999876520         00


Q ss_pred             ------CCCC-C-------CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEE
Q 007293          355 ------GFSS-G-------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI  420 (609)
Q Consensus       355 ------g~~~-g-------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I  420 (609)
                            ++.+ |       ...+...+....|+....|..-|.+|.++-.|...+|+.+.+...-+.-  .....+ +-+
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                  0111 1       0123446677889999999999999999999999999999998755521  223334 788


Q ss_pred             cCCHHHHHHHHHHHHHHhh
Q 007293          421 SGEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       421 ~G~~~~V~~A~~~I~~~Lr  439 (609)
                      .|....+..|-.+|..+..
T Consensus       296 ~g~~ls~~aa~g~L~~~~~  314 (402)
T KOG2191|consen  296 LGLGLSILAAEGVLAAKVA  314 (402)
T ss_pred             cchhhhhhhhhhHHHHhhc
Confidence            9999999999998887654

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

Probab=99.84  E-value=9.4e-20  Score=199.00  Aligned_cols=163  Identities=28%  Similarity=0.407  Sum_probs=138.5

Q ss_pred             EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc--
Q 007293          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG--  352 (609)
Q Consensus       275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~--  352 (609)
                      ++|++|+...+|.||||+|..||+|+.++.++|+|.+..+++.+|+|+|+|+... ...+++++|+.+.++++.....  
T Consensus        44 ~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~-~~~~~~~~al~ka~~~iv~~~~~d  122 (485)
T KOG2190|consen   44 TYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE-LNLSPATDALFKAFDMIVFKLEED  122 (485)
T ss_pred             eEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc-ccCCchHHHHHHHHHHHhhccccc
Confidence            4899999999999999999999999999999999999999999999999995322 2567889999999998865311  


Q ss_pred             -ccCCCCC-CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHH
Q 007293          353 -QQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNA  430 (609)
Q Consensus       353 -~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A  430 (609)
                       ....+.+ ......++.+|+||.+++|+||||+|+.||+|++.|||+|+|.+. .+|.   .++|.|+|.|.+++|.+|
T Consensus       123 ~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~a  198 (485)
T KOG2190|consen  123 DEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKA  198 (485)
T ss_pred             ccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHH
Confidence             1111111 122236899999999999999999999999999999999999986 6675   667889999999999999


Q ss_pred             HHHHHHHhhhcc
Q 007293          431 LSEVVGRLRHNL  442 (609)
Q Consensus       431 ~~~I~~~Lr~~~  442 (609)
                      +..|..+|+++.
T Consensus       199 l~~Is~~L~~~~  210 (485)
T KOG2190|consen  199 LVQISSRLLENP  210 (485)
T ss_pred             HHHHHHHHHhcC
Confidence            999999999975

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

Probab=99.59  E-value=2.1e-14  Score=140.75  Aligned_cols=159  Identities=21%  Similarity=0.377  Sum_probs=130.0

Q ss_pred             CCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhh
Q 007293          270 RKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVE  349 (609)
Q Consensus       270 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e  349 (609)
                      ....+.+++++..+.+|.||||+|++||.|+.+++|+|+|.++  ...+|+++|+..+          +.+..|++++.-
T Consensus        44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~----------~ti~~ilk~iip  111 (390)
T KOG2192|consen   44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADI----------ETIGEILKKIIP  111 (390)
T ss_pred             hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccH----------HHHHHHHHHHhh
Confidence            3456789999999999999999999999999999999999865  3578999999874          455556555532


Q ss_pred             cccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007293          350 VEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN  429 (609)
Q Consensus       350 ~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~  429 (609)
                      . ++.++    ...+.|..+|+|..+.+|.|||++|+.||++++.+.|+.+|.-. .   |...++|+|.|.|.+..|..
T Consensus       112 ~-lee~f----~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c---~p~stdrv~l~~g~~k~v~~  182 (390)
T KOG2192|consen  112 T-LEEGF----QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-C---CPHSTDRVVLIGGKPKRVVE  182 (390)
T ss_pred             h-hhhCC----CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-c---CCCCcceEEEecCCcchHHH
Confidence            1 11112    23467999999999999999999999999999999999999752 2   24688999999999999999


Q ss_pred             HHHHHHHHhhhcccCccccC
Q 007293          430 ALSEVVGRLRHNLKSGEILN  449 (609)
Q Consensus       430 A~~~I~~~Lr~~~~~~~~~~  449 (609)
                      ..+.|+..|.+..+..+..|
T Consensus       183 ~i~~il~~i~e~pikgsa~p  202 (390)
T KOG2192|consen  183 CIKIILDLISESPIKGSAQP  202 (390)
T ss_pred             HHHHHHHHhhcCCcCCcCCc
Confidence            99999999998766655443

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.47  E-value=1.4e-13  Score=132.27  Aligned_cols=138  Identities=18%  Similarity=0.205  Sum_probs=96.0

Q ss_pred             EEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEE---ccCcchhhhhhhccccccccCCCcchHHHHH
Q 007293           29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILV---VGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (609)
Q Consensus        29 ilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I---~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al  105 (609)
                      +.||.+++|.|||++|++|++|+++|||+|++.+.     +..|.|   +++++.                 +..|.+.+
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-----TGEVKIEEEDEDPLA-----------------VMKAREVV   59 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-----------------HHHHHHHH
Confidence            45799999999999999999999999999999753     245777   343333                 22343333


Q ss_pred             HHHHHHHhhhhhccCCCCCCCCceEEEE-Eeec---------ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCC
Q 007293          106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD  175 (609)
Q Consensus       106 ~~v~~~i~~~~~~~~~~~~~~~~vt~rl-lVP~---------~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~d  175 (609)
                      ..+..-   ...+..- .--...+++++ -|+.         ..+|+|||++|++++.|++.|||+|.|.         +
T Consensus        60 ~~i~~g---f~~e~A~-~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~  126 (172)
T TIGR03665        60 KAIGRG---FSPEKAL-KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G  126 (172)
T ss_pred             HHHHcC---CCHHHHH-HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence            332210   0011000 00001222222 2222         3789999999999999999999999993         3


Q ss_pred             ceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          176 QLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       176 R~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      +.|.|.|+++++..|..+|.+++.+.
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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=99.45  E-value=3.5e-13  Score=129.50  Aligned_cols=140  Identities=19%  Similarity=0.200  Sum_probs=98.1

Q ss_pred             EEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEc--ccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293          278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTIS--ALEYLDTRHSPVQNAAVLVFARSVEVEGQQG  355 (609)
Q Consensus       278 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIs--G~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g  355 (609)
                      +.||.+++|.|||++|++|+.|+++||++|.+.+.     +..|.|.  +. ++    ..++.|...+........+...
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~-d~----~~i~kA~~~I~~i~~gf~~e~A   71 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDE-DP----LAVMKAREVVKAIGRGFSPEKA   71 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCC-CH----HHHHHHHHHHHHHHcCCCHHHH
Confidence            56899999999999999999999999999999953     2468883  21 11    3344555544432211110000


Q ss_pred             CCCCCCCCCceEEEEEecc---------ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHH
Q 007293          356 FSSGENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKN  426 (609)
Q Consensus       356 ~~~g~~~~~~~t~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~  426 (609)
                      +  ..-.....-.-+.|+.         ..+|+|||++|++++.|++.|||+|.|..            +.|.|.|++++
T Consensus        72 ~--~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~  137 (172)
T TIGR03665        72 L--KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQ  137 (172)
T ss_pred             H--HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHH
Confidence            0  0000111122233443         47999999999999999999999999952            67999999999


Q ss_pred             HHHHHHHHHHHhhhc
Q 007293          427 VQNALSEVVGRLRHN  441 (609)
Q Consensus       427 V~~A~~~I~~~Lr~~  441 (609)
                      ++.|+++|...|.+.
T Consensus       138 ~~~A~~~i~~li~~~  152 (172)
T TIGR03665       138 VQIAREAIEMLIEGA  152 (172)
T ss_pred             HHHHHHHHHHHHcCC
Confidence            999999999988643

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=99.44  E-value=5.4e-13  Score=129.08  Aligned_cols=140  Identities=16%  Similarity=0.243  Sum_probs=98.3

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEc----cCcchhhhhhhccccccccCCCcch
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS  100 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~----G~~e~~~~~~~~~~~~~~e~~~~~~  100 (609)
                      +...+.||.+.+|.|||++|++|+.|+++|||+|++.+.     +..|.|.    ++++.                 +..
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-----TGEVIIEPTDGEDPLA-----------------VLK   60 (180)
T ss_pred             ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-----------------HHH
Confidence            467788999999999999999999999999999999853     2456665    33333                 223


Q ss_pred             HHHHHHHHHHHHhhhhh--ccCCCCCCCCceEEEEE-----ee-----cceeeeeeecCcchhhhcccccCcEEEecCCC
Q 007293          101 TQEAVIRVFERMWEVEA--EVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP  168 (609)
Q Consensus       101 A~~Al~~v~~~i~~~~~--~~~~~~~~~~~vt~rll-----VP-----~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p  168 (609)
                      |++.+..+..- .+.+.  ..-+     ..+..++.     .+     ...+|+|||++|++++.|++.|||+|.|..  
T Consensus        61 A~~~I~ai~~g-f~~e~A~~l~g-----d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--  132 (180)
T PRK13763         61 ARDIVKAIGRG-FSPEKALRLLD-----DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--  132 (180)
T ss_pred             HHHHHHHHhcC-CCHHHHHHHhC-----CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--
Confidence            43333332210 00000  0000     12222221     11     137899999999999999999999999954  


Q ss_pred             CCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          169 ACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       169 ~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                             +.|.|.|+++++..|...|..++++.
T Consensus       133 -------~~v~i~G~~~~~~~A~~~I~~li~g~  158 (180)
T PRK13763        133 -------KTVAIIGDPEQVEIAREAIEMLIEGA  158 (180)
T ss_pred             -------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence                   45899999999999999999999663

>PRK13763 putative RNA-processing protein; Provisional

Probab=99.39  E-value=2e-12  Score=125.22  Aligned_cols=145  Identities=18%  Similarity=0.217  Sum_probs=99.6

Q ss_pred             EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccccc
Q 007293          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ  354 (609)
Q Consensus       275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~  354 (609)
                      ...+.||.+.+|.|||++|++|+.|+++||++|.+.+.     +..|.|.-.... + ...++.|...+...........
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-----TGEVIIEPTDGE-D-PLAVLKARDIVKAIGRGFSPEK   76 (180)
T ss_pred             eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCC-C-HHHHHHHHHHHHHHhcCCCHHH
Confidence            56788999999999999999999999999999999954     256777611100 1 1334455554443332100000


Q ss_pred             CCCCCCCCCCceEEE-EEec---------cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCH
Q 007293          355 GFSSGENKGDAVAVS-ILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY  424 (609)
Q Consensus       355 g~~~g~~~~~~~t~~-l~VP---------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~  424 (609)
                      .+.  . ....+..+ +.|.         ...+|+|||++|++++.|++.|||+|.|..            +.|.|.|++
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 00111111 1111         147999999999999999999999999953            349999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q 007293          425 KNVQNALSEVVGRLRHN  441 (609)
Q Consensus       425 ~~V~~A~~~I~~~Lr~~  441 (609)
                      ++++.|...|...++.+
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=99.31  E-value=3.9e-12  Score=102.50  Aligned_cols=65  Identities=28%  Similarity=0.473  Sum_probs=58.8

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV  435 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~  435 (609)
                      +.+|+||.+.+|+|||++|++|++|+++|||+|++.+..+    ...++|+|+|+|++++|+.|+.+|.
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    2567899999999999999999873

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=99.29  E-value=4e-12  Score=102.44  Aligned_cols=64  Identities=31%  Similarity=0.549  Sum_probs=59.0

Q ss_pred             EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (609)
Q Consensus       130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I  194 (609)
                      ++||+||.+.+|+||||+|++|++|+++|||+|.+.+. ..+...+|+|+|+|++++|.+|+.+|
T Consensus         1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I   64 (65)
T cd02396           1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLI   64 (65)
T ss_pred             CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhh
Confidence            37899999999999999999999999999999999985 33467899999999999999999987

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=6.4e-11  Score=127.00  Aligned_cols=298  Identities=16%  Similarity=0.149  Sum_probs=200.9

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCC
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME  205 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~  205 (609)
                      ...+.+++.|+...+.+++||+|++|+.|+..++++|.+..+   ....++...+.|-+.++.+|...++.++.++.   
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            447889999999999999999999999999999999999775   22345555666689999999999999996631   


Q ss_pred             CCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEeccccc
Q 007293          206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA  285 (609)
Q Consensus       206 ~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~v  285 (609)
                                                                                         .+...+.+|...+
T Consensus       139 -------------------------------------------------------------------pvk~~lsvpqr~~  151 (608)
T KOG2279|consen  139 -------------------------------------------------------------------PVSEQLSVPQRSV  151 (608)
T ss_pred             -------------------------------------------------------------------cccccccchhhhc
Confidence                                                                               2234466889999


Q ss_pred             ccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhc---------------
Q 007293          286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV---------------  350 (609)
Q Consensus       286 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~---------------  350 (609)
                      ++|+|++|++++.|+..++|+|.+.......-.+...|.+..      ++...|..++.+++.+.               
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            999999999999999999999999977544556777887764      22223333333333211               


Q ss_pred             -------cc-----------------------ccCCCC-----------------------CC--CCCCceEEEEEeccc
Q 007293          351 -------EG-----------------------QQGFSS-----------------------GE--NKGDAVAVSILVGAD  375 (609)
Q Consensus       351 -------~~-----------------------~~g~~~-----------------------g~--~~~~~~t~~l~VP~~  375 (609)
                             .+                       ..+.+.                       +.  ......-.+|.||..
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                   00                       001000                       00  011234568899999


Q ss_pred             cccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcccCccccCCCCCCC
Q 007293          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNEARPRS  455 (609)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~~~~~~~  455 (609)
                      .+|.|||+.|..++.....|++.+.|--....-.  --.-.++.+.|+..-+..++.|+..+.-+    ..+..+.-...
T Consensus       306 lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~--v~~~qic~~egkqh~~n~vl~ml~~~~p~----~~f~eLnl~~~  379 (608)
T KOG2279|consen  306 LSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR--VLQLQICVNEGKQHYENSVLEMLTVHVPD----IVFAELNLNGS  379 (608)
T ss_pred             cccchhhhhhhhhhhhhhccCccceEEeccccch--hhhhhhheecchhHHHHHHHhhhhccCCc----cccccccccCc
Confidence            9999999999999999999999998865222000  01125688999999999999998754332    21111111110


Q ss_pred             CCCCCCCCCCCCCCCCCCCCcccccccccccccceeeecCCCCccccccCCCCCCCCCCCCCCCccccc
Q 007293          456 PSGRVGGPALHKLHQSVALSPEFEQETIAVQGVDQFVLPLNRSQTLQTEGRRHATPTTDGKPGSRMFEG  524 (609)
Q Consensus       456 ~~~~~g~p~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  524 (609)
                      -++..-.+++-...                .-+.-..||-+-.-.....+-+-+.+.+|+.|--|-|.-
T Consensus       380 ~~p~lps~al~~L~----------------td~~wL~fpd~i~cev~V~s~i~a~hlf~pq~tip~F~a  432 (608)
T KOG2279|consen  380 WYPALPSGALENLN----------------TDLYWLDFPDNIDCEVKVLSAIRADHLFLPQQTIPCFLA  432 (608)
T ss_pred             cCcccCcccccccC----------------CcceEEEcCCCceEEeeeehhhcccceeeccccchhhhh
Confidence            01111111121111                112234667777777777778889999999988886544

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

Probab=99.21  E-value=9.3e-11  Score=125.79  Aligned_cols=276  Identities=21%  Similarity=0.254  Sum_probs=173.7

Q ss_pred             CCCCCCCCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccC
Q 007293           16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG   95 (609)
Q Consensus        16 ~~~~~~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~   95 (609)
                      +..+...+++.+.+.|++..|-.+|||.|++|+.|+..|++||.+.+...+ ++++.++.|-...               
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            345667799999999999999999999999999999999999999765333 4677777765543               


Q ss_pred             CCcchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCC
Q 007293           96 GEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD  175 (609)
Q Consensus        96 ~~~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~d  175 (609)
                        +++|..++...   +...           ..+...+-+|...++.|+|++|.+++.|+.-++|+|.+..+  .-...+
T Consensus       123 --v~~a~a~~~~~---~~~~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~  184 (608)
T KOG2279|consen  123 --VCKAKAAIHQI---LTEN-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLS  184 (608)
T ss_pred             --CChHHHHHHHH---HhcC-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cccccc
Confidence              45554444332   2221           25667789999999999999999999999999999999875  234578


Q ss_pred             ceEEEeccHHHHHHHHHHHHHHHhccCCCCCC-------CcccCCCccccccCCCCCCCCCcCCCc------CCCCCCCC
Q 007293          176 QLIQITGATLAVKKALVAVTTCLQHLSTMEKS-------PICFNRPIEKVFYSNSSDPHREFFPHL------SLVPPLTG  242 (609)
Q Consensus       176 R~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~-------~~~~~~P~~~~~~~~~~~~~~~~~p~~------~~~P~~~~  242 (609)
                      ++..|.|...-+..|..++.+.+.++-...+.       ......|...+. .....+.....+|.      ++.|..++
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            89999999999999999999988764211111       001111111100 00000111111110      22222211


Q ss_pred             CCCCCCCccCC-CCCCCCCCCCCCCc-cCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCC---
Q 007293          243 NPSDNASEFHS-SSADADRDHPGLDK-KGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSG---  317 (609)
Q Consensus       243 ~~~~Ya~~~~p-~~~~~~~~~p~~~~-~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~---  317 (609)
                      ...+-.. +-- ......-..+..+. ........++|.+|...+|.+||+.|+.++.+...+++++.|......+.   
T Consensus       264 ~~~eg~d-m~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~  342 (608)
T KOG2279|consen  264 VTKEGGD-MAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQ  342 (608)
T ss_pred             cccCCCc-ceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhh
Confidence            1100000 000 00000000000000 11223346778899999999999999999999999999999975322222   


Q ss_pred             ccEEEEcccc
Q 007293          318 ERVVTISALE  327 (609)
Q Consensus       318 er~vtIsG~e  327 (609)
                      -.++.+.|+.
T Consensus       343 ~qic~~egkq  352 (608)
T KOG2279|consen  343 LQICVNEGKQ  352 (608)
T ss_pred             hhhheecchh
Confidence            2567777873

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=99.16  E-value=6.1e-11  Score=94.46  Aligned_cols=61  Identities=20%  Similarity=0.330  Sum_probs=55.6

Q ss_pred             EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007293          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV  435 (609)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~  435 (609)
                      .++.||.+++++|||++|++|++|+++|||+|.|++..       ..++.|+|+|+.++|..|+.+|.
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       45799999999999999999873

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=5e-11  Score=94.31  Aligned_cols=60  Identities=27%  Similarity=0.422  Sum_probs=54.8

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV  434 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I  434 (609)
                      |.+|.||.+++|+|||++|++|++|++.|||+|+|++.       + +...|+|+|++++|+.|+.+|
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=99.10  E-value=2.3e-10  Score=90.93  Aligned_cols=59  Identities=15%  Similarity=0.255  Sum_probs=53.8

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV  435 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~  435 (609)
                      .+..+.||.+++|+|||++|++|++|+++|||+|.|.+           ++.|.|+|+ +++++.|+.+|.
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=99.05  E-value=4.8e-10  Score=89.44  Aligned_cols=62  Identities=26%  Similarity=0.489  Sum_probs=56.5

Q ss_pred             EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007293          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV  434 (609)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I  434 (609)
                      .++.||.+++++|||++|++|++|++.|||+|.|+....     ...++.|+|.|+.+++..|+.+|
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            589999999999999999999999999999999987433     35689999999999999999887

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=98.99  E-value=4.4e-10  Score=89.52  Aligned_cols=60  Identities=27%  Similarity=0.354  Sum_probs=55.3

Q ss_pred             EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (609)
Q Consensus       131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I  194 (609)
                      .+|.||..++++|||++|++|++|+++|||+|.+...    ...++.|+|+|+.++|.+|+.+|
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            5689999999999999999999999999999999773    26789999999999999999886

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=98.98  E-value=2.2e-10  Score=90.63  Aligned_cols=60  Identities=23%  Similarity=0.418  Sum_probs=54.7

Q ss_pred             EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (609)
Q Consensus       130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I  194 (609)
                      |.+|.||..++|+|||++|++|++|+++|||+|.+...    + ....|+|+|+.++|.+|+.+|
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 ....

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.96  E-value=2.9e-09  Score=123.28  Aligned_cols=288  Identities=17%  Similarity=0.158  Sum_probs=196.3

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      ..+..++.+-......+||++|.+++.++.++.+.|+|++.....  ....|.|.....                 ..+.
T Consensus       199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~-----------------~~~~  259 (753)
T KOG2208|consen  199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSS-----------------SSIN  259 (753)
T ss_pred             eeEEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhccccccc-----------------eehh
Confidence            447888999999999999999999999999999999998754332  223444433221                 0111


Q ss_pred             HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec
Q 007293          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG  182 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G  182 (609)
                      --+...+.++..             .....+.++....-.++|..|..+..|+...--...+.+.   +.+.+..+.+.|
T Consensus       260 ~~i~~~~~~le~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~---~~s~~~~~~~~~  323 (753)
T KOG2208|consen  260 VEIQEALTRLES-------------EFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQN---YPSKDDSIVLSG  323 (753)
T ss_pred             hhhHHHHHHhcC-------------hhhhhhhhhccccccccccccchhhHHHhhcchhhhhhcc---ccccceeEeecc
Confidence            111122222111             2233456667777888999999999999887665555553   345667788888


Q ss_pred             cHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCC
Q 007293          183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH  262 (609)
Q Consensus       183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~  262 (609)
                      ....+..+...-...+...                                                             
T Consensus       324 ~~~~~~~~~~~~~~~~~~~-------------------------------------------------------------  342 (753)
T KOG2208|consen  324 FEVGAVLAKRDKTLLLKNS-------------------------------------------------------------  342 (753)
T ss_pred             cccchhhhhhHHHHHHHHh-------------------------------------------------------------
Confidence            8777766665554444331                                                             


Q ss_pred             CCCCccCCCcceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHH
Q 007293          263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVL  342 (609)
Q Consensus       263 p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~  342 (609)
                             ..+.+.+.+.+-...+..++||+|.+|.+|++++.+.+.+..  .++....+.++|..      ...+.|...
T Consensus       343 -------~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~------~~~~ka~~~  407 (753)
T KOG2208|consen  343 -------EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVS------ANDEKAVED  407 (753)
T ss_pred             -------hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccc------cchhHHHHH
Confidence                   012235567788999999999999999999999999999986  33456678888874      222333333


Q ss_pred             HHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhC-CeEEecCCCcccccCCCCCcEEEEc
Q 007293          343 VFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTG-TDIKLVGGEQVLGCAAQNDVVIQIS  421 (609)
Q Consensus       343 i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG-a~I~I~~~~~~P~~~~~~er~V~I~  421 (609)
                      +.....+..           .+.....+.+|...+.+|||.+|..|++|...+| .+|+.++..       .....+++.
T Consensus       408 v~~~~~ei~-----------n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~  469 (753)
T KOG2208|consen  408 VEKIIAEIL-----------NSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIR  469 (753)
T ss_pred             HHHHHHhhh-----------cccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEe
Confidence            333332210           1145778999999999999999999999999999 667666532       345667788


Q ss_pred             CCHHHHHHHHHHHHHHhh
Q 007293          422 GEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       422 G~~~~V~~A~~~I~~~Lr  439 (609)
                      |....+..+..++.....
T Consensus       470 ~~~~dv~~~~~~~~~~~~  487 (753)
T KOG2208|consen  470 GISKDVEKSVSLLKALKA  487 (753)
T ss_pred             ccccccchhHHHHHhhhh
Confidence            887777776666655443

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

Probab=98.91  E-value=2.2e-09  Score=85.58  Aligned_cols=62  Identities=31%  Similarity=0.532  Sum_probs=56.2

Q ss_pred             EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHH
Q 007293          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV  194 (609)
Q Consensus       131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I  194 (609)
                      .++.||..++++|||++|++|++|+++|||+|.|...  .....++.|.|.|..+++.+|+.+|
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            5799999999999999999999999999999999874  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.

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

Probab=98.91  E-value=2.4e-09  Score=85.10  Aligned_cols=58  Identities=26%  Similarity=0.343  Sum_probs=52.7

Q ss_pred             eEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHH
Q 007293          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV  194 (609)
Q Consensus       129 vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I  194 (609)
                      .+..+-||.+++|+||||+|++|++|+++|||+|.|..        ++.|.|+|. .+++.+|+.+|
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            45678899999999999999999999999999999955        367999998 99999999887

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

>PF13014 KH_3: KH domain

Probab=98.80  E-value=8e-09  Score=76.13  Aligned_cols=42  Identities=40%  Similarity=0.727  Sum_probs=38.6

Q ss_pred             cccceecCCChHHHHHHHHhCceEEEcC-CCCCCCceEEEEcc
Q 007293           35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG   76 (609)
Q Consensus        35 ~vG~IIGk~G~~Ik~IreeTga~I~V~~-~~~g~~eRvI~I~G   76 (609)
                      ++|+|||++|++|++|+++|||+|+|++ ..++..+|+|+|+|
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            5899999999999999999999999988 56678899999987

>KOG2208 consensus Vigilin [Lipid transport and metabolism]

Probab=98.76  E-value=3.8e-08  Score=114.08  Aligned_cols=287  Identities=17%  Similarity=0.197  Sum_probs=194.7

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHH
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA  104 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~A  104 (609)
                      ..+-..|+....-.++|..|..+++|+....-...+....+. ...++.++|....+..                ...+.
T Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s-~~~~~~~~~~~~~~~~----------------~~~~~  335 (753)
T KOG2208|consen  273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPS-KDDSIVLSGFEVGAVL----------------AKRDK  335 (753)
T ss_pred             hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccc-cceeEeecccccchhh----------------hhhHH
Confidence            344566777888889999999999999888544444333233 3456777777655311                11122


Q ss_pred             HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccH
Q 007293          105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGAT  184 (609)
Q Consensus       105 l~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~  184 (609)
                      . ..+....+.            .+.+.+-+....+..++||+|.+|.+|++++.|.+.+..    .+..+..+.++|..
T Consensus       336 ~-~~~~~~~~n------------n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~----~~~~~~~v~~~~~~  398 (753)
T KOG2208|consen  336 T-LLLKNSEEN------------NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK----QGSNNKKVVITGVS  398 (753)
T ss_pred             H-HHHHHhhcc------------ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc----ccCCCCCeEEeccc
Confidence            2 222221111            366778888999999999999999999999999999966    46788999999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCC
Q 007293          185 LAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPG  264 (609)
Q Consensus       185 e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~  264 (609)
                      .++.+|...|.....+....                                                            
T Consensus       399 ~~~~ka~~~v~~~~~ei~n~------------------------------------------------------------  418 (753)
T KOG2208|consen  399 ANDEKAVEDVEKIIAEILNS------------------------------------------------------------  418 (753)
T ss_pred             cchhHHHHHHHHHHHhhhcc------------------------------------------------------------
Confidence            99999999999999773210                                                            


Q ss_pred             CCccCCCcceEEEEEecccccccccccccchhhhhhhccC-eeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHH
Q 007293          265 LDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASG-ALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV  343 (609)
Q Consensus       265 ~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i  343 (609)
                              .....+.+|..++..+||.+|..|..|..+++ ..|++...  .+....+++.|.-   ..+..   +..++
T Consensus       419 --------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~--~~~~~~~~~~~~~---~dv~~---~~~~~  482 (753)
T KOG2208|consen  419 --------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN--NNSSDMVTIRGIS---KDVEK---SVSLL  482 (753)
T ss_pred             --------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC--CcccccceEeccc---cccch---hHHHH
Confidence                    12334679999999999999999999999999 55555543  3334456676653   11111   11111


Q ss_pred             Hh--hhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEc
Q 007293          344 FA--RSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS  421 (609)
Q Consensus       344 ~~--~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~  421 (609)
                      ..  ......         ..-...+...+.|..+.+..+|+.|..+...++..+..+..          ..++..++|.
T Consensus       483 ~~~~~~a~~~---------~~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~  543 (753)
T KOG2208|consen  483 KALKADAKNL---------KFRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIE  543 (753)
T ss_pred             Hhhhhhhhcc---------hhhhhhhccccchHHhhcccccCceeeeccCCceeeccccc----------ccccceeeec
Confidence            11  111100         01133566777788888888888777666555444444332          2567889999


Q ss_pred             CCHHHHHHHHHHHHHHhhh
Q 007293          422 GEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       422 G~~~~V~~A~~~I~~~Lr~  440 (609)
                      |..+.|.+|..++...+..
T Consensus       544 gk~~~v~~a~~~L~~~~~~  562 (753)
T KOG2208|consen  544 GKLELVLEAPAELKALIEA  562 (753)
T ss_pred             ccccchhhhHHHHHhcchh
Confidence            9999999999999886654

>smart00322 KH K homology RNA-binding domain

Probab=98.76  E-value=4e-08  Score=78.37  Aligned_cols=67  Identities=30%  Similarity=0.528  Sum_probs=60.0

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr  439 (609)
                      .+.++.||.++++++||++|++|++|++.||++|.+....       .....|+|.|+.++++.|+.+|...++
T Consensus         3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~~   69 (69)
T smart00322        3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEILE   69 (69)
T ss_pred             eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999997522       257889999999999999999988763

>PF13014 KH_3: KH domain

Probab=98.74  E-value=1.3e-08  Score=74.97  Aligned_cols=43  Identities=35%  Similarity=0.664  Sum_probs=37.8

Q ss_pred             cccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC
Q 007293          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG  422 (609)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G  422 (609)
                      +||+|||++|++|++|+++|||+|+|++ +..   ...+++.|+|+|
T Consensus         1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~---~~~~~~~v~I~G   43 (43)
T PF13014_consen    1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENE---PGSNERVVTITG   43 (43)
T ss_pred             CcCeEECCCChHHHHHHHHhCcEEEECC-ccC---CCCCceEEEEEC
Confidence            5899999999999999999999999998 221   357899999998

>smart00322 KH K homology RNA-binding domain

Probab=98.61  E-value=1.2e-07  Score=75.51  Aligned_cols=67  Identities=27%  Similarity=0.487  Sum_probs=60.4

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      .++.++.||...++.+||++|++|++|++.||++|.+...    ......+.|.|..+++..|..+|.+.+
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    226789999999999999999998876

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

Probab=98.51  E-value=1.9e-07  Score=89.67  Aligned_cols=148  Identities=18%  Similarity=0.220  Sum_probs=98.9

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      ....+.+.+|.+..+.+||+.|++.+.|.+.++++|.++     ..+..|.|.......+.            .....|.
T Consensus         6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp------------~~~~ka~   68 (194)
T COG1094           6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDP------------LALLKAR   68 (194)
T ss_pred             ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCCh------------HHHHHHH
Confidence            445677999999999999999999999999999999995     34577888765321110            0111222


Q ss_pred             HHHHHHHHHHhhhhhccCCC-CCCCCceEEEE-----Eee------cceeeeeeecCcchhhhcccccCcEEEecCCCCC
Q 007293          103 EAVIRVFERMWEVEAEVEGD-GDGDDVAYCGL-----LAN------TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC  170 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~~~-~~~~~~vt~rl-----lVP------~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~  170 (609)
                      +-+. .+.+    ++..+.+ .--+..+.+.+     ++.      ....|+|||++|.+-+.|++-|||+|.|..    
T Consensus        69 d~Vk-AIgr----GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----  139 (194)
T COG1094          69 DVVK-AIGR----GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----  139 (194)
T ss_pred             HHHH-HHhc----CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----
Confidence            2111 1111    1000000 00000112211     111      124699999999999999999999999954    


Q ss_pred             CCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       171 ~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                           ..|.|-|.+++|+.|...|..++...
T Consensus       140 -----~tVaiiG~~~~v~iAr~AVemli~G~  165 (194)
T COG1094         140 -----KTVAIIGGFEQVEIAREAVEMLINGA  165 (194)
T ss_pred             -----cEEEEecChhhhHHHHHHHHHHHcCC
Confidence                 57999999999999999999999764

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

Probab=98.50  E-value=1.1e-06  Score=84.38  Aligned_cols=142  Identities=18%  Similarity=0.223  Sum_probs=98.9

Q ss_pred             eEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccc
Q 007293          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ  353 (609)
Q Consensus       274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~  353 (609)
                      ....+.||.+.++.+||+.|+..+.|.+.+++++.++.     .+..|+|..++...++. ..+.|...+.      .+.
T Consensus         8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~-~~~ka~d~Vk------AIg   75 (194)
T COG1094           8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPL-ALLKARDVVK------AIG   75 (194)
T ss_pred             ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChH-HHHHHHHHHH------HHh
Confidence            35668899999999999999999999999999999983     34678887763222221 1222221111      112


Q ss_pred             cCCCCCC----CCCCceEEEE-E----e------ccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEE
Q 007293          354 QGFSSGE----NKGDAVAVSI-L----V------GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI  418 (609)
Q Consensus       354 ~g~~~g~----~~~~~~t~~l-~----V------P~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V  418 (609)
                      .|+++.-    -.. .....+ .    +      =....|+|||++|.+-+-|++.|||.|.|..            .+|
T Consensus        76 rGF~pe~A~~LL~d-~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tV  142 (194)
T COG1094          76 RGFPPEKALKLLED-DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTV  142 (194)
T ss_pred             cCCCHHHHHHHhcC-CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEE
Confidence            2332200    000 111111 1    1      1236799999999999999999999999963            679


Q ss_pred             EEcCCHHHHHHHHHHHHHHhhh
Q 007293          419 QISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       419 ~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      .|-|.+++|+.|++.|..+++.
T Consensus       143 aiiG~~~~v~iAr~AVemli~G  164 (194)
T COG1094         143 AIIGGFEQVEIAREAVEMLING  164 (194)
T ss_pred             EEecChhhhHHHHHHHHHHHcC
Confidence            9999999999999999998875

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

Probab=98.11  E-value=6.5e-06  Score=74.40  Aligned_cols=67  Identities=19%  Similarity=0.362  Sum_probs=53.1

Q ss_pred             ccccccccCCCchhHHHHHhhCCeEEecCCCcc-----------ccc-CCCCCcEEEEcCCH---HHHHHHHHHHHHHhh
Q 007293          375 DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGC-AAQNDVVIQISGEY---KNVQNALSEVVGRLR  439 (609)
Q Consensus       375 ~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~-----------P~~-~~~~er~V~I~G~~---~~V~~A~~~I~~~Lr  439 (609)
                      +++|.|||++|++||+|+++|||+|.|......           |.+ ...+.-.|.|++..   +++++|+.+|...|.
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            689999999999999999999999999875211           111 12334679999975   899999999999888


Q ss_pred             hc
Q 007293          440 HN  441 (609)
Q Consensus       440 ~~  441 (609)
                      ..
T Consensus        95 ~~   96 (120)
T cd02395          95 PA   96 (120)
T ss_pred             cC
Confidence            43

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=98.00  E-value=1.1e-05  Score=72.98  Aligned_cols=64  Identities=23%  Similarity=0.311  Sum_probs=51.7

Q ss_pred             ceeeeeeecCcchhhhcccccCcEEEecCCC-CC--------------CCCCCceEEEecc---HHHHHHHHHHHHHHHh
Q 007293          138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPPP-AC--------------AAIDDQLIQITGA---TLAVKKALVAVTTCLQ  199 (609)
Q Consensus       138 ~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p-~~--------------~~~~dR~V~I~G~---~e~V~~A~~~I~~~L~  199 (609)
                      +.+|.|||++|++||+|+++|||+|.|..+. ..              .....-.|.|++.   .+++.+|+.+|..++.
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            5789999999999999999999999998750 00              0122357889996   4999999999999997


Q ss_pred             cc
Q 007293          200 HL  201 (609)
Q Consensus       200 e~  201 (609)
                      ..
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.

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

Probab=97.94  E-value=9.8e-06  Score=82.15  Aligned_cols=150  Identities=18%  Similarity=0.254  Sum_probs=105.2

Q ss_pred             cceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHh---hhh
Q 007293          272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV  348 (609)
Q Consensus       272 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~---~i~  348 (609)
                      +.++..+.||..+++.|.|++|.+||.|+.+|...|+-+..   ..+-++.++|..      .-+..|...+..   .+.
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~------edv~~aRrei~saaeH~~   94 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH------EDVRRARREIPSAAEHFG   94 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc------hhHHHHhhcCccccceee
Confidence            56677888999999999999999999999999999876632   223578888873      112222211111   110


Q ss_pred             hcccccCCC---CCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHH
Q 007293          349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK  425 (609)
Q Consensus       349 e~~~~~g~~---~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~  425 (609)
                      --...+.+.   .+.....+.+..+.+|...+|.|.|..|.+|+.||+.+...|.-+-+        ..+.++-++|.+.
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   12223567888999999999999999999999999999999987653        3478899999999


Q ss_pred             H-HHHHH-HHHHHHh
Q 007293          426 N-VQNAL-SEVVGRL  438 (609)
Q Consensus       426 ~-V~~A~-~~I~~~L  438 (609)
                      + +++|. ..|+..+
T Consensus       167 nC~kra~s~eie~ta  181 (394)
T KOG2113|consen  167 NCVKRARSCEIEQTA  181 (394)
T ss_pred             chhhhccccchhhhh
Confidence            8 77776 5555443

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.81  E-value=2.9e-05  Score=72.17  Aligned_cols=103  Identities=14%  Similarity=0.158  Sum_probs=69.0

Q ss_pred             EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHH
Q 007293           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (609)
Q Consensus        26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al  105 (609)
                      .+.++|+...+|+.||++|++|+.|++..|-+|+|-....           .                       +.+-+
T Consensus        33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~-----------d-----------------------~~~fI   78 (140)
T PRK08406         33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD-----------D-----------------------PEEFI   78 (140)
T ss_pred             EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC-----------C-----------------------HHHHH
Confidence            4567889999999999999999999999998888743211           1                       11111


Q ss_pred             HHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEec
Q 007293          106 IRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (609)
Q Consensus       106 ~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~  165 (609)
                      ..++....-.....   ........+.+.|+....|..|||+|++|+.++.-+|-++.|.
T Consensus        79 ~n~l~Pa~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~  135 (140)
T PRK08406         79 KNIFAPAAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID  135 (140)
T ss_pred             HHHcCCCEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence            11111100000000   0011235667789999999999999999999999998877663

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.67  E-value=0.00016  Score=82.93  Aligned_cols=93  Identities=13%  Similarity=0.195  Sum_probs=72.1

Q ss_pred             ChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCC
Q 007293          334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ  413 (609)
Q Consensus       334 ~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~  413 (609)
                      ..+.++...|++.+.+.....   ...........++.||.+++|.|||+||.+||+|+++|||+|.|.+          
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            345566677777665542222   1122345678899999999999999999999999999999999954          


Q ss_pred             CCcEEEEcCC-HHHHHHHHHHHHHHhhh
Q 007293          414 NDVVIQISGE-YKNVQNALSEVVGRLRH  440 (609)
Q Consensus       414 ~er~V~I~G~-~~~V~~A~~~I~~~Lr~  440 (609)
                       +..|.|.+. .+++++|+.+|...++.
T Consensus       616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       616 -DGTVYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence             577888884 78999999999998885

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=97.48  E-value=0.00029  Score=80.85  Aligned_cols=94  Identities=18%  Similarity=0.232  Sum_probs=72.5

Q ss_pred             cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCce
Q 007293           98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL  177 (609)
Q Consensus        98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~  177 (609)
                      +..|.++..+++..+.+..... .......+....+-||.+.++.|||+||++||+|.++|||+|.|..        +..
T Consensus       548 L~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~  618 (719)
T TIGR02696       548 LKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGT  618 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcE
Confidence            3456666667766555443333 2222333667788899999999999999999999999999999954        477


Q ss_pred             EEEecc-HHHHHHHHHHHHHHHhc
Q 007293          178 IQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       178 V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      |.|.+. .+++.+|+.+|..++..
T Consensus       619 V~I~a~d~~~~~~A~~~I~~i~~~  642 (719)
T TIGR02696       619 VYIGAADGPSAEAARAMINAIANP  642 (719)
T ss_pred             EEEEeCCHHHHHHHHHHHHHhhCc
Confidence            888885 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.

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

Probab=97.43  E-value=0.00035  Score=71.14  Aligned_cols=155  Identities=19%  Similarity=0.197  Sum_probs=107.8

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      +.++..+-||..+++.|.|++|-+||.|+.+|.+.|+-+-..   .|=+..++|..+.+++|..++.-.         | 
T Consensus        24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~sa---------a-   90 (394)
T KOG2113|consen   24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPSA---------A-   90 (394)
T ss_pred             CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCccc---------c-
Confidence            888999999999999999999999999999999999864321   235777899998887765544221         1 


Q ss_pred             HHHHHHHHHHhhhhhccCC-CCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEe
Q 007293          103 EAVIRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT  181 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~~-~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~  181 (609)
                      +   ++-..+.......+- ........+...-+|-..+|++.|..|.+|+.|++.++..|.-.-.  |   .+.+..++
T Consensus        91 e---H~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~--~---~~~Vf~Vt  162 (394)
T KOG2113|consen   91 E---HFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--C---GEPVFCVT  162 (394)
T ss_pred             c---eeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--C---CCceEEEe
Confidence            0   000000000000000 0112345667777899999999999999999999999999887652  3   66788899


Q ss_pred             ccHHH-HHHHH-HHHHHHH
Q 007293          182 GATLA-VKKAL-VAVTTCL  198 (609)
Q Consensus       182 G~~e~-V~~A~-~~I~~~L  198 (609)
                      |-+.+ +++|- ..|..-+
T Consensus       163 g~~~nC~kra~s~eie~ta  181 (394)
T KOG2113|consen  163 GAPKNCVKRARSCEIEQTA  181 (394)
T ss_pred             cCCcchhhhccccchhhhh
Confidence            98877 55555 4444433

>PRK08406 transcription elongation factor NusA-like protein; Validated

Probab=97.41  E-value=0.00044  Score=64.31  Aligned_cols=102  Identities=16%  Similarity=0.163  Sum_probs=71.2

Q ss_pred             eEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhh--hhcc
Q 007293          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVE  351 (609)
Q Consensus       274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i--~e~~  351 (609)
                      ..+.++|+...+|..||++|++|+.|++..|-+|.+-....+                    ..+-+..++...  .+..
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                    111121111111  0000


Q ss_pred             cccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293          352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (609)
Q Consensus       352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~  402 (609)
                      ..       .........+.|+.+..|..|||+|++|+.++.-+|-++.|.
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       012235677889999999999999999999999999998774

>TIGR01952 nusA_arch NusA family KH domain protein, archaeal

Probab=97.25  E-value=0.00047  Score=64.05  Aligned_cols=102  Identities=14%  Similarity=0.159  Sum_probs=68.0

Q ss_pred             EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcch-hhhhhhccccccccCCCcchHHHH
Q 007293           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEA  104 (609)
Q Consensus        26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~-~~~~~~~~~~~~~e~~~~~~A~~A  104 (609)
                      -+-++|....+|..||++|++|+.|++..|-+|+|-..           +.+.+. +.+             .++||.  
T Consensus        34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~~fI~N-------------~l~PA~--   87 (141)
T TIGR01952        34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLEEFVAN-------------KLAPAE--   87 (141)
T ss_pred             EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHHHHHHH-------------cCCCce--
Confidence            44567888899999999999999999888988887432           111111 000             011110  


Q ss_pred             HHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEec
Q 007293          105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (609)
Q Consensus       105 l~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~  165 (609)
                             +.....     ...++...+.+.|+..+.+..|||+|.+|+..++-+|-++.|.
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     0011245677889999999999999999999999988877663

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=97.13  E-value=0.0011  Score=77.03  Aligned_cols=92  Identities=14%  Similarity=0.228  Sum_probs=66.2

Q ss_pred             HHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCC
Q 007293          336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND  415 (609)
Q Consensus       336 a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~e  415 (609)
                      +.++...|++.+.+........  .........++.||.++++.|||+||++||+|+++|||+|.|.+           +
T Consensus       523 a~~~~~~I~~~m~~~l~~~~~~--~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------d  589 (684)
T TIGR03591       523 AKEGRLHILGEMNKVISEPRAE--LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------D  589 (684)
T ss_pred             HHHHHHHHHHHHHHHHhhhhcc--ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------C
Confidence            4455555665554432111110  12234578899999999999999999999999999999999954           4


Q ss_pred             cEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293          416 VVIQISG-EYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       416 r~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (609)
                      -.|.|.+ ..+.+++|+++|.....+
T Consensus       590 G~V~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       590 GTVKIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence            5577766 467899999999987654

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=97.11  E-value=0.0016  Score=70.41  Aligned_cols=73  Identities=19%  Similarity=0.259  Sum_probs=58.6

Q ss_pred             ceEEEEEeec------ceeeeeeecCcchhhhcccccCcEEEecCC----C--------C--CCCCCCceEEEecc-HHH
Q 007293          128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP----P--------A--CAAIDDQLIQITGA-TLA  186 (609)
Q Consensus       128 ~vt~rllVP~------~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~----p--------~--~~~~~dR~V~I~G~-~e~  186 (609)
                      .++.++.||-      +.||+|||..|.|.|+|+++|||||.|..+    +        .  .....+=.|.|+++ .++
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            6777888886      579999999999999999999999999873    0        0  11123345778886 899


Q ss_pred             HHHHHHHHHHHHhc
Q 007293          187 VKKALVAVTTCLQH  200 (609)
Q Consensus       187 V~~A~~~I~~~L~e  200 (609)
                      |.+|+..|..+|.+
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=97.05  E-value=0.00097  Score=77.49  Aligned_cols=94  Identities=21%  Similarity=0.262  Sum_probs=68.8

Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V  178 (609)
                      ..|.++..+++..+.+...+.......-.+....+-||.+.++.|||+||++||+|+++|||+|.|..        +..|
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            34555555666554443333222222333667788999999999999999999999999999999954        4567


Q ss_pred             EEec-cHHHHHHHHHHHHHHHhc
Q 007293          179 QITG-ATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       179 ~I~G-~~e~V~~A~~~I~~~L~e  200 (609)
                      .|.+ ..+.+.+|+.+|..+..+
T Consensus       593 ~i~~~~~~~~~~a~~~I~~~~~~  615 (684)
T TIGR03591       593 KIAASDGEAAEAAIKMIEGITAE  615 (684)
T ss_pred             EEEECcHHHHHHHHHHHHhhhcc
Confidence            7776 589999999999888653

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=96.93  E-value=0.0025  Score=59.28  Aligned_cols=101  Identities=14%  Similarity=0.124  Sum_probs=69.9

Q ss_pred             EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHH--hhhhhccc
Q 007293          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG  352 (609)
Q Consensus       275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~--~~i~e~~~  352 (609)
                      .+-++|....+|..||++|.+|+.|++..|-+|.+-....+..                    +-+..++  .++.....
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            5667889999999999999999999988888887754211100                    0111100  01110000


Q ss_pred             ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEec
Q 007293          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV  402 (609)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~  402 (609)
                      .       ..++.....+.||.+..+..|||+|++|+...+-+|-++.|.
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       012335788999999999999999999999999999998774

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

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

Probab=96.77  E-value=0.007  Score=65.50  Aligned_cols=77  Identities=17%  Similarity=0.326  Sum_probs=58.6

Q ss_pred             ceEEEEEecc------ccccccccCCCchhHHHHHhhCCeEEecCCC---------ccccc--CCCCCcEEEEcCC-HHH
Q 007293          365 AVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE---------QVLGC--AAQNDVVIQISGE-YKN  426 (609)
Q Consensus       365 ~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~---------~~P~~--~~~~er~V~I~G~-~~~  426 (609)
                      ..+.+|.||-      +++|.|||..|.|.|+|+++|||+|.|-.+.         +.+.+  ..+++--+.|+.+ .|.
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            5677888875      6899999999999999999999999997621         10111  1334455777776 568


Q ss_pred             HHHHHHHHHHHhhhc
Q 007293          427 VQNALSEVVGRLRHN  441 (609)
Q Consensus       427 V~~A~~~I~~~Lr~~  441 (609)
                      |++|..+|..+|.+.
T Consensus       217 i~~Ai~vienli~~a  231 (554)
T KOG0119|consen  217 IKKAIAVIENLIQSA  231 (554)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999988863

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=96.66  E-value=0.0033  Score=61.35  Aligned_cols=102  Identities=19%  Similarity=0.247  Sum_probs=67.4

Q ss_pred             EEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHH
Q 007293           27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVI  106 (609)
Q Consensus        27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~  106 (609)
                      +-..+-.+.+|..||++|++|+.|.++.|-+|+|-...++           +..                   -..+|+.
T Consensus        78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~  127 (190)
T COG0195          78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALA  127 (190)
T ss_pred             EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcC
Confidence            3344455778999999999999999999977776332111           110                   0111111


Q ss_pred             HHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293          107 RVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (609)
Q Consensus       107 ~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~  166 (609)
                      -  .++......     ..+.. .+.+.||..+.+..|||+|.+++.+.+-||-++.|..
T Consensus       128 P--a~v~~V~~~-----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         128 P--AEVLSVNIK-----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             c--ceEeEEEEE-----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            0  000000000     00112 7788999999999999999999999999999999965

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

Probab=96.62  E-value=0.0023  Score=64.47  Aligned_cols=43  Identities=19%  Similarity=0.434  Sum_probs=37.9

Q ss_pred             CCCCCcEEEEEEecCC------cccceecCCChHHHHHHHHhCceEEEc
Q 007293           19 NLPDDVVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE   61 (609)
Q Consensus        19 ~~~~~~v~~RilvP~~------~vG~IIGk~G~~Ik~IreeTga~I~V~   61 (609)
                      ...+-.++.||+||.+      +||+|+|.+|.++|+|+++|+|+|-|.
T Consensus        86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir  134 (259)
T KOG1588|consen   86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR  134 (259)
T ss_pred             cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence            3445567889999997      799999999999999999999999984

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.54  E-value=0.0045  Score=72.85  Aligned_cols=93  Identities=14%  Similarity=0.178  Sum_probs=68.1

Q ss_pred             hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCe-EEecCCCcccccCCC
Q 007293          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQ  413 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~I~~~~~~P~~~~~  413 (609)
                      .+.++...|++.+.+..... .. ...........+.||.++++.|||.||.+||+|.++||+. |.+.+          
T Consensus       656 ~A~~g~~~Il~~M~~~i~~p-r~-~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------  723 (891)
T PLN00207        656 QAKDGRKHILAEMSKCSPPP-SK-RLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------  723 (891)
T ss_pred             HHHHHHHHHHHHHHHHHhhh-hh-hhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------
Confidence            34455566666665432111 00 1123456788999999999999999999999999999999 87743          


Q ss_pred             CCcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293          414 NDVVIQISG-EYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       414 ~er~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (609)
                       +-.|.|.+ +.+.+++|+.+|.....+
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             56688888 577899999999988764

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

Probab=96.47  E-value=0.0063  Score=68.78  Aligned_cols=98  Identities=13%  Similarity=0.159  Sum_probs=72.6

Q ss_pred             ChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCC
Q 007293          334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ  413 (609)
Q Consensus       334 ~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~  413 (609)
                      .++..|.++|+..+.+....+ . ........-..++.|+.+.++-+||++|.+||+|.++|||+|.|..          
T Consensus       522 ~QAk~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied----------  589 (692)
T COG1185         522 EQAKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED----------  589 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC----------
Confidence            344566666766665431110 0 0011234467888999999999999999999999999999999952          


Q ss_pred             CCcEEEEcCCH-HHHHHHHHHHHHHhhhcccC
Q 007293          414 NDVVIQISGEY-KNVQNALSEVVGRLRHNLKS  444 (609)
Q Consensus       414 ~er~V~I~G~~-~~V~~A~~~I~~~Lr~~~~~  444 (609)
                       +-+|.|.++. +.+++|+..|.++.++.-+.
T Consensus       590 -dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg  620 (692)
T COG1185         590 -DGTVKIAASDGESAKKAKERIEAITREVEVG  620 (692)
T ss_pred             -CCcEEEEecchHHHHHHHHHHHHHHhhcccc
Confidence             4668999987 68999999999999876544

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.46  E-value=0.0032  Score=74.02  Aligned_cols=95  Identities=14%  Similarity=0.199  Sum_probs=71.6

Q ss_pred             cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcE-EEecCCCCCCCCCCc
Q 007293           98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQ  176 (609)
Q Consensus        98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~-I~I~~~p~~~~~~dR  176 (609)
                      +..|.++...++..+.+.....-.......+....+-||.+.++.|||.||.+||.|.++||++ |.+..        +-
T Consensus       654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg  725 (891)
T PLN00207        654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DG  725 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Ce
Confidence            3456666777766655443322111222336678889999999999999999999999999999 88844        46


Q ss_pred             eEEEecc-HHHHHHHHHHHHHHHhc
Q 007293          177 LIQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       177 ~V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      .|.|.+. .+++.+|+.+|..++.+
T Consensus       726 ~V~I~a~d~~~i~~A~~~I~~l~~~  750 (891)
T PLN00207        726 TVKITAKDLSSLEKSKAIISSLTMV  750 (891)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence            7888884 99999999999999864

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

Probab=96.31  E-value=0.0094  Score=67.44  Aligned_cols=95  Identities=20%  Similarity=0.240  Sum_probs=70.9

Q ss_pred             cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCce
Q 007293           98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL  177 (609)
Q Consensus        98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~  177 (609)
                      +..|..|-++++..+.+...........-.+-...+-|+...+.-+||++|++|++|.++|||+|.|..        +..
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            455666666776665544322211111222445667889999999999999999999999999999953        467


Q ss_pred             EEEecc-HHHHHHHHHHHHHHHhc
Q 007293          178 IQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       178 V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      |.|.++ .+.+.+|+..|..+.++
T Consensus       593 v~i~~s~~~~~~~ak~~I~~i~~e  616 (692)
T COG1185         593 VKIAASDGESAKKAKERIEAITRE  616 (692)
T ss_pred             EEEEecchHHHHHHHHHHHHHHhh
Confidence            889887 69999999999999976

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

Probab=96.28  E-value=0.0041  Score=66.11  Aligned_cols=68  Identities=18%  Similarity=0.288  Sum_probs=56.2

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr  439 (609)
                      .....-|.|-+++||.+||++|+.|+.||..|.++|+|...        ..+..|+|.|...--.+|+..|..-++
T Consensus        45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~  112 (629)
T KOG0336|consen   45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD  112 (629)
T ss_pred             CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence            34566677889999999999999999999999999999874        347889999998877777777755433

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

Probab=96.21  E-value=0.0071  Score=48.00  Aligned_cols=37  Identities=22%  Similarity=0.261  Sum_probs=34.5

Q ss_pred             cEEEEEEecCCcccceecCCChHHHHHHHHhCceEEE
Q 007293           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC   60 (609)
Q Consensus        24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V   60 (609)
                      ...+.+.|+.+..|.+|||+|.+|+.+++.++.+|.|
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.

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

Probab=96.09  E-value=0.03  Score=56.63  Aligned_cols=81  Identities=20%  Similarity=0.295  Sum_probs=56.4

Q ss_pred             CCceEEEEEecc------ccccccccCCCchhHHHHHhhCCeEEecCCCc------------ccccC---CCCCcEEEEc
Q 007293          363 GDAVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ------------VLGCA---AQNDVVIQIS  421 (609)
Q Consensus       363 ~~~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~------------~P~~~---~~~er~V~I~  421 (609)
                      ....+.+|+||-      ++||+|+|..|.++|+++++|||+|-|-.+.-            .|.|.   ..-.-+|+..
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            456788899886      49999999999999999999999999976533            13322   1223567788


Q ss_pred             CCHHHHHHHHHHHHHHhhhccc
Q 007293          422 GEYKNVQNALSEVVGRLRHNLK  443 (609)
Q Consensus       422 G~~~~V~~A~~~I~~~Lr~~~~  443 (609)
                      .++..+..=+..-.+.|+++|+
T Consensus       169 ~p~~ea~~rl~~AleeI~klL~  190 (259)
T KOG1588|consen  169 APPAEAYARLAYALEEIKKLLV  190 (259)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcC
Confidence            8877666533344444454443

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

Probab=96.04  E-value=0.0067  Score=64.51  Aligned_cols=72  Identities=18%  Similarity=0.284  Sum_probs=58.7

Q ss_pred             CCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          124 DGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       124 ~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+.....+-+-+-+++||.+||++|++|++||..|+++|+|.+.     ..+-.|+|-|...--.+|...|-..+..
T Consensus        42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~-----~~e~kv~ifg~~~m~~kaka~id~~~~k  113 (629)
T KOG0336|consen   42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC-----DLEVKVTIFGINHMRKKAKASIDRGQDK  113 (629)
T ss_pred             cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc-----CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence            34556777888999999999999999999999999999999872     3567789999877777777666655543

>TIGR01953 NusA transcription termination factor NusA

Probab=96.02  E-value=0.011  Score=63.04  Aligned_cols=95  Identities=21%  Similarity=0.296  Sum_probs=63.7

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|+.|+.|.++. |-+|+|-....+..+   .|.       ++             ++||.         +
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~---fi~-------na-------------l~Pa~---------v  290 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE---FIA-------NA-------------LSPAK---------V  290 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------cCCce---------E
Confidence            458999999999999999998 778877432111100   000       00             11110         0


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~  166 (609)
                      .......      .....+.+.||..+.+..|||+|.+++....-||.+|.|..
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      01246889999999999999999999999999999999965

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.

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

Probab=96.00  E-value=0.009  Score=61.92  Aligned_cols=71  Identities=24%  Similarity=0.312  Sum_probs=60.3

Q ss_pred             ceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      .....+.|++.+.|.|||++|.+-++|+++|+++|.++++.+      ..+.++.+-++-++|..|.+.|...|-+.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            356788999999999999999999999999999999987432      55677777778899999999998877654

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.90  E-value=0.013  Score=62.83  Aligned_cols=96  Identities=19%  Similarity=0.274  Sum_probs=64.5

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|+.|+.|.++. |-+|+|-....+..+   .|.       ++             ++||.     +.   
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---fi~-------na-------------l~Pa~-----v~---  293 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---FVA-------NA-------------LSPAK-----VV---  293 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------CCCce-----EE---
Confidence            468999999999999999998 778887432211100   000       00             11110     00   


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                       .....     + .....+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus       294 -~v~i~-----~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        294 -SVEVD-----D-EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             -EEEEE-----c-CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence             00000     0 113468899999999999999999999999999999999774

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.87  E-value=0.011  Score=64.31  Aligned_cols=95  Identities=24%  Similarity=0.271  Sum_probs=63.4

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|+.|+.|.++. |-+|+|-....+..   ..|.       ++             +++|     ++.   
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~---~fI~-------Na-------------LsPA-----~V~---  325 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA---TYIA-------NA-------------LSPA-----RVD---  325 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HHHH-------Hh-------------cCCc-----eee---
Confidence            468999999999999999999 77887743221100   0000       00             1111     000   


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~  166 (609)
                       ......      .....+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus       326 -~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        326 -EVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             -EEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence             000000      11245789999999999999999999999999999999966

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

Probab=95.85  E-value=0.0073  Score=62.61  Aligned_cols=71  Identities=18%  Similarity=0.266  Sum_probs=58.6

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ....-++|+....|+|||++|.|-++|+++|+++|.+...   ....+.++.+.+..++|.+|...|...|.+.
T Consensus        56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p---~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~  126 (345)
T KOG2814|consen   56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP---NTNKEEIKIIGISRNCVIQALERIAKLIDSD  126 (345)
T ss_pred             cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC---CCCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence            3455689999999999999999999999999999999762   1234455555557999999999999999774

>COG0195 NusA Transcription elongation factor [Transcription]

Probab=95.84  E-value=0.0057  Score=59.67  Aligned_cols=101  Identities=21%  Similarity=0.258  Sum_probs=69.0

Q ss_pred             EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHh--hhhhccc
Q 007293          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEG  352 (609)
Q Consensus       275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~--~i~e~~~  352 (609)
                      .+-..+-.+.+|..||++|.+|+.|.++.|-+|.|-.-.             +      .++ +-+..++.  ++....+
T Consensus        77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~------d~~-~fI~nal~Pa~v~~V~~  136 (190)
T COG0195          77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------E------DPA-EFIKNALAPAEVLSVNI  136 (190)
T ss_pred             eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------C------CHH-HHHHHhcCcceEeEEEE
Confidence            344556678889999999999999999999666554321             1      111 11111111  1111000


Q ss_pred             ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (609)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~  403 (609)
                      .        ......+.+.||.+..+..|||+|.+++.+.+-||-+|.|..
T Consensus       137 ~--------~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~  179 (190)
T COG0195         137 K--------EDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET  179 (190)
T ss_pred             E--------eCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence            0        001127888999999999999999999999999999999975

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.80  E-value=0.013  Score=62.63  Aligned_cols=95  Identities=16%  Similarity=0.255  Sum_probs=64.2

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+..+   .|.       ++             ++||.  +..+    
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---fI~-------Na-------------l~Pa~--V~~V----  301 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---FIA-------RA-------------LAPAI--ISSV----  301 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---HHH-------Hh-------------CCCce--eeEE----
Confidence            458999999999999999998 778877432111100   000       00             11110  0000    


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                         .  .+     ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..-
T Consensus       302 ---~--i~-----~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~  346 (374)
T PRK12328        302 ---K--IE-----EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI  346 (374)
T ss_pred             ---E--Ec-----CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence               0  00     113467889999999999999999999999999999999874

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.60  E-value=0.019  Score=67.11  Aligned_cols=93  Identities=14%  Similarity=0.217  Sum_probs=66.3

Q ss_pred             hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCC
Q 007293          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~  414 (609)
                      .+.++...|++.+.+..... .. ...........+.||.+.++.+||.||.+||+|.++||+.|.+.+           
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-ELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-----------  591 (693)
T ss_pred             HHHHHHHHHHHHHHHHhcCC-hh-hhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----------
Confidence            34556666777665432111 00 011223456777889999999999999999999999999887632           


Q ss_pred             CcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293          415 DVVIQISG-EYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       415 er~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (609)
                      +-.|.|.+ ..+.+++|+++|.....+
T Consensus       592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        592 DGTVKIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             CceEEEEcccHHHHHHHHHHHHHhccc
Confidence            46688888 577899999999987754

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

Probab=95.58  E-value=0.016  Score=46.01  Aligned_cols=36  Identities=22%  Similarity=0.372  Sum_probs=34.0

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEe
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL  401 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I  401 (609)
                      ....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus        25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v   60 (61)
T cd02134          25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI   60 (61)
T ss_pred             cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence            688999999999999999999999999999998876

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.

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

Probab=95.57  E-value=0.033  Score=54.07  Aligned_cols=43  Identities=26%  Similarity=0.425  Sum_probs=36.1

Q ss_pred             CCCcEEEEEEecC------CcccceecCCChHHHHHHHHhCceEEEcCC
Q 007293           21 PDDVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG   63 (609)
Q Consensus        21 ~~~~v~~RilvP~------~~vG~IIGk~G~~Ik~IreeTga~I~V~~~   63 (609)
                      -+-.+.-+++||.      ++||.|||.+|+|.|+|++.|+|+|-|.-.
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            3445666788886      489999999999999999999999999643

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.43  E-value=0.013  Score=68.36  Aligned_cols=94  Identities=20%  Similarity=0.245  Sum_probs=67.3

Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V  178 (609)
                      ..|.++..+|++.+.+.....-.+.....+....+-|+.+.++.+||.||.+||+|.++||++|.+..        +-.|
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            35556666676665544322211111222444566679999999999999999999999999888733        4678


Q ss_pred             EEecc-HHHHHHHHHHHHHHHhc
Q 007293          179 QITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      .|.+. .+.+.+|+.+|..+..+
T Consensus       596 ~i~~~~~~~~~~a~~~I~~~~~~  618 (693)
T PRK11824        596 KIAATDGEAAEAAKERIEGITAE  618 (693)
T ss_pred             EEEcccHHHHHHHHHHHHHhccc
Confidence            88884 89999999999888854

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.36  E-value=0.03  Score=56.76  Aligned_cols=64  Identities=19%  Similarity=0.180  Sum_probs=54.6

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHhhhc
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHN  441 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~-~V~~A~~~I~~~Lr~~  441 (609)
                      -..+.||.++++.+||++|.+|+.|.+.+++.|.|-.           +-.|-|+++.. .+..|+.+|...-++.
T Consensus       146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            4678899999999999999999999999999998843           46688888855 8899999998766654

>PRK00468 hypothetical protein; Provisional

Probab=95.15  E-value=0.022  Score=47.14  Aligned_cols=35  Identities=29%  Similarity=0.442  Sum_probs=30.7

Q ss_pred             CCCcEEEEEEecCCcccceecCCChHHHHHHHHhC
Q 007293           21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK   55 (609)
Q Consensus        21 ~~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTg   55 (609)
                      .++.+.+++-|....+|.||||+|.+|+.||.--.
T Consensus        26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~   60 (75)
T PRK00468         26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK   60 (75)
T ss_pred             CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence            44668999999999999999999999999987643

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.01  E-value=0.032  Score=62.01  Aligned_cols=95  Identities=21%  Similarity=0.277  Sum_probs=63.3

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|+.|+.|.++. |-+|.|-...++-   ...|.       ++             +++|     .+    
T Consensus       245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~---~~fi~-------na-------------l~pa-----~v----  292 (470)
T PRK09202        245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDP---AQFII-------NA-------------LSPA-----EV----  292 (470)
T ss_pred             ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH---HHHHH-------Hh-------------CCCC-----EE----
Confidence            358999999999999999998 7788774321110   00000       00             1111     00    


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                      .....  +.     ..-.+.+.||..+.+..|||+|.+|+..++-||.+|.|...
T Consensus       293 ~~v~~--~~-----~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~  340 (470)
T PRK09202        293 SSVVV--DE-----DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE  340 (470)
T ss_pred             EEEEE--eC-----CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence            00000  00     02367899999999999999999999999999999999763

>TIGR01953 NusA transcription termination factor NusA

Probab=94.83  E-value=0.021  Score=60.84  Aligned_cols=95  Identities=19%  Similarity=0.289  Sum_probs=63.2

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~  361 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-....+..+-+  .       ...+|+         ++......       .
T Consensus       243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi--~-------nal~Pa---------~v~~v~i~-------~  297 (341)
T TIGR01953       243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFI--A-------NALSPA---------KVISVEVL-------D  297 (341)
T ss_pred             CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhcCCc---------eEEEEEEE-------c
Confidence            457999999999999999887 76776653221110000  0       000111         11000000       0


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~  403 (609)
                       .......+.||.++.+..|||+|.+++...+-||.+|.|.+
T Consensus       298 -~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s  338 (341)
T TIGR01953       298 -EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT  338 (341)
T ss_pred             -CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence             12247899999999999999999999999999999999976

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.

>PRK02821 hypothetical protein; Provisional

Probab=94.53  E-value=0.037  Score=46.01  Aligned_cols=35  Identities=17%  Similarity=0.288  Sum_probs=30.8

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC   56 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga   56 (609)
                      ++.+.+.|-|....+|.||||+|.+|+.||.--.+
T Consensus        28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            45588999999999999999999999999987544

>PRK12704 phosphodiesterase; Provisional

Probab=94.25  E-value=0.11  Score=58.57  Aligned_cols=67  Identities=13%  Similarity=0.229  Sum_probs=51.3

Q ss_pred             CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..+...|.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+          +...|.|+| .|-.-+.|...+...+.+
T Consensus       208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~d  276 (520)
T PRK12704        208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQD  276 (520)
T ss_pred             hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence            34566778888 89999999999999999999999999953          346688888 555545666555554443

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=94.23  E-value=0.03  Score=59.97  Aligned_cols=97  Identities=12%  Similarity=0.079  Sum_probs=65.3

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~  361 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-.++..+-+  .       +..+|+         ++.....        .
T Consensus       251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~fI--~-------Nal~Pa---------~V~~V~i--------~  304 (374)
T PRK12328        251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIFI--A-------RALAPA---------IISSVKI--------E  304 (374)
T ss_pred             ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eeeEEEE--------c
Confidence            457999999999999998887 77776653221110000  0       000111         1100000        0


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~  406 (609)
                       .......+.||.++.+..|||+|.+++.-.+-||.+|.|.+-+.
T Consensus       305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~  348 (374)
T PRK12328        305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS  348 (374)
T ss_pred             -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence             12247889999999999999999999999999999999988655

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.17  E-value=0.098  Score=56.24  Aligned_cols=96  Identities=19%  Similarity=0.210  Sum_probs=64.0

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~  361 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-...++..+-+  .       +..+|+         ++.....        .
T Consensus       245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi--~-------nal~Pa---------~v~~v~i--------~  298 (362)
T PRK12327        245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFV--A-------NALSPA---------KVVSVEV--------D  298 (362)
T ss_pred             CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eEEEEEE--------E
Confidence            457999999999999998888 77776653221110000  0       000111         1100000        0


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~  404 (609)
                      ........+.||.++.+.-|||+|.+++.-.+-||.+|.|.+.
T Consensus       299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~  341 (362)
T PRK12327        299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE  341 (362)
T ss_pred             cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence            0123478899999999999999999999999999999999764

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.96  E-value=0.14  Score=57.79  Aligned_cols=66  Identities=14%  Similarity=0.241  Sum_probs=50.4

Q ss_pred             CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhh
Q 007293          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLR  439 (609)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr  439 (609)
                      ..+...|.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+          +...|+|+| .|---+.|...|...+.
T Consensus       202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li~  269 (514)
T TIGR03319       202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLIQ  269 (514)
T ss_pred             hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence            44667788888 89999999999999999999999999953          345677888 55555555555544443

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.91  E-value=0.12  Score=56.38  Aligned_cols=95  Identities=21%  Similarity=0.232  Sum_probs=62.6

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~  361 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-.++..+-+  .       +.++|+         ++......       .
T Consensus       277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~~fI--~-------NaLsPA---------~V~~V~i~-------~  331 (449)
T PRK12329        277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPATYI--A-------NALSPA---------RVDEVRLV-------D  331 (449)
T ss_pred             ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhcCCc---------eeeEEEEE-------c
Confidence            457999999999999999888 76776653211110000  0       000111         11110000       0


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~  403 (609)
                       .......+.||.++.+.-|||+|.+++.-.+-||.+|.|.+
T Consensus       332 -~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s  372 (449)
T PRK12329        332 -PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD  372 (449)
T ss_pred             -CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence             12246789999999999999999999999999999999865

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

Probab=93.78  E-value=0.063  Score=44.42  Aligned_cols=32  Identities=25%  Similarity=0.443  Sum_probs=29.1

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e  157 (609)
                      +..+.++|-+....+|.||||+|.+|+.||.-
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl   58 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL   58 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence            55788999999999999999999999999854

>PRK01064 hypothetical protein; Provisional

Probab=93.78  E-value=0.071  Score=44.46  Aligned_cols=34  Identities=26%  Similarity=0.527  Sum_probs=30.6

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhC
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK   55 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTg   55 (609)
                      ++.+.+++-|.....|.+|||+|.+|+.||.-..
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            5678999999999999999999999999998643

>PRK00468 hypothetical protein; Provisional

Probab=93.74  E-value=0.067  Score=44.30  Aligned_cols=33  Identities=15%  Similarity=0.275  Sum_probs=29.0

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhh
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT  395 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T  395 (609)
                      +..+..++.|.++-+|+||||+|.+|+.|+.--
T Consensus        27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv   59 (75)
T PRK00468         27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV   59 (75)
T ss_pred             CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence            355788999999999999999999999998654

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

Probab=93.67  E-value=0.078  Score=43.87  Aligned_cols=33  Identities=27%  Similarity=0.458  Sum_probs=29.8

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHh
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT   54 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeT   54 (609)
                      +..+.++|-+.....|.||||+|.+|+.||---
T Consensus        27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll   59 (76)
T COG1837          27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL   59 (76)
T ss_pred             CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence            567889999999999999999999999998753

>PRK00106 hypothetical protein; Provisional

Probab=93.62  E-value=0.18  Score=56.94  Aligned_cols=66  Identities=15%  Similarity=0.283  Sum_probs=50.7

Q ss_pred             CceEEEEEecc-ccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhh
Q 007293          364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLR  439 (609)
Q Consensus       364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr  439 (609)
                      ..+...|.+|+ ++-|+|||+.|.+|+-+...||+.+.|.+          +...|+|+| .|---+.|...+...+.
T Consensus       223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li~  290 (535)
T PRK00106        223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLIK  290 (535)
T ss_pred             hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence            44667788898 89999999999999999999999999953          346688888 56555555555544443

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.52  E-value=1.3  Score=43.82  Aligned_cols=86  Identities=19%  Similarity=0.317  Sum_probs=65.1

Q ss_pred             HHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc
Q 007293          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA  183 (609)
Q Consensus       104 Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~  183 (609)
                      .+.+|+..+........-    +..-.+.+.++....-+|+..+|..++.|....||+|.+..       .+..|.|+|+
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            455666666655433211    11223444456888899999999999999888999999977       5678999999


Q ss_pred             HHHHHHHHHHHHHHHhc
Q 007293          184 TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       184 ~e~V~~A~~~I~~~L~e  200 (609)
                      ...+..+...|.+++..
T Consensus        74 k~~~~~i~~~i~~~l~~   90 (210)
T PF14611_consen   74 KSTAEYIEASINEILSN   90 (210)
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999999965

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=93.39  E-value=0.12  Score=52.43  Aligned_cols=63  Identities=21%  Similarity=0.260  Sum_probs=53.3

Q ss_pred             EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhcc
Q 007293          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e~  201 (609)
                      +.+-||...++.+||++|.+|+.|.++++++|.|-.        +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus       147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~  210 (235)
T PRK04163        147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA  210 (235)
T ss_pred             EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence            347789999999999999999999999999999944        356889887 668888888888777653

>PRK02821 hypothetical protein; Provisional

Probab=93.35  E-value=0.079  Score=44.06  Aligned_cols=34  Identities=18%  Similarity=0.336  Sum_probs=29.6

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCC
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGT  397 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa  397 (609)
                      ..+..++.|.++-+|+||||+|.+|+.|+.--.|
T Consensus        29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a   62 (77)
T PRK02821         29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA   62 (77)
T ss_pred             CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence            4478999999999999999999999999876544

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

Probab=93.30  E-value=0.29  Score=47.71  Aligned_cols=42  Identities=24%  Similarity=0.460  Sum_probs=35.3

Q ss_pred             CCceEEEEEec------cccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293          363 GDAVAVSILVG------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (609)
Q Consensus       363 ~~~~t~~l~VP------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~  404 (609)
                      +...+-++.||      .++||.|||..|.+.|++++.|+|+|-|-..
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            44566677776      3799999999999999999999999999653

>PF14611 SLS: Mitochondrial inner-membrane-bound regulator

Probab=93.24  E-value=0.85  Score=45.18  Aligned_cols=128  Identities=15%  Similarity=0.104  Sum_probs=85.9

Q ss_pred             EEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293          276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG  355 (609)
Q Consensus       276 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g  355 (609)
                      +.+.++....-.+...+|..++.|....||+|.+...     +..+.|+|++      +.+ +.+......+.       
T Consensus        28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k------~~~-~~i~~~i~~~l-------   88 (210)
T PF14611_consen   28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK------STA-EYIEASINEIL-------   88 (210)
T ss_pred             eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH------HHH-HHHHHHHHHHH-------
Confidence            3445567778889999999999998889999999843     4579999985      222 22222222221       


Q ss_pred             CCCCCCCCCceEEEEEecccccccccc----CCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEc-----CCHHH
Q 007293          356 FSSGENKGDAVAVSILVGADFVGCLTG----SGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKN  426 (609)
Q Consensus       356 ~~~g~~~~~~~t~~l~VP~~~vG~IIG----kgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~-----G~~~~  426 (609)
                             ....+.++.++.-.--.-.+    .....+++|++.|++.|+..+.          ...+.|+     -....
T Consensus        89 -------~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~  151 (210)
T PF14611_consen   89 -------SNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKR  151 (210)
T ss_pred             -------hhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccch
Confidence                   12356677776532221221    1467899999999999998653          2234444     46778


Q ss_pred             HHHHHHHHHHHhh
Q 007293          427 VQNALSEVVGRLR  439 (609)
Q Consensus       427 V~~A~~~I~~~Lr  439 (609)
                      ++.|++++...+.
T Consensus       152 ~~~a~RlL~~a~~  164 (210)
T PF14611_consen  152 ADRAKRLLLWALD  164 (210)
T ss_pred             HHHHHHHHHHhcc
Confidence            9999999998875

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=93.19  E-value=0.17  Score=56.38  Aligned_cols=96  Identities=20%  Similarity=0.242  Sum_probs=63.4

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN  361 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~  361 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-.-.++...  +              +..|+.-  ..+.....        .
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            347999999999999999887 767766532111100  0              0000000  00100000        0


Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCC
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~  405 (609)
                       ...-...+.||.++.+.-|||+|.+|+...+.||.+|.|....
T Consensus       299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~  341 (470)
T PRK09202        299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE  341 (470)
T ss_pred             -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence             1123788999999999999999999999999999999997643

>PRK01064 hypothetical protein; Provisional

Probab=93.10  E-value=0.1  Score=43.60  Aligned_cols=33  Identities=27%  Similarity=0.503  Sum_probs=29.3

Q ss_pred             CCCceEEEEEeecceeeeeeecCcchhhhcccc
Q 007293          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE  157 (609)
Q Consensus       125 ~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e  157 (609)
                      ....+.+++.|.....|.+|||+|.+|+.||.-
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

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=93.03  E-value=0.25  Score=55.72  Aligned_cols=65  Identities=15%  Similarity=0.305  Sum_probs=50.0

Q ss_pred             eEEEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHHhc
Q 007293          129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~~L~e  200 (609)
                      .+..+-+|+ .+-|.||||.|.+|+.++.-||+.+.|..       +...|.|+| +|---+-|...+..++.+
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            334455666 78999999999999999999999999966       445688888 466556666666666654

>PRK00106 hypothetical protein; Provisional

Probab=92.86  E-value=0.3  Score=55.10  Aligned_cols=65  Identities=12%  Similarity=0.329  Sum_probs=50.7

Q ss_pred             eEEEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHHhc
Q 007293          129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       129 vt~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~~L~e  200 (609)
                      .+..+-+|+ .+-|.||||.|.+|+.++.-||+.+.|..       +...|.|+| +|---+-|...+..++.+
T Consensus       225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d  291 (535)
T PRK00106        225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD  291 (535)
T ss_pred             eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence            344456666 78999999999999999999999999966       445688998 466666666666666654

>PRK12704 phosphodiesterase; Provisional

Probab=92.85  E-value=0.25  Score=55.92  Aligned_cols=63  Identities=16%  Similarity=0.308  Sum_probs=48.7

Q ss_pred             EEEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293          131 CGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       131 ~rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      ..+-+|+ .+-|.||||.|.+|+.++.-||+.|.|..       +...|.|+|. +---+.|...+...+.+
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            3345565 89999999999999999999999999966       4567889994 55545666666666654

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

Probab=92.63  E-value=0.53  Score=52.31  Aligned_cols=93  Identities=17%  Similarity=0.230  Sum_probs=68.3

Q ss_pred             hHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEE
Q 007293          100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ  179 (609)
Q Consensus       100 ~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~  179 (609)
                      .|.+|-..|++.+..+....-.......++...|-|+.+....+||.+|...|+|..|||+.-++         ++..+.
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            44455555555554433332222334457888899999999999999999999999999966665         456677


Q ss_pred             Eecc-HHHHHHHHHHHHHHHhcc
Q 007293          180 ITGA-TLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       180 I~G~-~e~V~~A~~~I~~~L~e~  201 (609)
                      |--. ..+..+|...|..++...
T Consensus       639 i~A~~~~am~~Ak~~I~~i~~~~  661 (760)
T KOG1067|consen  639 IFAPTQAAMEEAKEFIDGIIKDD  661 (760)
T ss_pred             EEecCHHHHHHHHHHHHHHhcCc
Confidence            7664 889999999999998763

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

Probab=90.40  E-value=0.12  Score=61.11  Aligned_cols=71  Identities=17%  Similarity=-0.032  Sum_probs=60.0

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ....+.+|.....+|||++|.+|+.++..|||.|.|.+-..    ....||.+.+.|.++.++.|...|.-.+.+
T Consensus      1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~----~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP----DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC----ccchhhhcccCCCChhhhhhhccccceeec
Confidence            34567789989999999999999999999999999977322    135689999999999999999988776654

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=90.10  E-value=0.17  Score=41.47  Aligned_cols=35  Identities=17%  Similarity=0.273  Sum_probs=29.5

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhCc
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC   56 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga   56 (609)
                      .+...+.+-|.....|.||||+|.+++.||.-.+.
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            45567777889999999999999999999977654

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

Probab=88.83  E-value=0.66  Score=36.48  Aligned_cols=35  Identities=17%  Similarity=0.274  Sum_probs=28.0

Q ss_pred             cEEEEEEecCCcccceecCCChHHHHHHHHhCceE
Q 007293           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI   58 (609)
Q Consensus        24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I   58 (609)
                      .....+.+.....|.+||++|.+++.|+..++-.+
T Consensus        24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            35555666666789999999999999999998544

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.

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

Probab=88.38  E-value=0.28  Score=47.52  Aligned_cols=54  Identities=28%  Similarity=0.417  Sum_probs=48.6

Q ss_pred             cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293          374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       374 ~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr  439 (609)
                      +..+|+|+||+|.+---|.+.|.++|.+.+            ..|.|-|..++++.|...|+..|-
T Consensus       177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIl  230 (252)
T KOG3273|consen  177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLIL  230 (252)
T ss_pred             HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhc
Confidence            468999999999999999999999998853            569999999999999999988664

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

Probab=87.89  E-value=1.3  Score=49.25  Aligned_cols=89  Identities=15%  Similarity=0.130  Sum_probs=64.3

Q ss_pred             HHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcE
Q 007293          338 NAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVV  417 (609)
Q Consensus       338 ~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~  417 (609)
                      +|...|.+.+.+....+-..  ..+...+..++.|+.++...+||.+|...|+|..+||+.-.+            ++.+
T Consensus       571 ~ar~~Il~~m~k~i~~Pr~~--~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t  636 (760)
T KOG1067|consen  571 EARLQILDIMEKNINSPRGS--DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGT  636 (760)
T ss_pred             HHHHHHHHHHHhhcCCcccC--ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCce
Confidence            44556666665442211111  123567889999999999999999999999999999955444            2456


Q ss_pred             EEEcCC-HHHHHHHHHHHHHHhhh
Q 007293          418 IQISGE-YKNVQNALSEVVGRLRH  440 (609)
Q Consensus       418 V~I~G~-~~~V~~A~~~I~~~Lr~  440 (609)
                      +.|.-. +...++|++.|.+.+..
T Consensus       637 ~~i~A~~~~am~~Ak~~I~~i~~~  660 (760)
T KOG1067|consen  637 FSIFAPTQAAMEEAKEFIDGIIKD  660 (760)
T ss_pred             EEEEecCHHHHHHHHHHHHHHhcC
Confidence            666654 67889999999998775

>PRK12705 hypothetical protein; Provisional

Probab=86.49  E-value=0.85  Score=51.23  Aligned_cols=62  Identities=15%  Similarity=0.262  Sum_probs=44.3

Q ss_pred             EEEeec-ceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293          132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       132 rllVP~-~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      .+-+|+ .+-|.||||.|.+|+.++..||+.+.|...       .+.|.|++. +..-+.|...+..++.+
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            344454 789999999999999999999999999763       344666664 44444555555555543

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

Probab=86.40  E-value=0.56  Score=38.22  Aligned_cols=35  Identities=26%  Similarity=0.377  Sum_probs=27.5

Q ss_pred             EEEEecCCc-----ccceecCCChHHHHHHHHh-CceEEEc
Q 007293           27 FRLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCE   61 (609)
Q Consensus        27 ~RilvP~~~-----vG~IIGk~G~~Ik~IreeT-ga~I~V~   61 (609)
                      ..+.|-+..     +|..||++|+.|+.|.++. |-+|+|=
T Consensus         5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV   45 (69)
T PF13184_consen    5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV   45 (69)
T ss_dssp             EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred             EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence            345566666     9999999999999999999 8888874

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

Probab=86.21  E-value=0.7  Score=44.87  Aligned_cols=56  Identities=29%  Similarity=0.388  Sum_probs=50.3

Q ss_pred             cceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          137 TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       137 ~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      +..+|.|+||+|.+--.|++-|-++|.+.         +..|.|-|..++++-|...|+.++-..
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            45689999999999999999999999994         457999999999999999999999764

>PF13083 KH_4: KH domain; PDB: 3GKU_B

Probab=84.85  E-value=0.46  Score=38.85  Aligned_cols=36  Identities=11%  Similarity=0.255  Sum_probs=30.0

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeE
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI  399 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I  399 (609)
                      ......+.+..+..|.||||+|.+++.||.-..+-+
T Consensus        27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~   62 (73)
T PF13083_consen   27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA   62 (73)
T ss_dssp             TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence            346788889999999999999999999997665433

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

Probab=84.21  E-value=1.5  Score=34.45  Aligned_cols=34  Identities=12%  Similarity=0.273  Sum_probs=28.4

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeE
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI  399 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I  399 (609)
                      ....+.+.....|.+||++|++|+.|+..++-.+
T Consensus        25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~   58 (68)
T cd02409          25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL   58 (68)
T ss_pred             EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence            5666667766789999999999999999998554

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=84.19  E-value=1  Score=36.66  Aligned_cols=37  Identities=22%  Similarity=0.341  Sum_probs=30.1

Q ss_pred             EEEEEecccc-----ccccccCCCchhHHHHHhh-CCeEEecC
Q 007293          367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVG  403 (609)
Q Consensus       367 t~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-Ga~I~I~~  403 (609)
                      ...+.|-+..     +|..||++|+.|+.|+++. |-+|+|-.
T Consensus         4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~   46 (69)
T PF13184_consen    4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE   46 (69)
T ss_dssp             EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred             eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence            4566666666     9999999999999999999 99999976

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

Probab=84.15  E-value=0.29  Score=58.15  Aligned_cols=69  Identities=17%  Similarity=0.114  Sum_probs=59.0

Q ss_pred             EEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       131 ~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .++-+|-....+|||++|++|..++.-|||.|.+.+- ......||.+.+.|.++.++.|-..|.-.+.+
T Consensus      1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm-q~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM-QPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred             cccccchhhhhhhhccCcchhhhHhhccceEEehhhc-CCccchhhhcccCCCChhhhhhhccccceeec
Confidence            4577888889999999999999999999999999873 11225789999999999999999888777765

>PF07650 KH_2: KH domain syndrome, contains KH motifs

Probab=80.72  E-value=0.97  Score=37.33  Aligned_cols=33  Identities=27%  Similarity=0.428  Sum_probs=28.3

Q ss_pred             EEEEecCCcccceecCCChHHHHHHHHhCceEE
Q 007293           27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH   59 (609)
Q Consensus        27 ~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~   59 (609)
                      ..+.+.....|.|||++|++|++|+++.+-.+.
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            457778999999999999999999998876554

; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

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	609
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	3e-27
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	4e-20
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	2e-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	8e-04
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-25
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	3e-21
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	1e-06
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	3e-24
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	7e-23
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	2e-08
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	6e-06
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	4e-23
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-20
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	1e-13
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	3e-07
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	2e-21
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	4e-16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	3e-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-	7e-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	5e-08
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	1e-06
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	7e-09
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	7e-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	4e-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	5e-06
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	1e-07
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	9e-06
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
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	1e-07
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	4e-06
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	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	5e-06
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	6e-05
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	1e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	7e-07
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	2e-04
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	1e-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	5e-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	3e-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	5e-05
1tua_A	191	Hypothetical protein APE0754; structural genomics,	9e-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 =  107 bits (269), Expect = 3e-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 = 87.2 bits (216), Expect = 4e-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 = 65.3 bits (159), Expect = 2e-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 = 8e-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 (253), Expect = 3e-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 = 89.8 bits (223), Expect = 3e-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 = 47.8 bits (114), Expect = 1e-06
 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 = 98.7 bits (246), Expect = 3e-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 = 94.5 bits (235), Expect = 7e-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 = 2e-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 = 45.5 bits (108), Expect = 6e-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 = 4e-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 = 68.4 bits (167), Expect = 1e-13
 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 = 3e-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 = 90.6 bits (225), Expect = 2e-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 = 75.2 bits (185), Expect = 4e-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 = 3e-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 = 7e-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 = 45.0 bits (107), 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 = 52.7 bits (127), 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 = 49.2 bits (118), Expect = 5e-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

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

 Score = 51.5 bits (124), Expect = 7e-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 = 7e-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 = 45.4 bits (108), 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 = 4e-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 = 5e-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

>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 = 43.6 bits (103), Expect = 9e-06
 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

>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 = 1e-07
 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 = 4e-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 = 39.2 bits (92), 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

>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 = 43.9 bits (104), Expect = 5e-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 = 40.8 bits (96), Expect = 6e-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 = 48.0 bits (115), 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 = 46.1 bits (110), Expect = 7e-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 = 2e-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 = 1e-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 = 44.0 bits (104), 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 = 5e-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 = 45.1 bits (107), 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 = 38.2 bits (89), 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 = 3e-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 = 43.9 bits (103), Expect = 5e-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 = 42.7 bits (100), Expect = 9e-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 = 40.8 bits (95), 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	609
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	99.9
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	99.9
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	99.89
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	99.89
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	99.89
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;	99.87
3n89_A	376	Defective in GERM LINE development protein 3, ISO;	99.8
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.7
2qnd_A	144	FMR1 protein; KH domain, eukaryotic KH domains, ta	99.67
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.54
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	99.51
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.47
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.46
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	99.44
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	99.42
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.4
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-	99.39
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.39
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	99.38
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	99.38
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	99.38
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	99.37
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.36
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.35
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	99.33
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.33
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.33
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	99.31
1tua_A	191	Hypothetical protein APE0754; structural genomics,	99.31
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	99.3
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	99.3
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	99.3
1we8_A	104	Tudor and KH domain containing protein; structural	99.29
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.29
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	99.28
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.27
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.26
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.24
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	99.24
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	99.22
1we8_A	104	Tudor and KH domain containing protein; structural	99.21
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	99.15
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	99.11
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	99.11
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	99.1
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.07
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	99.04
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.98
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	98.97
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	98.81
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	98.79
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.78
2cpq_A	91	FragIle X mental retardation syndrome related prot	98.5
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.45
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.31
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	98.28
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	98.2
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.93
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	97.83
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.66
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	97.56
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	97.54
2cxc_A	144	NUSA; transcription termination, RNA binding prote	97.45
3v69_A	140	Protein filia; RNA-binding, embryogenesis, KH doma	96.99
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.87
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	96.76
2cxc_A	144	NUSA; transcription termination, RNA binding prote	96.69
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	95.51
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.33
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	93.9
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	93.39
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	93.1
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	93.06
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.98
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	92.46
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	91.65
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	89.57

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=99.92  E-value=4.5e-25  Score=212.01  Aligned_cols=161  Identities=20%  Similarity=0.388  Sum_probs=126.4

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCC---CCCCCceEEEEccCcchhhhhhhccccccccCCCc
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG---FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV   98 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~---~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~   98 (609)
                      ++.++++|+||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|+|+|+|+.+++.+               
T Consensus         3 ~~~~~~~i~vp~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G~~~~v~~---------------   67 (178)
T 2anr_A            3 GSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA---------------   67 (178)
T ss_dssp             CCCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEECHHHHHH---------------
T ss_pred             CCCEEEEEEEChhHeeeeECCCcHHHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEeCHHHHHH---------------
Confidence            678999999999999999999999999999999999999753   46788999999998776432               


Q ss_pred             chHHHHHHHHHHHHhhhhhccC-----------CCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293           99 SSTQEAVIRVFERMWEVEAEVE-----------GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~-----------~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                        |..   .+.+.+.+......           .........+++|+||.+++|+||||+|++|++|+++|||+|+|.+.
T Consensus        68 --A~~---~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Vp~~~vg~iIGkgG~~Ik~i~~~tga~I~i~~~  142 (178)
T 2anr_A           68 --VHG---FIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQK  142 (178)
T ss_dssp             --HHH---HHHHHHTCCCCC-----------------CGGGGEEEEEEEHHHHHHHHCGGGHHHHHHHHHSSCEEEECCC
T ss_pred             --HHH---HHHHHHhccCCccccCCcccccCCccCCCCCCceEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEeCC
Confidence              322   22222222110000           00012235789999999999999999999999999999999999885


Q ss_pred             CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhccC
Q 007293          168 PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLS  202 (609)
Q Consensus       168 p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~  202 (609)
                      +.++...++.|+|+|++++|.+|+.+|.++|++++
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=3.6e-24  Score=202.76  Aligned_cols=154  Identities=20%  Similarity=0.312  Sum_probs=126.3

Q ss_pred             cEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCC-CCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG-FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~-~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      .-+++|+||.+++|.||||+|++|++|+++|||+|+|.+. .+++.+|+|+|+|+.++                    +.
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 67889999999998766                    33


Q ss_pred             HHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCC-ceEEEe
Q 007293          103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD-QLIQIT  181 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~d-R~V~I~  181 (609)
                      .|...++..+.+....   .......++++|+||..++|+||||+|++|++|+++|||+|.|..+ ..+...+ +.|+|+
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            4455555554443111   1123346788999999999999999999999999999999999875 2233344 589999


Q ss_pred             ccHHHHHHHHHHHHHHHhcc
Q 007293          182 GATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       182 G~~e~V~~A~~~I~~~L~e~  201 (609)
                      |++++|.+|+.+|.+++++.
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=99.90  E-value=3.7e-24  Score=202.06  Aligned_cols=155  Identities=18%  Similarity=0.346  Sum_probs=126.0

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.  ++.+|+|+|+|+.+++                    .
T Consensus         3 ~~~~~~~~vp~~~~g~iIGkgG~~Ik~i~~~tg~~I~i~~~--~~~~r~v~I~G~~~~v--------------------~   60 (160)
T 2jzx_A            3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAI--------------------F   60 (160)
T ss_dssp             CEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCSEEEEECC--TTTEEEEEEEEEHHHH--------------------H
T ss_pred             ccEEEEEEEchhheeeeECCCcHHHHHHHHHHCCEEEEcCC--CCCceEEEEEeCHHHH--------------------H
Confidence            46899999999999999999999999999999999999875  5679999999986653                    2


Q ss_pred             HHHHHHHHHHhhhhhcc-C-CCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEE
Q 007293          103 EAVIRVFERMWEVEAEV-E-GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI  180 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~-~-~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I  180 (609)
                      .|...+.+.+.+..... . +.......++++|+||.+++|+||||+|++|++|+++|||+|+|.++ ..+...++.|+|
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            33334443333321110 0 00112336899999999999999999999999999999999999874 456778999999


Q ss_pred             eccHHHHHHHHHHHHHHHhc
Q 007293          181 TGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       181 ~G~~e~V~~A~~~I~~~L~e  200 (609)
                      +|++++|.+|+.+|.+++.+
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=99.90  E-value=4.8e-24  Score=204.12  Aligned_cols=159  Identities=21%  Similarity=0.323  Sum_probs=123.7

Q ss_pred             CcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        23 ~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      +..+++|+||.+++|.||||+|++|++|+++|||+|+|.+..+++.+|+|+|+|+.+++.                 .|.
T Consensus         1 g~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~~~v~-----------------~A~   63 (174)
T 1j4w_A            1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ-----------------HAA   63 (174)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECHHHHH-----------------HHH
T ss_pred             CCeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCHHHHH-----------------HHH
Confidence            457899999999999999999999999999999999998766678899999999977643                 344


Q ss_pred             HHHHHHHHHHhhhhhccC------------C--CCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-
Q 007293          103 EAVIRVFERMWEVEAEVE------------G--DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-  167 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~~------------~--~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-  167 (609)
                      .++..++...........            .  .......++++|+||.+++|+||||+|++|++|+++|||+|+|.+. 
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            444444333211000000            0  0001224689999999999999999999999999999999999886 


Q ss_pred             CCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          168 PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       168 p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      +.+....++.|+|+|++++|.+|+.+|.++|
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            3455678899999999999999999998874

>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=99.89  E-value=8.8e-24  Score=202.96  Aligned_cols=162  Identities=21%  Similarity=0.338  Sum_probs=128.3

Q ss_pred             CcceEEEEEecccccccccccccchhhhhhhccCeeEEEecC---CCCCCccEEEEcccccccCCCChHHHHHHHHHhhh
Q 007293          271 KQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS  347 (609)
Q Consensus       271 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~---~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i  347 (609)
                      ..+++++|.||.+++|.||||+|++|++|+++|||+|+|.+.   .+++.+|.|+|+|+.      ..+..|..++.+.+
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            467899999999999999999999999999999999999853   356789999999984      34566766676666


Q ss_pred             hhcccccC-------CCC--CCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEE
Q 007293          348 VEVEGQQG-------FSS--GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVI  418 (609)
Q Consensus       348 ~e~~~~~g-------~~~--g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V  418 (609)
                      .+......       +.+  ........+.+|+||.+++|+||||+|++||+|++.|||+|+|.+..+.   ...+++.|
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  0112235789999999999999999999999999999999999875432   24578999


Q ss_pred             EEcCCHHHHHHHHHHHHHHhhhc
Q 007293          419 QISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       419 ~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      +|+|++++|++|+.+|.++|++.
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            99999999999999999999875

>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=99.89  E-value=6.5e-24  Score=200.91  Aligned_cols=154  Identities=15%  Similarity=0.220  Sum_probs=121.7

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCC--CCCCCceEEEEccCcchhhhhhhccccccccCCCcchHH
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG--FPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ  102 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~--~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~  102 (609)
                      ++++|+||.+++|.||||+|++|++|+++|||+|+|.+.  .++..+|+|+|+|+.+++                    .
T Consensus         2 ~~~~~~Vp~~~~g~iIGk~G~~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G~~~~v--------------------~   61 (164)
T 2jvz_A            2 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKV--------------------Q   61 (164)
T ss_dssp             EEEEEEECTTCHHHHTCTTTHHHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEECHHHH--------------------H
T ss_pred             eEEEEEechhheeEEECCChHHHHHHHHHhCCeEEEecCCCCCCCCceEEEEEcCHHHH--------------------H
Confidence            689999999999999999999999999999999999753  346779999999987663                    2


Q ss_pred             HHHHHHHHHHhhhhhcc---CCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEE
Q 007293          103 EAVIRVFERMWEVEAEV---EGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ  179 (609)
Q Consensus       103 ~Al~~v~~~i~~~~~~~---~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~  179 (609)
                      .|...+...+.+.....   .++......++++|+||...+|+||||+|++|++|+++|||+|.|.+.  .+...++.|+
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            33334444333321110   000011113568899999999999999999999999999999999874  3445689999


Q ss_pred             EeccHHHHHHHHHHHHHHHhc
Q 007293          180 ITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       180 I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      |+|++++|.+|+.+|.+++++
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=99.89  E-value=3.7e-23  Score=195.78  Aligned_cols=154  Identities=21%  Similarity=0.314  Sum_probs=128.4

Q ss_pred             eEEEEEecccccccccccccchhhhhhhccCeeEEEecC-CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc
Q 007293          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (609)
Q Consensus       274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~  352 (609)
                      .+++|+||.+++|.|||++|++|++|+++|||+|+|.+. .+++.+|.|+|+|+.      ..+..|..++.+.+.+...
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 567899999999974      4566777777777755421


Q ss_pred             ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHH
Q 007293          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALS  432 (609)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~  432 (609)
                      .     +.......+.+|.||.+++|+|||++|++|++|++.|||+|+|++.. .|.  ..+++.|+|+|++++|+.|+.
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     11223457889999999999999999999999999999999997643 232  344568999999999999999


Q ss_pred             HHHHHhhhc
Q 007293          433 EVVGRLRHN  441 (609)
Q Consensus       433 ~I~~~Lr~~  441 (609)
                      +|.++|++.
T Consensus       149 ~I~~~i~~~  157 (163)
T 3krm_A          149 KIRDILAQV  157 (163)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999864

>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=2e-23  Score=196.92  Aligned_cols=156  Identities=21%  Similarity=0.399  Sum_probs=127.7

Q ss_pred             cceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcc
Q 007293          272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE  351 (609)
Q Consensus       272 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~  351 (609)
                      ..++++|.||.+++|.|||++|++|++|+++|||+|+|.+.  ++.+|.|+|+|+.      ..+.+|..++.+.+.+..
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  4678999999984      455677777776665432


Q ss_pred             cccCCCC-CCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHH
Q 007293          352 GQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNA  430 (609)
Q Consensus       352 ~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A  430 (609)
                      . ...+. ........+.+|.||.+++|+|||++|++|++|++.|||+|+|.+. ..|   ..+++.|+|+|++++|++|
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 11111 1112346899999999999999999999999999999999999763 333   4678999999999999999


Q ss_pred             HHHHHHHhhh
Q 007293          431 LSEVVGRLRH  440 (609)
Q Consensus       431 ~~~I~~~Lr~  440 (609)
                      +.+|.+.|.+
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=6.2e-23  Score=196.38  Aligned_cols=158  Identities=19%  Similarity=0.312  Sum_probs=123.8

Q ss_pred             ceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc
Q 007293          273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (609)
Q Consensus       273 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~  352 (609)
                      ..+++|.||.+++|.||||+|++|++|+++|||+|+|.+..+++.+|.|+|+|+.      ..+..|..+|.+.+.+...
T Consensus         2 ~~~~~~~vp~~~vg~iIGkgG~~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~~------~~v~~A~~~I~~~~~~~~~   75 (174)
T 1j4w_A            2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPP------DRAQHAAEIITDLLRSVQA   75 (174)
T ss_dssp             CEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEEECCTTSCSEEEEEEEECH------HHHHHHHHHHHHHHHHHC-
T ss_pred             CeEEEEEEChhheeeeecCCchHHHHHHHHhCCEEEEecCCCCCCccEEEEEeCH------HHHHHHHHHHHHHHHhccc
Confidence            3578999999999999999999999999999999999876667789999999984      3455666666655543310


Q ss_pred             cc-C--------CCCC------CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcE
Q 007293          353 QQ-G--------FSSG------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVV  417 (609)
Q Consensus       353 ~~-g--------~~~g------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~  417 (609)
                      .. +        +..+      ......++.+|.||.+++|+||||+|++||+|++.|||+|+|.+..  +.+...+++.
T Consensus        76 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGkgG~~Ik~I~~~tga~I~i~~~~--~~~~~~~~~~  153 (174)
T 1j4w_A           76 GNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNP--PPNADPNMKL  153 (174)
T ss_dssp             ----------------------------CEEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCC--TTTSCTTEEE
T ss_pred             CCCCCCCCCCCCCCCCCCccccCCCCCcEEEEEEEChHHcCeeECCCchHHHHHHHHHCCEEEECCCC--CCCCCCCceE
Confidence            00 0        0000      0012346889999999999999999999999999999999998743  3334577899


Q ss_pred             EEEcCCHHHHHHHHHHHHHHh
Q 007293          418 IQISGEYKNVQNALSEVVGRL  438 (609)
Q Consensus       418 V~I~G~~~~V~~A~~~I~~~L  438 (609)
                      |+|+|++++|+.|+.+|.++|
T Consensus       154 v~I~G~~~~v~~A~~~I~~~i  174 (174)
T 1j4w_A          154 FTIRGTPQQIDYARQLIEEKI  174 (174)
T ss_dssp             EEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEECCHHHHHHHHHHHHHhC
Confidence            999999999999999999875

>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=1.6e-22  Score=191.31  Aligned_cols=156  Identities=17%  Similarity=0.251  Sum_probs=125.4

Q ss_pred             eEEEEEecccccccccccccchhhhhhhccCeeEEEecC--CCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcc
Q 007293          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE  351 (609)
Q Consensus       274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~--~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~  351 (609)
                      ++++|.||.+++|.|||++|++|++|+++|||+|+|.+.  .++..+|.|+|+|+.      ..+..|...+.+.+.+..
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            578999999999999999999999999999999999753  345678999999974      455677777777665432


Q ss_pred             cccCCCCCC--CCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHH
Q 007293          352 GQQGFSSGE--NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQN  429 (609)
Q Consensus       352 ~~~g~~~g~--~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~  429 (609)
                       ..++.+..  ......+.+|.||.+++|+||||+|++|++|++.|||+|+|.+.++     ...++.|+|+|++++|+.
T Consensus        76 -~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~i~~~tg~~I~i~~~~~-----~~~~~~v~I~G~~~~v~~  149 (164)
T 2jvz_A           76 -QGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEH  149 (164)
T ss_dssp             -SCCCSSCSSCTTSCSSSBCCEEETTTHHHHHCSSSHHHHHHHHHTCCEEEECCCCT-----TSSEEEEEEESCHHHHHH
T ss_pred             -CCCCCCccccCCCCCceEEEEEChhhccccCCCCcHhHHHHHHHHCCeEEEeCCCC-----CCCcEEEEEEcCHHHHHH
Confidence             11121110  0111356889999999999999999999999999999999987432     355799999999999999


Q ss_pred             HHHHHHHHhhhc
Q 007293          430 ALSEVVGRLRHN  441 (609)
Q Consensus       430 A~~~I~~~Lr~~  441 (609)
                      |+.+|.++|++.
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=99.87  E-value=9.1e-22  Score=206.73  Aligned_cols=225  Identities=17%  Similarity=0.106  Sum_probs=160.0

Q ss_pred             CCceEEEEEeecceeeeeeecCc--chhhhcccccCcEEEecCCC---CCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGG--RNVTRMRIESGAKIVMLPPP---ACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG--~~Ik~I~~eSGa~I~I~~~p---~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ...+|+.+-||...++.||||+|  ++|++|+++|||+|++....   ..+......|+|+|..++|++|..+|.+++- 
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  99999999999999996531   1122455789999999999999999877431 


Q ss_pred             cCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCccCCCcceEEEEEe
Q 007293          201 LSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLF  280 (609)
Q Consensus       201 ~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~V  280 (609)
                                                                                               .++.+.+
T Consensus       106 -------------------------------------------------------------------------l~i~~el  112 (376)
T 3n89_A          106 -------------------------------------------------------------------------FTVFMAL  112 (376)
T ss_dssp             -------------------------------------------------------------------------EEEEEEC
T ss_pred             -------------------------------------------------------------------------ceEEEEc
Confidence                                                                                     1223333


Q ss_pred             cccccccccccccchhhhhhhccCeeEEEecCCC--CCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccCCCC
Q 007293          281 SGWTASGIIGKRGAIVRSLQNASGALISFAAPLT--KSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSS  358 (609)
Q Consensus       281 P~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~--~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~  358 (609)
                      |...+..  ...+..|.+ ++.++++|.|.....  +.....|+|+|.+   .....+.+|+..+.+.+.+..       
T Consensus       113 p~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~~~~~~sd~V~IrG~~---~nv~~akeA~~~Ll~~l~~~e-------  179 (376)
T 3n89_A          113 SKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPEKNGIVTTYLRITARE---KNQHELIEAAKRLNEILFRES-------  179 (376)
T ss_dssp             TTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-----CEEEEEEEEEG---GGHHHHHHHHHHHHHHHCC---------
T ss_pred             cccccCc--chhhhhhcc-ceeCceEEEeCCcccccCCCCCEEEEEcCh---hhHHHHHHHHHHHHHHHHhhh-------
Confidence            3322221  111234444 678999999865321  1235679999985   223345677777776664321       


Q ss_pred             CCCCCCceEEEEEeccccccccccCCC--chhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHH
Q 007293          359 GENKGDAVAVSILVGADFVGCLTGSGS--SAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVG  436 (609)
Q Consensus       359 g~~~~~~~t~~l~VP~~~vG~IIGkgG--~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~  436 (609)
                       ......++.+|.|+..+|.+|||++|  ..|++|+++|||+|.+++.++... ...+...|+|+|+.++|..|++.|.+
T Consensus       180 -~~~~~~~s~~v~V~~~~H~~IIGk~G~n~~IkkIr~eTGv~I~FP~~~d~~d-~~~~~~~ItItGs~e~V~~Ark~I~~  257 (376)
T 3n89_A          180 -PAPENNFTLHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNE-TRGNIYEIKVVGNIDNVLKARRYIMD  257 (376)
T ss_dssp             -CCCSSCEEEEEEEEGGGHHHHTCCTTSCCHHHHHHHHHTCEEECC----------CCEEEEEEESCHHHHHHHHHHHHH
T ss_pred             -cccccceEEEEEeCHHHHHHhhcCCCcchHHHHHHHhhCCEEECCCCCCccc-ccCCceEEEEEeCHHHHHHHHHHHHh
Confidence             01134589999999999999999999  567999999999999987544110 11345789999999999999999999


Q ss_pred             Hhh
Q 007293          437 RLR  439 (609)
Q Consensus       437 ~Lr  439 (609)
                      .|=
T Consensus       258 lLP  260 (376)
T 3n89_A          258 LLP  260 (376)
T ss_dssp             TSE
T ss_pred             hCC
Confidence            775

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

Probab=99.80  E-value=3.4e-19  Score=187.19  Aligned_cols=297  Identities=10%  Similarity=0.093  Sum_probs=188.7

Q ss_pred             CCCCCCCcEEEEEEecCCcccceecCCC--hHHHHHHHHhCceEEEcCCC-----CCCCceEEEEccCcchhhhhhhccc
Q 007293           17 PLNLPDDVVSFRLVCPTPVVGGLIGRSG--SIISSIRRDTKCRIHCEGGF-----PGSDHRVILVVGSGSIDRRIMFCEN   89 (609)
Q Consensus        17 ~~~~~~~~v~~RilvP~~~vG~IIGk~G--~~Ik~IreeTga~I~V~~~~-----~g~~eRvI~I~G~~e~~~~~~~~~~   89 (609)
                      ........+++.+-||..+++.||||+|  ++|++|+++|||+|+|++..     +......|+|+|..++++       
T Consensus        22 ~le~~~~~VTl~v~Ip~~~Hs~IIGkgG~~sNIkkImeEtgv~I~fPD~~~~~~~~~~ks~~VtItG~~enVE-------   94 (376)
T 3n89_A           22 MIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVD-------   94 (376)
T ss_dssp             CCCCCTTEEEEEEECCGGGHHHHHSCCSSSCSHHHHHHHHTCEEECCCCCCCSSSCCTTTTEEEEEEEHHHHH-------
T ss_pred             EEEecCCEEEEEEEEchhhhhhhccCCChHHHHHHHHHHhCCeEECCCCcccccCCcCCCCeEEEEcCHHHHH-------
Confidence            3445578899999999999999999999  99999999999999998764     113457899999998843       


Q ss_pred             cccccCCCcchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCC
Q 007293           90 DVVVEGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPA  169 (609)
Q Consensus        90 ~~~~e~~~~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~  169 (609)
                                .|..+|..+.                  ++++.+-+|...++.  ..-+..|.+ ++..|++|.+...+.
T Consensus        95 ----------~AR~~I~~l~------------------Pl~i~~elp~~~i~~--~~l~~~I~q-q~~y~V~I~Fp~~~~  143 (376)
T 3n89_A           95 ----------RARMLMRRNC------------------HFTVFMALSKMKMPL--HELQAHVRQ-NPIQNVEMSFVDAPE  143 (376)
T ss_dssp             ----------HHHHHHHHSC------------------EEEEEEECTTCSSCH--HHHHHHHHH-CCCTTCEEEEEEEC-
T ss_pred             ----------HHHHHHHhcC------------------CceEEEEccccccCc--chhhhhhcc-ceeCceEEEeCCccc
Confidence                      3544443211                  455556566543322  111345555 678999999855211


Q ss_pred             CCCCCCceEEEeccHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCC
Q 007293          170 CAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNAS  249 (609)
Q Consensus       170 ~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~P~~~~~~~~Ya~  249 (609)
                      ..+...-.|+|+|...+|.+|+.++..+++......                                            
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            111124579999998777766666555554311000                                            


Q ss_pred             ccCCCCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccc--chhhhhhhccCeeEEEecCCC----CCCccEEEE
Q 007293          250 EFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRG--AIVRSLQNASGALISFAAPLT----KSGERVVTI  323 (609)
Q Consensus       250 ~~~p~~~~~~~~~p~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G--~~Ik~I~~~tGa~I~i~~~~~----~s~er~vtI  323 (609)
                                        ......++..|.|+..+|..|||++|  ..|++|+++||++|.|++...    ......|+|
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                              00124568889999999999999999  566999999999999986422    123468999


Q ss_pred             cccccccCCCChHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293          324 SALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (609)
Q Consensus       324 sG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~  403 (609)
                      +|++      ..+.+|...|.+.+                 .+...|.++.+..-.-...--..|-.+.++.++-|.|.+
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            9996      45556666665544                 366777766654333333444456667889999999976


Q ss_pred             CCcccccCCCC---CcEEEEcCC---HHHHHHHHHHHHH
Q 007293          404 GEQVLGCAAQN---DVVIQISGE---YKNVQNALSEVVG  436 (609)
Q Consensus       404 ~~~~P~~~~~~---er~V~I~G~---~~~V~~A~~~I~~  436 (609)
                      ..--|.....+   -..|.|++-   .-++..|.+.+..
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            43212100111   144666654   4555566655544

>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=4.6e-17  Score=150.77  Aligned_cols=137  Identities=16%  Similarity=0.142  Sum_probs=100.8

Q ss_pred             ceEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccc
Q 007293          273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG  352 (609)
Q Consensus       273 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~  352 (609)
                      .++.++.||.+.+|.+||++|++|+.|++++|..|.....    +...+.+.|.       +|+  ++..+.. +.+.  
T Consensus         3 ~~~~~~~Vp~~~vG~~IG~~G~~I~~i~~e~gI~ii~~~~----~~~~~i~~~~-------~p~--~v~~~~~-~l~~--   66 (144)
T 2qnd_A            3 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDE----DTCTFHIYGE-------DQD--AVKKARS-FLEF--   66 (144)
T ss_dssp             -CEEEEECCGGGHHHHHCGGGHHHHHHHTSTTEEEEEEET----TTTEEEEEES-------SHH--HHHHHHH-HHCE--
T ss_pred             ceEEEEEECCcceeeEECCChhHHHHHHHHHCCeEeccCC----CchheeeccC-------CHH--HHHHHHH-hhhc--
Confidence            4578899999999999999999999999999944332222    1234556664       222  2222211 1111  


Q ss_pred             ccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCC-eEEecCCCcccccCCCCC--cEEEEcCCHHHHHH
Q 007293          353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGT-DIKLVGGEQVLGCAAQND--VVIQISGEYKNVQN  429 (609)
Q Consensus       353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa-~I~I~~~~~~P~~~~~~e--r~V~I~G~~~~V~~  429 (609)
                                   ...++.||.+++|++|||+|++|+.|++.||| +|+|.+.++...  ..++  +.|+|+|++++|+.
T Consensus        67 -------------~e~~v~Vp~~~~g~~IGK~G~nIr~i~~~tG~~~I~i~~~~~~~~--~~~~~~~~vtI~G~~~~v~~  131 (144)
T 2qnd_A           67 -------------AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNV--PQEEGMVPFVFVGTKDSIAN  131 (144)
T ss_dssp             -------------EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHTCSEEEEEEECTTCC--CCCTTEEEEEEEEEHHHHHH
T ss_pred             -------------ceEEEEECHHHcCeeECCCCHHHHHHHHHHCCEEEEEcCCCCCCc--cccCCeeEEEEEeCHHHHHH
Confidence                         24899999999999999999999999999997 999987544211  1233  35899999999999


Q ss_pred             HHHHHHHHhhh
Q 007293          430 ALSEVVGRLRH  440 (609)
Q Consensus       430 A~~~I~~~Lr~  440 (609)
                      |+.+|..+|..
T Consensus       132 Ak~li~~~l~~  142 (144)
T 2qnd_A          132 ATVLLDYHLNY  142 (144)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHh
Confidence            99999999874

>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=99.67  E-value=5.9e-17  Score=150.00  Aligned_cols=136  Identities=14%  Similarity=0.140  Sum_probs=99.9

Q ss_pred             cEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHH
Q 007293           24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQE  103 (609)
Q Consensus        24 ~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~  103 (609)
                      .++.+++||.+.+|++||++|++|++|++++|  |++-... +.+++.+...+.++.+                      
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            46789999999999999999999999999999  5543221 1234544443334332                      


Q ss_pred             HHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCc-EEEecCCC-CCCCCCCc--eEE
Q 007293          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGA-KIVMLPPP-ACAAIDDQ--LIQ  179 (609)
Q Consensus       104 Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa-~I~I~~~p-~~~~~~dR--~V~  179 (609)
                        ..+.. +..             ...+++.||..++|++|||+|++|+.|++.||| +|.|.... ......++  .|+
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             EeccHHHHHHHHHHHHHHHhc
Q 007293          180 ITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       180 I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      |+|+.++|.+|+.+|..+|..
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=99.54  E-value=7e-15  Score=144.77  Aligned_cols=147  Identities=16%  Similarity=0.220  Sum_probs=99.7

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHH
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA  104 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~A  104 (609)
                      -+.++.||.+++|.|||++|++|+.|+++|||+|+|+.     +++.|.|.++....+      .      ..+..|.+.
T Consensus        34 ~i~~i~IP~~kig~lIG~gGk~Ik~I~e~tgvkI~I~~-----~~g~V~I~~~~~t~d------~------~~i~kA~~~   96 (219)
T 2e3u_A           34 QEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDS-----ETGEVWITSTKETED------P------LAVWKARDI   96 (219)
T ss_dssp             CEEEEECCHHHHHHHHCGGGHHHHHHHHHHTEEEEECT-----TTCEEEEEECTTCCS------H------HHHHHHHHH
T ss_pred             EEEEEEeCHHHhhhhhcccHHHHHHHHHHHCcEEEEEc-----CCCEEEEecCCCCCC------H------HHHHHHHHH
Confidence            35689999999999999999999999999999999963     256788887641100      0      002223333


Q ss_pred             HHHHHHHHhhhhhccCCCCCCCCceEEE-EEe-----ec------ceeeeeeecCcchhhhcccccCcEEEecCCCCCCC
Q 007293          105 VIRVFERMWEVEAEVEGDGDGDDVAYCG-LLA-----NT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA  172 (609)
Q Consensus       105 l~~v~~~i~~~~~~~~~~~~~~~~vt~r-llV-----P~------~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~  172 (609)
                      +..+.   .....+....-- .+...+. +-+     +.      ..+|+||||+|++|+.|++.|||+|.|.       
T Consensus        97 I~~i~---rg~~~e~g~~ll-~dd~~~e~i~i~~~~v~~~~~~~~r~~GriIGk~G~tik~ie~~Tg~~I~v~-------  165 (219)
T 2e3u_A           97 VLAIG---RGFSPERAFRLL-NEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVY-------  165 (219)
T ss_dssp             HHHHH---TTCCHHHHGGGG-STTCEEEEEEGGGCC------CHHHHHHHHHCGGGHHHHHHHHHHCCEEEEE-------
T ss_pred             HHHHh---ccCCccccceec-cCCccceeEEcccccccCCchhhhhhhheeECCCchHHHHHHHHhCceEEEC-------
Confidence            32222   000000000000 0011121 222     22      3689999999999999999999999994       


Q ss_pred             CCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          173 IDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       173 ~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                        ++.|.|.|++++|+.|..+|.+++.+.
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              367999999999999999999999663

>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=1.9e-14  Score=141.61  Aligned_cols=146  Identities=15%  Similarity=0.175  Sum_probs=105.2

Q ss_pred             EEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhccccc
Q 007293          275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ  354 (609)
Q Consensus       275 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~  354 (609)
                      ...+.||.+.+|.|||++|.+|+.|+++||++|.++..     ++.|+|.++....+ ...++.|...+...+.......
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            56799999999999999999999999999999999732     46799988731111 1345566655555432111110


Q ss_pred             CCCCCCCCCCceEEEEEec-----------cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC
Q 007293          355 GFSSGENKGDAVAVSILVG-----------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE  423 (609)
Q Consensus       355 g~~~g~~~~~~~t~~l~VP-----------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~  423 (609)
                      +... . .....-..+.++           ...+|+||||+|++|+.|++.|||+|.|..            +.|.|.|+
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 011122233333           237999999999999999999999999953            67999999


Q ss_pred             HHHHHHHHHHHHHHhhh
Q 007293          424 YKNVQNALSEVVGRLRH  440 (609)
Q Consensus       424 ~~~V~~A~~~I~~~Lr~  440 (609)
                      +++++.|+.+|..+|..
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            99999999999999965

>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=99.47  E-value=4.5e-14  Score=115.32  Aligned_cols=71  Identities=18%  Similarity=0.421  Sum_probs=65.3

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      +..++.+|+||.+++|+|||++|++||+|+++|||+|+|.+.       ...+|.|+|+|++++|.+|+.+|.++|++
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       24589999999999999999999999986

>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=99.46  E-value=1.3e-13  Score=115.08  Aligned_cols=73  Identities=19%  Similarity=0.390  Sum_probs=66.1

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..++.+|.||.+++|+||||+|++||+|+++|||+|+|.+..     ...+++.|+|+|++++|++|+.+|.+++++.
T Consensus         5 ~~~~~~i~Vp~~~vg~iIGkgG~~Ik~I~~~tga~I~i~~~~-----~~~~~~~v~I~G~~~~v~~A~~~I~~~i~~~   77 (82)
T 1zzk_A            5 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQNAQYLLQNSVKQY   77 (82)
T ss_dssp             CCEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCTT-----SCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEChHhcCeeECCCchHHHHHHHHHCCEEEEcCCC-----CCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            468999999999999999999999999999999999997531     2457899999999999999999999999874

>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=113.94  Aligned_cols=73  Identities=22%  Similarity=0.361  Sum_probs=64.7

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+.++..  .+..++.|+|+|++++|++|+.+|.++|++
T Consensus         3 ~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~--~~~~~~~v~I~G~~~~v~~A~~~I~~~i~e   75 (76)
T 1dtj_A            3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTY   75 (76)
T ss_dssp             EEEEEEEETTTHHHHHCSTTHHHHHHHHHHCCEEEECCTTCCS--TTCCEEEEEEEESHHHHHHHHHHHHHHCC-
T ss_pred             eEEEEEEChHHcceEECCCchHHHHHHHHhCCEEEECcCCCCC--CCCceeEEEEEeCHHHHHHHHHHHHHHHhc
Confidence            6889999999999999999999999999999999998754321  246789999999999999999999998864

>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=114.86  Aligned_cols=72  Identities=21%  Similarity=0.433  Sum_probs=65.7

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..++.+|.||.+++|+|||++|++|++|++.|||+|+|.+.  .   ...+++.|+|+|++++|++|+.+|.++|++
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 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP--V---EGSTDRQVTITGSAASISLAQYLINVRLSS   74 (76)
T ss_dssp             CCEEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCC--C---TTCSEEEEEEEECHHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEEChHHcceEECCCChHHHHHHHHHCCEEEEcCC--C---CCCCeEEEEEEeCHHHHHHHHHHHHHHHHc
Confidence            45899999999999999999999999999999999999863  1   356789999999999999999999999875

>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=99.44  E-value=1.1e-13  Score=115.52  Aligned_cols=73  Identities=16%  Similarity=0.387  Sum_probs=65.3

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..++.+|.||.+++|+||||+|++|++|++.|||+|+|.+..     ...+++.|+|+|++++|++|+.+|.+++++.
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     2467899999999999999999999998864

>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=99.42  E-value=7.7e-14  Score=113.93  Aligned_cols=70  Identities=30%  Similarity=0.458  Sum_probs=65.5

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ..++++|+||.+.+|.||||+|++|++|+++|||+|+|.+.    +..+|+|+|+|++++|.+|+.+|.++|++
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

>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=99.40  E-value=1.9e-13  Score=114.28  Aligned_cols=70  Identities=21%  Similarity=0.347  Sum_probs=63.6

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|++.+        +++.|+|+|++++|++|+++|.++++.
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            4668999999999999999999999999999999999998632        368999999999999999999998764

>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=5.2e-13  Score=113.98  Aligned_cols=74  Identities=16%  Similarity=0.258  Sum_probs=67.0

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...++.+|.||.+++|+||||+|++|++|+++|||+|+|.+..+     ...++.|+|+|++++|++|+.+|.++|++.
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            45689999999999999999999999999999999999987432     356899999999999999999999999874

>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=2.9e-13  Score=114.30  Aligned_cols=75  Identities=23%  Similarity=0.355  Sum_probs=66.6

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ++.+|.||.+++|+|||++|++|++|++.|||+|+|.+.++..  .+..++.|+|+|++++|+.|+.+|.++|.+.-
T Consensus         3 ~t~~i~IP~~~vG~IIGkgG~~Ik~I~~~tga~I~I~~~~~~~--~g~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~   77 (87)
T 1ec6_A            3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFL--PGTRNRRVTITGSPAATQAAQYLISQRVTYEQ   77 (87)
T ss_dssp             SEEEEEEEHHHHHHHHCGGGHHHHHHHHHHCCEEEECCTTCBS--TTSCEEEEEEESSHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEChHHcCeeECCCcHhHHHHHHHhCCEEEEccCCCCC--CCCCceEEEEEcCHHHHHHHHHHHHHHHhccc
Confidence            5789999999999999999999999999999999998754321  24678999999999999999999999998753

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=99.39  E-value=2.8e-13  Score=114.93  Aligned_cols=74  Identities=20%  Similarity=0.414  Sum_probs=67.0

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...++.+|.||.+++|+||||+|++||+|+++|||+|+|.+..     ...+++.|+|+|++++|++|+.+|.+++++.
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            4678999999999999999999999999999999999997531     2467899999999999999999999999875

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

Probab=99.39  E-value=4.8e-13  Score=117.39  Aligned_cols=74  Identities=15%  Similarity=0.220  Sum_probs=65.7

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      +.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+ | +.+.++++|+|+|++++|++|+.+|.++|++..
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-P-NGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL   81 (107)
T ss_dssp             CEEEEEEGGGTTTTSTTTTCHHHHHHHHSSSEEEECCCCC-T-TCCTTEEEEEEESCHHHHHHHHHHHHHHSCSCC
T ss_pred             eEEEEECHHHcCccCCCCcHHHHHHHHHhCCEEEEcCccC-C-CCCCCceEEEEECCHHHHHHHHHHHHHHHhccc
Confidence            7899999999999999999999999999999999987432 1 134568999999999999999999999998754

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

Probab=99.38  E-value=2.2e-13  Score=112.11  Aligned_cols=71  Identities=23%  Similarity=0.363  Sum_probs=66.9

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .++.+|+||.+.+|+||||+|++|++|+++|||+|+|.+  .+++..+|.|+|+|++++|.+|+.+|.+++.+
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

>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=99.38  E-value=2.9e-13  Score=113.03  Aligned_cols=73  Identities=23%  Similarity=0.369  Sum_probs=66.7

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ..++.+|+||.+.+|+||||+|++|++|+++|||+|+|.+.  +++..+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus         4 ~~~~~~i~Ip~~~vg~IIGkgG~~Ik~I~~~sga~I~i~~~--~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~   76 (82)
T 1wvn_A            4 SQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--VEGSSGRQVTITGSAASISLAQYLINARLSSE   76 (82)
T ss_dssp             TCEEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CTTCSEEEEEEEECHHHHHHHHHHHHHHTC--
T ss_pred             CcEEEEEEEchHhccceeCCCchhHHHHHHHhCCEEEEecC--CCCCCceEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            37899999999999999999999999999999999999873  56778999999999999999999999999774

>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=99.38  E-value=4.3e-13  Score=112.01  Aligned_cols=72  Identities=24%  Similarity=0.414  Sum_probs=67.0

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ..++++|+||.+.+|+||||+|++|++|+++|||+|+|.+  .+++..+|.|+|+|++++|.+|+.+|.+++.+
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  34567889999999999999999999999987

>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=99.37  E-value=3.3e-13  Score=110.92  Aligned_cols=73  Identities=18%  Similarity=0.311  Sum_probs=65.8

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .++++|+||.+.+|+||||+|++|++|+++|||+|+|.+. ...++..+|.|+|+|++++|.+|+.+|.+++.+
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            4678999999999999999999999999999999999875 234567899999999999999999999999864

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

Probab=99.36  E-value=1.5e-12  Score=109.46  Aligned_cols=74  Identities=22%  Similarity=0.368  Sum_probs=65.5

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ...+.+|.||.+++|+||||+|++||+|+++|||+|.|.+....   ....+|.|+|+|+++++++|+.+|.+++++
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            45788999999999999999999999999999999999874321   246789999999999999999999998864

>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=99.35  E-value=1.5e-12  Score=111.51  Aligned_cols=76  Identities=18%  Similarity=0.344  Sum_probs=67.6

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...++.+|.||.+++|+||||+|++||+|+++|||+|+|.+....   ...++|.|+|+|++++|++|+.+|.++|++.
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   1346899999999999999999999999864

>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=99.33  E-value=6.5e-13  Score=112.68  Aligned_cols=74  Identities=23%  Similarity=0.403  Sum_probs=68.1

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ...++.+|+||.+.+|.||||+|++|++|+++|||+|+|.+  .++...+|.|+|+|++++|.+|+.+|.+++.+.
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 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE--PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   84 (89)
T ss_dssp             CCEEEEEEEEEHHHHHHHHCGGGHHHHHHHHHTCCEEEECS--CCSSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEChhhcceeECCCCHhHHHHHHHhCCeEEecC--CCCCCCccEEEEEcCHHHHHHHHHHHHHHHHhh
Confidence            44789999999999999999999999999999999999987  345678999999999999999999999999873

>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=113.96  Aligned_cols=72  Identities=14%  Similarity=0.230  Sum_probs=64.4

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      .+.+|.||.+++++||||+|++||+|+++|||+|+|.+...     ...+|.|+|+|++++|++|+.+|.+++++.-
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~~~-----~~~er~V~I~G~~e~v~~A~~~I~~ii~~~~   82 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG-----TGPEKIAHIMGPPDRCEHAARIINDLLQSLR   82 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSSCS-----SSSEEEEEEESSHHHHHHHHHHHHHHHHHHC
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecCCC-----CCceeEEEEEeCHHHHHHHHHHHHHHHhccc
Confidence            47899999999999999999999999999999999986432     3568999999999999999999999998753

>1tua_A Hypothetical protein APE0754; structural genomics, protein structure initiative, MCSG, four layers alpha-beta sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1 d.51.1.1

Probab=99.33  E-value=1.2e-12  Score=125.78  Aligned_cols=145  Identities=15%  Similarity=0.151  Sum_probs=100.3

Q ss_pred             EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHH
Q 007293           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV  105 (609)
Q Consensus        26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al  105 (609)
                      .++++||.+.+|.|||++|++++.|++++||+|+++.     .++.++|.......+.            ..+..|.+.+
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            3689999999999999999999999999999999963     4677888732211000            0022344433


Q ss_pred             HHHHHHHhhhhhccCCCCCCCCceEEEEE-ee----------cceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCC
Q 007293          106 IRVFERMWEVEAEVEGDGDGDDVAYCGLL-AN----------TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAID  174 (609)
Q Consensus       106 ~~v~~~i~~~~~~~~~~~~~~~~vt~rll-VP----------~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~  174 (609)
                      ..+..- ...+...   .-..+.+.+.++ ++          ....|+||||+|.+|+.|+..|||+|.|.         
T Consensus        68 ~ai~rg-f~~e~A~---~Ll~Dd~~~e~i~i~~~~~~~~~~~~r~~GrIIGk~G~tik~iE~~Tg~~I~v~---------  134 (191)
T 1tua_A           68 KAISLG-FPPEKAF---RLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVG---------  134 (191)
T ss_dssp             HHHHHT-CCHHHHG---GGGSTTEEEEEEETHHHHTTCHHHHHHHHHHHHCGGGHHHHHHHHHHTCEEEEC---------
T ss_pred             HHHHcC-CCHHHhh---hcccCcceeEEEEcccccccCchhHHHHhhheeCCCccHHHHHHHHHCceEEEc---------
Confidence            322211 0000000   000013334332 33          24689999999999999999999999994         


Q ss_pred             CceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          175 DQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       175 dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ++.|.|.|+++++..|...|.+++..
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

>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=99.31  E-value=8.1e-13  Score=111.57  Aligned_cols=74  Identities=18%  Similarity=0.294  Sum_probs=67.1

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .++++|+||.+.+|+||||+|++|++|+++|||+|.|.++ ...++..+|.|+|+|++++|.+|+.+|.+++.+.
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            3578999999999999999999999999999999999875 2346678999999999999999999999999763

>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=99.31  E-value=2.3e-12  Score=123.84  Aligned_cols=145  Identities=19%  Similarity=0.225  Sum_probs=102.9

Q ss_pred             EEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHhhhhhcccccC
Q 007293          276 LRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQG  355 (609)
Q Consensus       276 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~~i~e~~~~~g  355 (609)
                      +++.||.+.+|.|||++|++++.|++.+|++|+++.     .++.|+|..+....++ ..++.|...+.........+..
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-----ENSMVIVEPEAEGIPP-VNLMKAAEVVKAISLGFPPEKA   79 (191)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEET-----TTTEEEEEESSTTSCH-HHHHHHHHHHHHHHHTCCHHHH
T ss_pred             eEEECCHHHhhHHHhcCHhHHHHHHHHHCcEEEEEc-----CCCeEEEEeCCCCCCH-HHHHHHHHHHHHHHcCCCHHHh
Confidence            578999999999999999999999999999999973     3678888744211111 3445555555332221110000


Q ss_pred             CCCCCCCCCceEEEEEec----------cccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHH
Q 007293          356 FSSGENKGDAVAVSILVG----------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK  425 (609)
Q Consensus       356 ~~~g~~~~~~~t~~l~VP----------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~  425 (609)
                      .  ..-.+...-..+.++          ....|+|||++|.+|+.|++.|||+|.|..            +.|.|.|+++
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  000112223334444          246899999999999999999999999953            4899999999


Q ss_pred             HHHHHHHHHHHHhhh
Q 007293          426 NVQNALSEVVGRLRH  440 (609)
Q Consensus       426 ~V~~A~~~I~~~Lr~  440 (609)
                      +++.|+..|..++..
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

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

Probab=99.30  E-value=2.3e-12  Score=108.27  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=66.8

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ....+.+|.||.+.+|+||||+|++|++|+++|||+|.|..+...+...+|.|+|+|++++|.+|+.+|.+++.+
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            446789999999999999999999999999999999999885223456899999999999999999999998854

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

Probab=99.30  E-value=1.6e-12  Score=114.01  Aligned_cols=72  Identities=22%  Similarity=0.331  Sum_probs=65.0

Q ss_pred             EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      +++|+||.+++|+||||+|++||+|+++|||+|+|.++ .......+|+|+|+|+.++|.+|+.+|.+++.+.
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 2233457899999999999999999999999774

>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=99.30  E-value=1.6e-12  Score=110.91  Aligned_cols=74  Identities=22%  Similarity=0.390  Sum_probs=67.7

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ...++.+|+||.+.+|+||||+|++|++|+++|||+|+|..+  .++..+|.|+|+|++++|.+|+.+|.+++.+.
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  34567899999999999999999999999874

>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=99.29  E-value=4.2e-12  Score=110.85  Aligned_cols=77  Identities=19%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ....+.+|.||.+++|+||||+|++||+|+++|||+|+|.+..+.   ...+++.|+|+|++++|++|+.+|.+++++..
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            456899999999999999999999999999999999999874331   12358999999999999999999999998643

>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=99.29  E-value=4.3e-12  Score=108.82  Aligned_cols=75  Identities=15%  Similarity=0.243  Sum_probs=67.3

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ...++.+|.||.+++|.|||++|++|++|+++|||+|+|++..+      .+++.|+|+|++++|++|+++|...++++.
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            46789999999999999999999999999999999999976432      347899999999999999999999998875


Q ss_pred             c
Q 007293          443 K  443 (609)
Q Consensus       443 ~  443 (609)
                      -
T Consensus        88 ~   88 (95)
T 2ctm_A           88 A   88 (95)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.28  E-value=1.7e-12  Score=111.15  Aligned_cols=77  Identities=26%  Similarity=0.430  Sum_probs=68.3

Q ss_pred             CCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       125 ~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ....++.+|+||.+.+|+||||+|++||+|+++|||+|.|.++.......+|.|+|+|++++|.+|+.+|.+++.+.
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            45678999999999999999999999999999999999998852112457899999999999999999999999773

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.27  E-value=9.3e-12  Score=107.19  Aligned_cols=73  Identities=15%  Similarity=0.221  Sum_probs=65.0

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..++.+|.||.++++.|||++|++|++|+++|||+|+|++..+ |   ...++.|+|+|+.+++++|+.+|...+++
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-G---NQPQDQITITGYEKNTEAARDAILRIVGE   87 (97)
T ss_dssp             TTCEEEEECCTTTHHHHSCSSSCHHHHHHHHHTCEEECCCTTT-C---SSCSSEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             cceeEEEEECHHHhhhcCCCCchhHHHHHHHHCCEEEecCCCC-C---CCCccEEEEEeCHHHHHHHHHHHHHHHHH
Confidence            3479999999999999999999999999999999999987543 1   24679999999999999999999998875

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

Probab=99.26  E-value=5.5e-12  Score=102.29  Aligned_cols=68  Identities=19%  Similarity=0.298  Sum_probs=61.0

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L  438 (609)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++..       ..++.|+|+|+.++|++|+.+|...+
T Consensus         3 ~~~~~~i~I~~~~ig~iIG~gG~~I~~I~e~tg~~I~i~~~g-------~~~~~V~I~G~~~~v~~A~~~I~~i~   70 (71)
T 1vig_A            3 RMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-------EKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CCEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCCCC-------SSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             ceEEEEEEECHHHhhhhcCCCCccHHHHHHHHCCEEEECCCC-------CcccEEEEEcCHHHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999998632       35689999999999999999998753

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.24  E-value=8.9e-12  Score=106.72  Aligned_cols=73  Identities=15%  Similarity=0.211  Sum_probs=65.1

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ...++.+|.||.+++|.|||++|++||+|+++|||+|+|++.+       ..++.|+|+|++++|++|+.+|..++++..
T Consensus        14 ~~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~~-------~~~~~V~I~G~~e~v~~A~~~I~~i~~~~~   86 (94)
T 2cte_A           14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-------DPSNQIKITGTKEGIEKARHEVLLISAEQD   86 (94)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCTT-------SSCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCCC-------CCCCeEEEEECHHHHHHHHHHHHHHhhccc
Confidence            3568999999999999999999999999999999999997632       235799999999999999999999988753

>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=99.24  E-value=3.2e-12  Score=106.74  Aligned_cols=70  Identities=17%  Similarity=0.237  Sum_probs=63.5

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ...++.+|.||.+.+|+||||+|++||+|+++|||+|+|.+.     .++++|+|+|++++|++|+.+|.+++..
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            447899999999999999999999999999999999999752     2478999999999999999999998764

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

Probab=99.22  E-value=5.5e-12  Score=110.29  Aligned_cols=71  Identities=18%  Similarity=0.321  Sum_probs=64.3

Q ss_pred             eEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       129 vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .+++|+||.+.+++||||+|++||+|+++|||+|+|.++  .....+|.|+|+|++++|.+|+.+|.+++.+.
T Consensus        11 ~~~~i~Ip~~~iG~IIGkgG~~Ik~I~~~TGakI~I~~~--~~~~~er~V~I~G~~e~v~~A~~~I~~ii~~~   81 (106)
T 2hh3_A           11 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD--DGTGPEKIAHIMGPPDRCEHAARIINDLLQSL   81 (106)
T ss_dssp             -CEEEEEETTTHHHHHTTTTHHHHHHHHHHTCEEEECSS--CSSSSEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEECHHHcCccCCCCcHHHHHHHHHHCcEEEEecC--CCCCceeEEEEEeCHHHHHHHHHHHHHHHhcc
Confidence            468899999999999999999999999999999999874  34557899999999999999999999999873

>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=99.21  E-value=8.7e-12  Score=108.83  Aligned_cols=75  Identities=21%  Similarity=0.298  Sum_probs=66.2

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .+++.+|+||.+.+|+||||+|++|++|+++|||+|.|.+........++.|+|+|+.++|.+|+.+|.+++.+.
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            378899999999999999999999999999999999998741111236899999999999999999999999774

>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=99.15  E-value=4.2e-11  Score=104.39  Aligned_cols=71  Identities=21%  Similarity=0.285  Sum_probs=63.6

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...+.+|.||.+++|.|||++|++|++|+++|||+|+|++..       ...+.|+|+|+.++|++|+.+|...+++.
T Consensus        15 ap~~~~i~Ip~~~ig~IIG~gG~~Ir~I~eetg~~I~I~~~g-------~~~~~V~I~G~~e~v~~A~~~I~~i~~e~   85 (104)
T 2ctk_A           15 VPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-------LQSDIIAITGLAANLDRAKAGLLERVKEL   85 (104)
T ss_dssp             SCEEEEEECCHHHHHHHHCSSSHHHHHHHHHTCCEEECCCTT-------TTCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEEEChHHccceeCCCchHHHHHHHHHCCEEEecCCC-------CCcceEEEEcCHHHHHHHHHHHHHHHhhH
Confidence            458999999999999999999999999999999999998632       23469999999999999999999988764

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

Probab=99.11  E-value=3.6e-11  Score=97.44  Aligned_cols=67  Identities=19%  Similarity=0.318  Sum_probs=60.7

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      ..+..|.||...+|.|||++|++|++|+++|||+|.|.++    +..+|.|+|+|..++|.+|+.+|.+++
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    336789999999999999999998764

>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=99.11  E-value=6.5e-11  Score=101.90  Aligned_cols=72  Identities=17%  Similarity=0.178  Sum_probs=64.8

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+++.|.||...++.||||+|++|++|+++|||+|+|.++ ..+...++.|+|+|..+++.+|+.+|..++.+
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

>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=99.10  E-value=4.4e-11  Score=102.36  Aligned_cols=71  Identities=21%  Similarity=0.269  Sum_probs=64.4

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ..++.+|.||...+|.|||++|++|++|+++|||+|+|.+.    ...++.|+|+|..++|.+|+.+|.+++.+.
T Consensus        15 ~~~t~~i~Ip~~~ig~IIG~gG~~Ik~I~~etg~~I~i~~~----~~~~~~V~I~G~~e~v~~A~~~I~~i~~~~   85 (94)
T 2cte_A           15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP----DDPSNQIKITGTKEGIEKARHEVLLISAEQ   85 (94)
T ss_dssp             SCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCCT----TSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEChHHeeeeECCCChhHHHHHHHHCCEEEeCCC----CCCCCeEEEEECHHHHHHHHHHHHHHhhcc
Confidence            47899999999999999999999999999999999999762    234689999999999999999999999774

>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=99.07  E-value=1e-10  Score=100.23  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=65.3

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ...++..|.||...++.|||++|++|++|+++|||+|+|..+   ....++.|+|+|..++|.+|+.+|..++.+.
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            447899999999999999999999999999999999999663   2235789999999999999999999999774

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=99.04  E-value=2.1e-10  Score=98.17  Aligned_cols=72  Identities=14%  Similarity=0.240  Sum_probs=64.9

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhh-CCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT-GTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T-Ga~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      .+.++.+|.||.++++.|||++|++||+|+++| ||+|.|++.       +...+.|+|+|+.++|++|+.+|...+.+.
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            467899999999999999999999999999999 999999762       234678999999999999999999988864

>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=7.7e-10  Score=95.98  Aligned_cols=68  Identities=12%  Similarity=0.193  Sum_probs=61.3

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHh-hCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..++.+|.||.++|++|||++|++||+|+++ ++++|+|++          +++.|+|+|+++.|.+|+.+|...+++.
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            3489999999999999999999999999996 599999875          2578999999999999999999988764

>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=98.97  E-value=3.1e-10  Score=98.83  Aligned_cols=69  Identities=17%  Similarity=0.240  Sum_probs=62.8

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      +++..|.||...++.|||++|++|++|+++|||+|.|.+.    +...+.|+|+|..++|.+|+.+|..++.+
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

>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=98.81  E-value=2.4e-09  Score=91.58  Aligned_cols=72  Identities=17%  Similarity=0.183  Sum_probs=64.9

Q ss_pred             CCCceEEEEEeecceeeeeeecCcchhhhccccc-CcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIES-GAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       125 ~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eS-Ga~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .++.++..|.||..+++.|||++|++|++|+++| ||+|.|..+    +...+.|+|.|..++|.+|+.+|.+++.+
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 999999663    44567899999999999999999999976

>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=98.79  E-value=4.2e-09  Score=91.34  Aligned_cols=67  Identities=18%  Similarity=0.274  Sum_probs=60.9

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccc-cCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIE-SGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e-SGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .++.+|.||..+++.|||++|++|++|+++ ++++|.+..       .++.|+|+|+++.|.+|..+|..++.+.
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 599999844       4679999999999999999999999763

>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=98.78  E-value=2.7e-09  Score=89.94  Aligned_cols=73  Identities=19%  Similarity=0.192  Sum_probs=63.3

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCe-EEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHhhh
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr~  440 (609)
                      ...+..+|.||.+++|.+||++|++|++|++.|||+ |.|.+          ++..|+|.| +.+++++|+.+|...-..
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            356899999999999999999999999999999998 99953          358899999 899999999999885555


Q ss_pred             cccCc
Q 007293          441 NLKSG  445 (609)
Q Consensus       441 ~~~~~  445 (609)
                      +.+++
T Consensus        82 ~~vp~   86 (91)
T 2cpq_A           82 IQVPS   86 (91)
T ss_dssp             CCCCS
T ss_pred             EecCh
Confidence            55554

>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=98.50  E-value=6.1e-08  Score=81.68  Aligned_cols=66  Identities=23%  Similarity=0.253  Sum_probs=58.2

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcE-EEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHHHH
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCL  198 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~-I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~~L  198 (609)
                      ...+...|.||.+.+|.+||++|++|++|+++|||+ |.|..       ++..|+|.| +.+++.+|+.+|..+-
T Consensus        12 ~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e~tGv~~IdI~e-------ddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           12 AAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDE-------DTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             SCSEEEEEECCHHHHHHHHTTTTHHHHHHHTSTTEEEEEEET-------TTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             cCceEEEEEEChHHhhhhcCCCcHHHHHHHHHhCCeEEEEEc-------CCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            346888999999999999999999999999999998 99954       458999999 7999999998875544

>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=98.45  E-value=3.5e-07  Score=82.65  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=63.3

Q ss_pred             CceEEEEEeccc------cccccccCCCchhHHHHHhhCCeEEecCCCcc-----------cccCCCCCcEEEEcC-CHH
Q 007293          364 DAVAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGCAAQNDVVIQISG-EYK  425 (609)
Q Consensus       364 ~~~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~-----------P~~~~~~er~V~I~G-~~~  425 (609)
                      ..++.+|.||.+      ++|.|||++|.+||+|+++|||+|.|....-.           +.....++-.|.|++ +.+
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            347899999988      88999999999999999999999999763210           001123467888999 588


Q ss_pred             HHHHHHHHHHHHhhhcc
Q 007293          426 NVQNALSEVVGRLRHNL  442 (609)
Q Consensus       426 ~V~~A~~~I~~~Lr~~~  442 (609)
                      .+++|+.+|...|.+.+
T Consensus        85 ~~~~A~~~I~~ll~~~~  101 (131)
T 1k1g_A           85 NVKKAVEQIRNILKQGI  101 (131)
T ss_dssp             HHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHhccC
Confidence            99999999999998754

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

Probab=98.31  E-value=1.9e-06  Score=76.36  Aligned_cols=77  Identities=22%  Similarity=0.216  Sum_probs=58.4

Q ss_pred             CceEEEEEeccc-------cccccccCCCchhHHHHHhhCCeEEecCCCcc---c--ccCCCCCcEEEEcC-CHHHHHHH
Q 007293          364 DAVAVSILVGAD-------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV---L--GCAAQNDVVIQISG-EYKNVQNA  430 (609)
Q Consensus       364 ~~~t~~l~VP~~-------~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~---P--~~~~~~er~V~I~G-~~~~V~~A  430 (609)
                      ...+.+|.||-+       ++|.|||++|.+||+|+++|||+|.|..+...   +  .....++-.|.|++ +.+++++|
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            357888888765       88999999999999999999999999643110   0  00112345677775 58999999


Q ss_pred             HHHHHHHhhh
Q 007293          431 LSEVVGRLRH  440 (609)
Q Consensus       431 ~~~I~~~Lr~  440 (609)
                      +.+|...|.+
T Consensus        90 ~~~Ie~Ll~~   99 (119)
T 2yqr_A           90 KKLCENLLQT   99 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHhhc
Confidence            9999998885

>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=98.28  E-value=6.4e-07  Score=80.96  Aligned_cols=73  Identities=18%  Similarity=0.215  Sum_probs=61.4

Q ss_pred             ceEEEEEeecc------eeeeeeecCcchhhhcccccCcEEEecCCC--------------CCCCCCCceEEEecc-HHH
Q 007293          128 VAYCGLLANTT------KIGVVVGKGGRNVTRMRIESGAKIVMLPPP--------------ACAAIDDQLIQITGA-TLA  186 (609)
Q Consensus       128 ~vt~rllVP~~------~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p--------------~~~~~~dR~V~I~G~-~e~  186 (609)
                      .++.++.||..      .+|.|||++|.+||+|+++|||+|.|..+.              ......+-.|.|++. .++
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      788999999999999999999999997630              001123668889995 999


Q ss_pred             HHHHHHHHHHHHhc
Q 007293          187 VKKALVAVTTCLQH  200 (609)
Q Consensus       187 V~~A~~~I~~~L~e  200 (609)
                      +.+|+.+|.++|.+
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=98.20  E-value=1.4e-06  Score=77.23  Aligned_cols=73  Identities=21%  Similarity=0.189  Sum_probs=58.5

Q ss_pred             ceEEEEEeecc-------eeeeeeecCcchhhhcccccCcEEEecCCC--------CCCCCCCceEEEecc-HHHHHHHH
Q 007293          128 VAYCGLLANTT-------KIGVVVGKGGRNVTRMRIESGAKIVMLPPP--------ACAAIDDQLIQITGA-TLAVKKAL  191 (609)
Q Consensus       128 ~vt~rllVP~~-------~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p--------~~~~~~dR~V~I~G~-~e~V~~A~  191 (609)
                      .++.+|.||-.       .+|.|||++|.+||+|+++|||+|.|..+.        ......+-.|.|.+. .+++.+|+
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            57888988875       788999999999999999999999997420        001123456778765 99999999


Q ss_pred             HHHHHHHhc
Q 007293          192 VAVTTCLQH  200 (609)
Q Consensus       192 ~~I~~~L~e  200 (609)
                      .+|.++|.+
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=97.93  E-value=8.9e-06  Score=73.96  Aligned_cols=74  Identities=23%  Similarity=0.324  Sum_probs=55.7

Q ss_pred             eEEEEEeccc------cccccccCCCchhHHHHHhhCCeEEecCCCcc------------cccC-CCCCcEEEEcCC-HH
Q 007293          366 VAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV------------LGCA-AQNDVVIQISGE-YK  425 (609)
Q Consensus       366 ~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~------------P~~~-~~~er~V~I~G~-~~  425 (609)
                      ++.+|.||.+      ++|.|||++|.++|+|+++|||+|.|-.+.-.            |.+. ..+.--|.|++. ++
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            5678888854      49999999999999999999999999864421            1111 123347888884 32


Q ss_pred             -----HHHHHHHHHHHHhh
Q 007293          426 -----NVQNALSEVVGRLR  439 (609)
Q Consensus       426 -----~V~~A~~~I~~~Lr  439 (609)
                           .+++|+.+|...|.
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                 79999999999886

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

Probab=97.83  E-value=7.7e-06  Score=74.39  Aligned_cols=72  Identities=22%  Similarity=0.290  Sum_probs=56.3

Q ss_pred             eEEEEEeecce------eeeeeecCcchhhhcccccCcEEEecCCCCC----------------CCCCCceEEEecc-H-
Q 007293          129 AYCGLLANTTK------IGVVVGKGGRNVTRMRIESGAKIVMLPPPAC----------------AAIDDQLIQITGA-T-  184 (609)
Q Consensus       129 vt~rllVP~~~------vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~----------------~~~~dR~V~I~G~-~-  184 (609)
                      ++.++.||-+.      +|.|||++|.++|+|+++|||+|.|..+...                ....+=-|.|++. . 
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            56788999766      8999999999999999999999999875110                0112237788885 3 


Q ss_pred             ----HHHHHHHHHHHHHHhc
Q 007293          185 ----LAVKKALVAVTTCLQH  200 (609)
Q Consensus       185 ----e~V~~A~~~I~~~L~e  200 (609)
                          ..+.+|+.+|..+|..
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                3799999999999964

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

Probab=97.66  E-value=4.6e-05  Score=85.69  Aligned_cols=91  Identities=11%  Similarity=0.099  Sum_probs=65.9

Q ss_pred             hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCC
Q 007293          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~  414 (609)
                      .+.++...|++.+.+..... .. ...........+.||.+++|.|||+||++||+|+++|||+|.|.+           
T Consensus       538 ~A~~g~~~I~~~m~~al~~~-~~-~~~~~ap~~~~~~I~~~kI~~vIG~gG~~Ik~I~e~tg~~I~I~d-----------  604 (630)
T 3u1k_A          538 QASVAKKEILQIMNKTISKP-RA-SRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVD-----------  604 (630)
T ss_dssp             HHHHHHHHHHHHHHHHCSSC-CS-SCCTTCCEEEEEECCHHHHHHHHCGGGHHHHHHHHHHCCEEEECS-----------
T ss_pred             HHHHHHHHHHHHHHHHHHHH-Hh-hhcccCCeEEEEEeChhHhheeECCCChhHHHHHHHHCCEEEEcC-----------
Confidence            34455556666554432111 10 112234578899999999999999999999999999999999953           


Q ss_pred             CcEEEEcCC-HHHHHHHHHHHHHHh
Q 007293          415 DVVIQISGE-YKNVQNALSEVVGRL  438 (609)
Q Consensus       415 er~V~I~G~-~~~V~~A~~~I~~~L  438 (609)
                      +-.|.|.|+ .+.+++|+.+|.+++
T Consensus       605 ~G~V~I~~~~~~~~~~A~~~I~~i~  629 (630)
T 3u1k_A          605 EETFSVFAPTPSAMHEARDFITEIC  629 (630)
T ss_dssp             SSEEEEEESSHHHHHHHHHHTTC--
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHHh
Confidence            467999987 678999999987654

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

Probab=97.56  E-value=4.3e-05  Score=85.94  Aligned_cols=92  Identities=15%  Similarity=0.192  Sum_probs=67.7

Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V  178 (609)
                      ..|.++...++..+.+...+.......-.+....+-||.+.++.|||+||++||+|+++|||+|.|..        +..|
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            45666666666655443322211112233567788999999999999999999999999999999954        4689


Q ss_pred             EEecc-HHHHHHHHHHHHHHH
Q 007293          179 QITGA-TLAVKKALVAVTTCL  198 (609)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L  198 (609)
                      .|.|. .+++.+|+.+|..++
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            99987 789999999987664

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

Probab=97.54  E-value=0.00018  Score=64.18  Aligned_cols=67  Identities=12%  Similarity=0.069  Sum_probs=59.7

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhh
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR  439 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr  439 (609)
                      ...|.|.++.++.|+|++|+.|+.|+..|+|.|+|..-+.      ++...|+|.|++..-..|+.+|.....
T Consensus        57 PlVF~vE~~lve~IFGp~Gs~Ip~IE~~SqTLIqV~~~~s------~g~tEVtIfG~~~~Q~rak~MI~sLA~  123 (140)
T 3v69_A           57 PKRLYVEPRLLEIMFGKDGEHIPHLESMLHTLIHVNVWGP------ERRAEIWIFGPPPFRRDVDRMLTDLAH  123 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECCCT------TSCEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEeccCC------CCcEEEEEECCHHHHHHHHHHHHHHHH
Confidence            4578899999999999999999999999999999987432      467899999999999999999987654

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

Probab=97.45  E-value=3.6e-05  Score=70.37  Aligned_cols=103  Identities=17%  Similarity=0.234  Sum_probs=71.8

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcch-hhhhhhccccccccCCCcchHHH
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQE  103 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e~-~~~~~~~~~~~~~e~~~~~~A~~  103 (609)
                      -.+.++|+...+|+.||++|+.|+.|+++.|-+|+|-....+           ++. +.++             ++||. 
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            356788999999999999999999999999999988443111           111 0000             11110 


Q ss_pred             HHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEec
Q 007293          104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML  165 (609)
Q Consensus       104 Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~  165 (609)
                              +.......    . ++...+.+.||..+.+..|||+|.+++...+-||.+|.|.
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=96.99  E-value=0.00065  Score=60.69  Aligned_cols=68  Identities=13%  Similarity=0.042  Sum_probs=59.8

Q ss_pred             EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+.+.|.+..++.|+|++|+.|+.|+..|++.|++...   ..+..--|+|.|++..=.+|+.+|..+..-
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---GPERRAEIWIFGPPPFRRDVDRMLTDLAHY  124 (140)
T ss_dssp             CEEEEECGGGHHHHHCGGGTTHHHHHHHHTSEEEEECC---CTTSCEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEehhhhhcccCCCcCccchHHhhcceeEEEecc---CCCCcEEEEEECCHHHHHHHHHHHHHHHHH
Confidence            35688899999999999999999999999999999884   223567799999999999999999988854

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

Probab=96.87  E-value=0.00061  Score=77.53  Aligned_cols=95  Identities=13%  Similarity=0.156  Sum_probs=23.2

Q ss_pred             hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCC
Q 007293          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~  414 (609)
                      .+.++...|++.+.+... .... ..........++.||.++++.|||+||.+||+|+++|||+|.|.+           
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 QAKEGRAHILGEMNKAMD-APRA-DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND-----------  607 (726)
T ss_dssp             HHHHHHHHHHHHHHTTCS-SCCS-SCCSSCCC------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHH-hhhh-hhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC-----------
Confidence            344555666666544321 1110 112233457789999999999999999999999999999998853           


Q ss_pred             CcEEEEcCC-HHHHHHHHHHHHHHhhhcc
Q 007293          415 DVVIQISGE-YKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       415 er~V~I~G~-~~~V~~A~~~I~~~Lr~~~  442 (609)
                      +..|.|.+. .+++++|+.+|...+.+.-
T Consensus       608 dG~v~I~~~~~~~~~~A~~~i~~i~~~~~  636 (726)
T 4aid_A          608 DGVVKVSASDGAKIKAAIDWIKSITDEAE  636 (726)
T ss_dssp             ------CCSCHHHHHHHHHC---------
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhhhhc
Confidence            455777776 7889999999998876543

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

Probab=96.76  E-value=0.00063  Score=77.47  Aligned_cols=95  Identities=17%  Similarity=0.246  Sum_probs=24.9

Q ss_pred             cchHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCce
Q 007293           98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL  177 (609)
Q Consensus        98 ~~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~  177 (609)
                      +..|.++...++..+.+.............+....+-||.+.++.|||+||.+||+|.++||++|.|..        +..
T Consensus       539 L~~A~~g~~~I~~~m~~al~~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~d--------dG~  610 (726)
T 4aid_A          539 LAQAKEGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIND--------DGV  610 (726)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSSCCSSCCSSCCC------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhcccCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEEC--------Cce
Confidence            345556666666655443322111111222445678899999999999999999999999999999954        456


Q ss_pred             EEEecc-HHHHHHHHHHHHHHHhc
Q 007293          178 IQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       178 V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      |.|.+. .+++.+|+.+|..++.+
T Consensus       611 v~I~~~~~~~~~~A~~~i~~i~~~  634 (726)
T 4aid_A          611 VKVSASDGAKIKAAIDWIKSITDE  634 (726)
T ss_dssp             ---CCSCHHHHHHHHHC-------
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhhh
Confidence            777776 99999999999988864

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

Probab=96.69  E-value=0.00077  Score=61.57  Aligned_cols=103  Identities=20%  Similarity=0.210  Sum_probs=72.8

Q ss_pred             eEEEEEecccccccccccccchhhhhhhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHH--hhhhhcc
Q 007293          274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVE  351 (609)
Q Consensus       274 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~--~~i~e~~  351 (609)
                      ..+.+.|+...+|..||++|++|+.|+++.|-+|.+-....+                   +. .-+...+  .++....
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            367788999999999999999999999999999877643211                   10 1111110  0111110


Q ss_pred             cccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecC
Q 007293          352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG  403 (609)
Q Consensus       352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~  403 (609)
                      ..       ..+......+.||.++.+..|||+|++++...+-||.+|.|.+
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       0023467889999999999999999999999999999987753

>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=95.51  E-value=0.0037  Score=61.97  Aligned_cols=96  Identities=13%  Similarity=0.077  Sum_probs=63.2

Q ss_pred             CcccceecCCChHHHHH-HHHhCceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSI-RRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~I-reeTga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+-||++|++|+.| ++-.|-+|+|-....+           ++.                          .+...+
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-----------p~~--------------------------fi~nal  168 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-----------PAR--------------------------FVANAL  168 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-----------HHH--------------------------HHHHHT
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC-----------HHH--------------------------HHHhcc
Confidence            45899999999999999 5666888887433211           100                          111111


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                      .......- .-.......+.+.||..+.+.-|||+|.+|+.-..-||.+|.|...
T Consensus       169 sPA~V~~V-~i~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  222 (251)
T 2asb_A          169 SPAKVVSV-SVIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  222 (251)
T ss_dssp             TTSCCSEE-EEEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEES
T ss_pred             CCcceEEE-EEEcCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEH
Confidence            10000000 0000012468899999999999999999999999999999999764

>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=95.33  E-value=0.0048  Score=64.51  Aligned_cols=96  Identities=13%  Similarity=0.081  Sum_probs=64.9

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||++|++|+.|.++. |-+|+|-....+           +                      +    ..+...+
T Consensus       249 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-----------p----------------------~----~fi~nal  291 (366)
T 1k0r_A          249 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-----------P----------------------A----RFVANAL  291 (366)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-----------H----------------------H----HHHHHHT
T ss_pred             CCcccccCCcchHHHHHHHHhCCCeEEEEEcCCC-----------H----------------------H----HHHHHhc
Confidence            568999999999999999999 888887432111           0                      0    0011111


Q ss_pred             hhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC
Q 007293          113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP  167 (609)
Q Consensus       113 ~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~  167 (609)
                      .......-. ........+.+.||..+.+..|||+|.+++....-||.+|.|...
T Consensus       292 sPA~V~~V~-~~~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~  345 (366)
T 1k0r_A          292 SPAKVVSVS-VIDQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGD  345 (366)
T ss_dssp             TTSCCSEEE-EEETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHCCEEEEEES
T ss_pred             CCcceeEEE-EEcCCCcEEEEEEChHHhhhccCCCcHHHHHHHHHHCCeeeeeEH
Confidence            100000000 000014578899999999999999999999999999999999764

>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=93.90  E-value=0.057  Score=53.46  Aligned_cols=96  Identities=20%  Similarity=0.194  Sum_probs=65.4

Q ss_pred             cccccccccccchhhhh-hhccCeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHHh--hhhhcccccCCCCC
Q 007293          283 WTASGIIGKRGAIVRSL-QNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEGQQGFSSG  359 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I-~~~tGa~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~~--~i~e~~~~~g~~~g  359 (609)
                      +-+|.-||++|.+|+.| ++-.|-+|.|-...++                   ++ .-+...+.  ++......      
T Consensus       126 DpvGacIG~~G~rI~~i~~eL~gekIDIi~~s~d-------------------p~-~fi~nalsPA~V~~V~i~------  179 (251)
T 2asb_A          126 NAKGACIGPMGQRVRNVMSELSGEKIDIIDYDDD-------------------PA-RFVANALSPAKVVSVSVI------  179 (251)
T ss_dssp             CHHHHHHCGGGHHHHHHHHHTTTCEEEEEECCSS-------------------HH-HHHHHHTTTSCCSEEEEE------
T ss_pred             CHHHHHhCCCchHHHHHHHHhCCCeEEEEEecCC-------------------HH-HHHHhccCCcceEEEEEE------
Confidence            45799999999999999 6777888877643211                   11 11111110  11100000      


Q ss_pred             CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (609)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~  406 (609)
                        .....+..+.||.++.+.-|||+|++|+.-.+-||.+|.|.+..+
T Consensus       180 --~~~~~~a~V~V~~~qlslAIGk~GqNvrLA~~Ltg~~idI~~~~~  224 (251)
T 2asb_A          180 --DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDAP  224 (251)
T ss_dssp             --ETTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESSC
T ss_pred             --cCCCcEEEEEEChHHhhhhhcCCcCcHHHHHHHHCCEecceEHHH
Confidence              011247899999999999999999999999999999999987554

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=93.39  E-value=0.025  Score=58.81  Aligned_cols=94  Identities=19%  Similarity=0.221  Sum_probs=63.2

Q ss_pred             CcccceecCCChHHHHHHHHh-CceEEEcCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcchHHHHHHHHHHHH
Q 007293           34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM  112 (609)
Q Consensus        34 ~~vG~IIGk~G~~Ik~IreeT-ga~I~V~~~~~g~~eRvI~I~G~~e~~~~~~~~~~~~~~e~~~~~~A~~Al~~v~~~i  112 (609)
                      +-+|+.||.+|+.|+.+.++. |-+|.|-....+           +                      +    ..+...+
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~d-----------~----------------------~----~fi~nal  287 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDD-----------P----------------------K----QLIANAL  287 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSS-----------H----------------------H----HHHHHHT
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCCC-----------H----------------------H----HHHHHhc
Confidence            468999999999999999998 777776332111           0                      0    0111111


Q ss_pred             hhhhhccCCCCC-CCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecC
Q 007293          113 WEVEAEVEGDGD-GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP  166 (609)
Q Consensus       113 ~~~~~~~~~~~~-~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~  166 (609)
                      ......  ...- ......+.+.||..+.+.-|||+|.+++.-..-||.+|.|..
T Consensus       288 ~Pa~v~--~v~~~d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s  340 (344)
T 1hh2_P          288 APATVI--EVEILDKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP  340 (344)
T ss_dssp             CSSCCS--EEEEEETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEE
T ss_pred             CccEEE--EEEEEcCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceee
Confidence            000000  0000 011457889999999999999999999999999999999865

>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=93.10  E-value=0.083  Score=55.17  Aligned_cols=96  Identities=20%  Similarity=0.180  Sum_probs=66.0

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHH--hhhhhcccccCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG  359 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~--~~i~e~~~~~g~~~g  359 (609)
                      +-+|..||++|.+|+.|.++. |-+|.|-....+                   ++ .-+...+  .++.....       
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 777776532111                   11 1111111  01110000       


Q ss_pred             CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCc
Q 007293          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ  406 (609)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~  406 (609)
                       .........+.||.++.+..|||+|.+++...+-||.+|.|....+
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             0012357899999999999999999999999999999999987544

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

Probab=93.06  E-value=0.03  Score=63.95  Aligned_cols=93  Identities=20%  Similarity=0.242  Sum_probs=9.2

Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V  178 (609)
                      ..|.++...++..+.+........-..-.+....+-||.+.++.+||++|.+|+.|.+++|+.|.|..        +..|
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            34555555555554443222111111122445667889999999999999999999999999998843        4567


Q ss_pred             EEecc-HHHHHHHHHHHHHHHh
Q 007293          179 QITGA-TLAVKKALVAVTTCLQ  199 (609)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L~  199 (609)
                      .|.+. .+.+.+|..+|..++.
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 6778888877776654

>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=92.98  E-value=0.023  Score=65.20  Aligned_cols=91  Identities=19%  Similarity=0.245  Sum_probs=33.4

Q ss_pred             chHHHHHHHHHHHHhhhhhccCCCCCCCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceE
Q 007293           99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI  178 (609)
Q Consensus        99 ~~A~~Al~~v~~~i~~~~~~~~~~~~~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V  178 (609)
                      ..|.++...++..+.+..... .....-.+....+-||.+.++.+||++|.+||+|.+++|+.|.|..        +..|
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            445556666665554433222 1111122334457789999999999999999999999999998843        4667


Q ss_pred             EEecc-HHHHHHHHHHHHHHH
Q 007293          179 QITGA-TLAVKKALVAVTTCL  198 (609)
Q Consensus       179 ~I~G~-~e~V~~A~~~I~~~L  198 (609)
                      .|+.. .+...+|...|..+.
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            77765 777777776666554

>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=92.46  E-value=0.019  Score=65.77  Aligned_cols=89  Identities=15%  Similarity=0.246  Sum_probs=32.0

Q ss_pred             hHHHHHHHHHhhhhhcccccCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCC
Q 007293          335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN  414 (609)
Q Consensus       335 ~a~~A~~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~  414 (609)
                      .+.++...|++.+.+.....   ............+.||.+++|.+||++|.+||+|++.+|+.|.|..           
T Consensus       570 ~A~~~~~~I~~~m~~al~~~---~~~~~~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-----------  635 (757)
T 1e3p_A          570 QARDARLHILDVMMEAIDTP---DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-----------  635 (757)
T ss_dssp             HHHHHHHHHHHHHHHHCSSC---CCCCTTSCBCCCC------------------CTTCCCCCSCC---------------
T ss_pred             HHHHHHHHHHHHHHHHhccc---ccccccCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-----------
Confidence            34455555665554432211   1111223445678899999999999999999999999999998853           


Q ss_pred             CcEEEEcCC-HHHHHHHHHHHHHH
Q 007293          415 DVVIQISGE-YKNVQNALSEVVGR  437 (609)
Q Consensus       415 er~V~I~G~-~~~V~~A~~~I~~~  437 (609)
                      +..|.|+.. .+..++|+..|...
T Consensus       636 dG~v~Is~~~~~~~~~a~~~i~~i  659 (757)
T 1e3p_A          636 DGTIYIGAADGPAAEAARATINGI  659 (757)
T ss_dssp             ----CCCBSSHHHHCC--------
T ss_pred             CceEEEecCCHHHHHHHHHHHHHh
Confidence            355777665 55666776666553

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

Probab=91.65  E-value=0.057  Score=61.66  Aligned_cols=66  Identities=18%  Similarity=0.296  Sum_probs=0.0

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~~~Lr~  440 (609)
                      ......+.||.++++.+||++|.+|+.|.++||+.|.|..           +..|.|.+. .+.+++|+..|...+.+
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            3456788999999999999999999999999999997743           355667665 55777888877665543

>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=89.57  E-value=0.068  Score=55.59  Aligned_cols=94  Identities=18%  Similarity=0.185  Sum_probs=63.4

Q ss_pred             cccccccccccchhhhhhhcc-CeeEEEecCCCCCCccEEEEcccccccCCCChHHHHHHHHH--hhhhhcccccCCCCC
Q 007293          283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSSG  359 (609)
Q Consensus       283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~s~er~vtIsG~e~p~~~~~~a~~A~~~i~--~~i~e~~~~~g~~~g  359 (609)
                      +-+|..||.+|.+|+.+.++. |-+|.+-.-.+                   .++ .-+...+  .++....+.      
T Consensus       245 DpvGacvg~~G~ri~~i~~el~ge~Idii~~s~-------------------d~~-~fi~nal~Pa~v~~v~~~------  298 (344)
T 1hh2_P          245 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSD-------------------DPK-QLIANALAPATVIEVEIL------  298 (344)
T ss_dssp             CHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCS-------------------SHH-HHHHHHTCSSCCSEEEEE------
T ss_pred             cccceeeccCCcEeHHHHHHhCCCeeeEEecCC-------------------CHH-HHHHHhcCccEEEEEEEE------
Confidence            457999999999999999887 66666543211                   111 1111110  011111000      


Q ss_pred             CCCCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCC
Q 007293          360 ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG  404 (609)
Q Consensus       360 ~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~  404 (609)
                        .....+..+.||.++.+.-|||+|.+++.-.+-||.+|.|...
T Consensus       299 --d~~~~~~~v~v~~~~~s~AIGk~G~Nvrla~~Ltg~~idi~s~  341 (344)
T 1hh2_P          299 --DKENKAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPI  341 (344)
T ss_dssp             --ETTTTEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEEC
T ss_pred             --cCCCCEEEEEEChHHcchhhcCCCccHHHHHHHHCCEeceeec
Confidence              0123478999999999999999999999999999999999753

---

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	609
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	7e-07
d1wvna1	70	d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {Huma	2e-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	6e-09
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-07
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	3e-05
d1x4na1	79	d.51.1.1 (A:8-86) Far upstream binding element, FB	1e-04
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-08
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	1e-07
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	2e-05
d2axya1	71	d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Hum	3e-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	2e-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	3e-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	3e-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	5e-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	4e-05
d1zzka1	75	d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapie	9e-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,	1e-06
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	3e-06
d1dtja_	74	d.51.1.1 (A:) Neuro-oncological ventral antigen 2,	0.003
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,	5e-07
d1j4wa2	71	d.51.1.1 (A:104-174) Far upstream binding element,	8e-05
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	1e-05
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	3e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	7e-05
d2ctea1	81	d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [T	0.002
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	4e-05
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	5e-04
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	0.001
d2ctka1	91	d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [T	0.002
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	2e-04
d1viga_	71	d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId	0.003
d2ba0a3	84	d.51.1.1 (A:136-219) Exosome complex RNA-binding p	6e-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 = 7e-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 = 37.9 bits (88), Expect = 2e-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 = 37.5 bits (87), 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 = 50.6 bits (121), Expect = 6e-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 = 47.1 bits (112), Expect = 1e-07
 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 = 40.6 bits (95), Expect = 3e-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 = 38.6 bits (90), Expect = 1e-04
 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 = 2e-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 = 1e-07
 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 = 40.9 bits (96), Expect = 2e-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 = 40.1 bits (94), Expect = 3e-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 = 2e-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 = 37.5 bits (87), 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 = 3e-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 = 48.8 bits (116), 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 = 3e-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 = 5e-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 = 43.3 bits (102), 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 = 39.9 bits (93), Expect = 4e-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 = 36.0 bits (83), Expect = 9e-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 = 46.7 bits (111), 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 = 1e-06
 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 = 43.3 bits (102), Expect = 3e-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 = 34.4 bits (79), Expect = 0.003
 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 = 45.3 bits (107), Expect = 5e-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 = 8e-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

>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 = 41.8 bits (98), Expect = 1e-05
 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 = 37.9 bits (88), 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 = 40.5 bits (95), Expect = 3e-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 = 39.3 bits (92), Expect = 7e-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 = 35.5 bits (82), Expect = 0.002
 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 = 35.1 bits (81), 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 = 40.2 bits (94), Expect = 4e-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 = 37.1 bits (86), Expect = 5e-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 = 36.3 bits (84), Expect = 0.001
 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 = 35.6 bits (82), Expect = 0.002
 Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 8/67 (11%)

Query: 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS 347
           +IG++G+ +R + +     I    P  +    ++ I+ L       + +  A   +  R 
Sbjct: 24  VIGQKGSGIRKMMDEFEVNIHV--PAPELQSDIIAITGLA------ANLDRAKAGLLERV 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 = 37.8 bits (88), Expect = 2e-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 = 34.3 bits (79), 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

>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 = 37.0 bits (86), Expect = 6e-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 = 35.2 bits (81), 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 = 34.5 bits (79), 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	609
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) [	99.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.5
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.5
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.49
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.49
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	99.49
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	99.45
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.45
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	99.44
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	99.43
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	99.43
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	99.43
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.41
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	99.41
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	99.37
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	99.33
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.18
d2cpqa1	78	Fragile X mental retardation syndrome related prot	99.16
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.15
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.13
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.11
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	99.09
d2cpqa1	78	Fragile X mental retardation syndrome related prot	98.96
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	98.93
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.91
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.81
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	98.48
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.46
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.38
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	98.36
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	98.32
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.27
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	98.21
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.78
d1k1ga_	122	RNA splicing factor 1 {Human (Homo sapiens) [TaxId	97.77
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.27
d2bl5a1	134	Quaking protein A (Xqua) {African clawed frog (Xen	97.05
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	94.02
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.92
d2asba3	67	Transcription factor NusA, C-terminal domains {Myc	93.55
d1hh2p3	68	Transcription factor NusA, C-terminal domains {The	93.27
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	81.62

>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=4.2e-15  Score=120.14  Aligned_cols=73  Identities=19%  Similarity=0.398  Sum_probs=66.5

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..+|.+|.||.+++|+|||++|++|++|+++|||+|+|.+..+     ..+++.|+|+|++++|++|+.+|.++|++|
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=5.1e-15  Score=117.98  Aligned_cols=68  Identities=18%  Similarity=0.420  Sum_probs=62.6

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHh
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L  438 (609)
                      .|.+|.||.+++|+|||++|.+|++|++.|||+|+|.+..+     ..++|.|+|+|++++|++|+.+|..+|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-----GSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCCCT-----TCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCCCC-----CCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            68999999999999999999999999999999999976433     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=99.51  E-value=6.9e-15  Score=117.55  Aligned_cols=70  Identities=19%  Similarity=0.425  Sum_probs=64.1

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..++.+|+||.+++|+|||++|++|++|++.|||+|+|++.       ...+|+|+|+|++++|.+|+.+|.++|+|
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            35899999999999999999999999999999999999763       24579999999999999999999999975

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=1.1e-14  Score=116.36  Aligned_cols=70  Identities=17%  Similarity=0.293  Sum_probs=62.3

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHh
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L  438 (609)
                      +.+|.||.+++|+||||+|++|++|++.|||+|+|++..+ + +...++|.|+|+|++++|++|+.+|.++|
T Consensus         2 ~~~~~IP~~~vg~IIGk~G~~Ik~I~~~sga~I~i~~~~~-~-~~~~~~r~v~I~G~~~~v~~A~~~I~e~i   71 (71)
T d1j4wa2           2 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPP-P-NADPNMKLFTIRGTPQQIDYARQLIEEKI   71 (71)
T ss_dssp             EEEEEEETTTHHHHHCGGGHHHHHHHHHHCCEEEEECCCT-T-TSCTTEEEEEEECCHHHHHHHHHHHHHHC
T ss_pred             EEEEEEChHhcceEECCCCcChHHHHhhcCcEEEEeecCC-C-CCCCCeEEEEEEeCHHHHHHHHHHHHhhC
Confidence            5689999999999999999999999999999999987543 2 24567899999999999999999999875

>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=9.6e-15  Score=119.81  Aligned_cols=75  Identities=19%  Similarity=0.333  Sum_probs=67.9

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      +..++.+|+||.+++|+|||++|++|++|++.|||+|+|.+..+.+   ...+|.|+|+|++++|.+|+.+|.++|++
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            4679999999999999999999999999999999999998754433   45689999999999999999999999976

>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=116.25  Aligned_cols=71  Identities=23%  Similarity=0.382  Sum_probs=63.7

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHh
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL  438 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L  438 (609)
                      .+.+|.||.+++|+|||++|++|++|++.|||+|+|.+.++..  ...++|.|+|+|++++|++|+.+|.++|
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            4679999999999999999999999999999999998765532  2467899999999999999999999876

>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=99.49  E-value=1.2e-14  Score=117.01  Aligned_cols=71  Identities=17%  Similarity=0.290  Sum_probs=64.9

Q ss_pred             ceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..+.+|.||.+++|+|||++|++|++|+++|||+|+|.+.++     ...++.|+|+|++++|++|+.+|.++|++
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            368899999999999999999999999999999999987543     45679999999999999999999999875

>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=99.49  E-value=6.4e-15  Score=117.78  Aligned_cols=70  Identities=30%  Similarity=0.458  Sum_probs=65.0

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+++++|+||.+++|+||||+|++|++|+++|||+|+|.+.    ...+|+|+|+|++++|.+|+.+|.++|+|
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    45689999999999999999999999975

>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=99.45  E-value=1.8e-14  Score=118.13  Aligned_cols=76  Identities=26%  Similarity=0.443  Sum_probs=69.5

Q ss_pred             CCCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       125 ~~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ....++.+|+||..++|+||||+|++|++|+++|||+|.|.+....+...+|+|+|+|++++|.+|+.+|.++|++
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            4568999999999999999999999999999999999999876345567899999999999999999999999976

>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=114.88  Aligned_cols=74  Identities=16%  Similarity=0.258  Sum_probs=67.3

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...++.+|.||.+++|+|||++|.+|++|++.|||+|.|++.+.     +.+++.|+|+|++++|+.|+.+|.++|++.
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            45689999999999999999999999999999999999987433     467899999999999999999999999864

>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=99.44  E-value=3.6e-14  Score=114.53  Aligned_cols=72  Identities=25%  Similarity=0.451  Sum_probs=66.8

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .+|.++.||..++|+||||+|++|++|+++|||+|+|...  .+...+|+|+|+|++++|.+|+.+|.++++++
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 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP--LEGSEDRIITITGTQDQIQNAQYLLQNSVKQY   74 (75)
T ss_dssp             CEEEEEEEETTTGGGGTCGGGHHHHHHHHHHCCEEEECCT--TSCSSEEEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEChHhcCeeECCCCchHHHHHhhcCCeEEEccC--CCCCCceEEEEEeCHHHHHHHHHHHHHHHHhc
Confidence            6789999999999999999999999999999999999773  45678999999999999999999999999873

>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=6.9e-14  Score=114.56  Aligned_cols=74  Identities=15%  Similarity=0.248  Sum_probs=66.9

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ...++.++.||.++|++|||++|++|++|++.|||+|+|++.++      .+.+.|+|+|++++|++|+.+|.+.+++|+
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            35678999999999999999999999999999999999987543      346789999999999999999999999885

>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=99.43  E-value=2.7e-14  Score=114.03  Aligned_cols=69  Identities=25%  Similarity=0.419  Sum_probs=62.5

Q ss_pred             EEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       130 t~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      +++|+||++.+|+||||+|++|++|+++|||+|+|.++ .......+|+|+|+|++++|.+|+.+|.++|
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 3445678899999999999999999998874

>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=99.43  E-value=3.4e-14  Score=113.13  Aligned_cols=68  Identities=25%  Similarity=0.414  Sum_probs=63.3

Q ss_pred             eEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       129 vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      .|.+|+||.+.+|+||||+|++|++|+++|||+|.|.+.  .+...+|+|+|+|++++|.+|+.+|.++|
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 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANP--VEGSSGRQVTITGSAASISLAQYLINARL   69 (70)
T ss_dssp             EEEEEEEEGGGHHHHHCGGGHHHHHHHHHHCCEEEECCC--CTTCSEEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEChHhcceeECCCChHHHHHHHHcCcEEEEcCC--CCCCCcEEEEEEeCHHHHHHHHHHHHHHc
Confidence            578999999999999999999999999999999999773  56678999999999999999999999876

>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=99.43  E-value=4.3e-14  Score=113.82  Aligned_cols=70  Identities=19%  Similarity=0.342  Sum_probs=64.0

Q ss_pred             eEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCC-CCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       129 vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~-p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      .+++|+||+.++|+||||+|++|++|+++|||+|+|.+. ...+...+|+|+|+|++++|.+|+.+|.++|
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            357999999999999999999999999999999999876 3456678999999999999999999999876

>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=117.48  Aligned_cols=77  Identities=19%  Similarity=0.263  Sum_probs=68.5

Q ss_pred             CCCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ....++.+|.||.+++|+|||++|.+||+|++.|||+|.|.+..+.   ....+|+|+|+|++++|++|+.+|.++|++.
T Consensus        11 ~~~~v~~~i~IP~~~vg~vIGk~G~~Ik~I~~~tga~I~i~~~~~~---~~~~~r~v~I~G~~~~v~~A~~~I~~~i~e~   87 (104)
T d1we8a_          11 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG---TLLLSRLIKISGTQKEVAAAKHLILEKVSED   87 (104)
T ss_dssp             SSCEEEEEEEEETTTHHHHHTTTSHHHHHHHHHHCCEEEECCSSCC---SSSSEEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEECHHHhcceECCCCcchHHHHHHcCCEEEECCCCCC---CCCCccEEEEEeCHHHHHHHHHHHHHHHhCc
Confidence            4567899999999999999999999999999999999999875442   2456799999999999999999999999864

>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=99.41  E-value=4.6e-14  Score=113.64  Aligned_cols=71  Identities=20%  Similarity=0.375  Sum_probs=65.6

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      ..+++|+||.+++|+||||+|++|++|+++|||+|+|...  .+...+|+|+|+|++++|.+|..+|.++|++
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            5689999999999999999999999999999999999874  3466789999999999999999999999976

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=5.5e-13  Score=109.84  Aligned_cols=73  Identities=15%  Similarity=0.231  Sum_probs=65.6

Q ss_pred             ceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..+.+|.||..++++|||++|++|++|++.|||+|+|++...    ...+++.|+|+|+.++|+.|+.+|.+.+++.
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            368899999999999999999999999999999999976544    3567889999999999999999999988763

>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=99.37  E-value=1.8e-13  Score=111.51  Aligned_cols=73  Identities=22%  Similarity=0.396  Sum_probs=67.5

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ..++.+|+||...+|+|||++|++|++|+++|||+|.|.+.  .++..+|+|+|+|++++|.+|+.+|.++|+++
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  45678899999999999999999999999863

>d2ctea1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=6.7e-13  Score=108.57  Aligned_cols=72  Identities=15%  Similarity=0.218  Sum_probs=65.2

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ...++.+|.||.+++|+|||++|++|++|+++|||+|.|++.       +..++.|+|+|++++|++|+.+|.+.+.+.
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            355899999999999999999999999999999999999763       345789999999999999999999988864

>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=99.33  E-value=4.4e-13  Score=114.99  Aligned_cols=76  Identities=21%  Similarity=0.304  Sum_probs=67.9

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ..+++.+|+||..++|+||||+|.+|++|+++|||+|.|.+........+|+|+|+|++++|.+|+.+|.++|++.
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

>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=99.31  E-value=1.3e-12  Score=104.14  Aligned_cols=67  Identities=19%  Similarity=0.312  Sum_probs=60.8

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHH
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGR  437 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~  437 (609)
                      ...+.+|.||.+++++|||++|++|++|+++|||+|+|++.       ..+++.|+|+|++++|++|+.+|.+.
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       34578999999999999999999874

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.3e-12  Score=107.14  Aligned_cols=72  Identities=14%  Similarity=0.237  Sum_probs=64.0

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHh-hCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      .+.++.+|.||.++||+|||++|++|++|+++ ++++|++++.       +.+++.|+|+|++++|++|+.+|.+++++.
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       346789999999999999999999998864

>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=99.26  E-value=3e-12  Score=107.01  Aligned_cols=71  Identities=20%  Similarity=0.268  Sum_probs=64.5

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      ..++.+|.||.++|++|||++|++|++|++.|||+|.|++.       +.+++.|+|+|++++|+.|+.+|..++++.
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            45899999999999999999999999999999999999763       345789999999999999999999988763

>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=99.25  E-value=2.6e-12  Score=105.71  Aligned_cols=72  Identities=17%  Similarity=0.178  Sum_probs=66.2

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+++++.||..++++|||++|++|++|+++|||+|+|.+. ......++.|+|+|+.++|.+|..+|.+++.+
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            5788999999999999999999999999999999999774 44567889999999999999999999999976

>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=99.18  E-value=6e-12  Score=102.77  Aligned_cols=72  Identities=19%  Similarity=0.236  Sum_probs=65.6

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ...++.++.||..++|+|||++|++|++|+++|||+|.+.+    .+..++.|+|+|+.++|.+|+.+|.+++.+.
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 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR----PDDPSNQIKITGTKEGIEKARHEVLLISAEQ   78 (81)
T ss_dssp             CSCEEEEEECCTTTHHHHHCSSSCHHHHHHHHTTCCCBCCC----TTSSCCEEEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCceEEEEEECHHHHhhccCCCChhHHHHHHHhCCEEEECC----CCCCCCEEEEEeCHHHHHHHHHHHHHHHHHH
Confidence            34689999999999999999999999999999999999966    3557789999999999999999999999773

>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=99.18  E-value=6.6e-12  Score=102.52  Aligned_cols=73  Identities=14%  Similarity=0.193  Sum_probs=64.7

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ++.++..+.||..++++|||++|++|++|+++|||+|+|.+.   ....++.|+|+|++++|.+|+.+|.++++++
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            347788999999999999999999999999999999999663   2234578999999999999999999999874

>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=99.16  E-value=4.7e-12  Score=102.43  Aligned_cols=64  Identities=19%  Similarity=0.231  Sum_probs=57.6

Q ss_pred             CceEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHH
Q 007293          364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVG  436 (609)
Q Consensus       364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~  436 (609)
                      +.++.+|.||.+++|+|||++|++||+|++.|||+|.+.+         .+++.|+|.| ++++|++|+.+|..
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            4579999999999999999999999999999999998864         3457899999 69999999999954

>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=99.15  E-value=9.4e-12  Score=101.82  Aligned_cols=72  Identities=17%  Similarity=0.197  Sum_probs=64.7

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhcccc-cCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE-SGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~e-SGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      ...++..|.||..++|+||||+|++|++|+++ ++|+|.+..    .+..++.|+|+|++++|.+|+.+|.+++++.
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            34778999999999999999999999999988 599999965    3557899999999999999999999999874

>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=99.14  E-value=1.1e-11  Score=98.68  Aligned_cols=67  Identities=19%  Similarity=0.320  Sum_probs=61.0

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHH
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL  198 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L  198 (609)
                      ..+++|.||..++++|||++|++|++|+++|||+|++.+    +...++.|+|+|++++|.+|+.+|.++.
T Consensus         4 ~~~~ei~V~~~~~~~iIG~~G~~i~~I~~~tg~~I~i~~----~~~~~~~v~I~G~~~~v~~A~~~I~~i~   70 (71)
T d1viga_           4 MDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPP----DSEKSNLIRIEGDPQGVQQAKRELLELA   70 (71)
T ss_dssp             CEEEEEEECSSHHHHHTCSSCCHHHHHHHHTCCEEECCC----CCSSSEEEEEEESSHHHHHHHHHHHHTC
T ss_pred             eEEEEEEECHHHhcccCCCCCchHHHHHHHhCCEEEeCC----CCCCCCEEEEECCHHHHHHHHHHHHHHh
Confidence            567899999999999999999999999999999999966    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=99.13  E-value=4.4e-11  Score=99.46  Aligned_cols=69  Identities=12%  Similarity=0.192  Sum_probs=62.4

Q ss_pred             CCceEEEEEeccccccccccCCCchhHHHHHh-hCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhc
Q 007293          363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDV-TGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~-TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~  441 (609)
                      .+.+|.+|.||..+|++|||++|++|++|+++ +|++|.+++          ++..|+|+|++++|+.|+.+|.+.+++.
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

>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=97.87  Aligned_cols=64  Identities=13%  Similarity=0.101  Sum_probs=58.2

Q ss_pred             EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      ..+.||.+++|.|||++|++|++|+++|||+|+|.+           +..|+|+|++++++.|+.+|...+++..
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           4679999999999999999999888754

>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=99.09  E-value=2.8e-11  Score=100.92  Aligned_cols=69  Identities=16%  Similarity=0.205  Sum_probs=64.1

Q ss_pred             ceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       128 ~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .++..+.||...++.|||++|++|++|+++|||+|.+.+    .+..++.|+|+|+.++|.+|+.+|.+++.+
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=98.96  E-value=1.3e-10  Score=93.82  Aligned_cols=64  Identities=23%  Similarity=0.291  Sum_probs=57.6

Q ss_pred             CceEEEEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEec-cHHHHHHHHHHHHH
Q 007293          127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTT  196 (609)
Q Consensus       127 ~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G-~~e~V~~A~~~I~~  196 (609)
                      +.++.++.||.+.+|+|||++|++|++|+++|||+|.+..+      .++.|+|.| +.++|.+|+.+|..
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            46789999999999999999999999999999999998653      568899999 69999999999843

>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=98.93  E-value=4.7e-10  Score=93.09  Aligned_cols=68  Identities=16%  Similarity=0.255  Sum_probs=61.9

Q ss_pred             CCceEEEEEeecceeeeeeecCcchhhhccccc-CcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIES-GAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       126 ~~~vt~rllVP~~~vG~IIGkgG~~Ik~I~~eS-Ga~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .+.++..+.||...+++|||++|++|++|++++ |++|.+..       .+..|+|+|++++|.+|+.+|.+++.+
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 89999955       356899999999999999999999976

>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=98.91  E-value=2.5e-10  Score=93.40  Aligned_cols=62  Identities=24%  Similarity=0.253  Sum_probs=57.0

Q ss_pred             EEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhcc
Q 007293          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       132 rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      -+.||.+.+|.||||+|++|++|+++|||+|.|.+        ++.|.|+|++++|.+|..+|..++++.
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        357999999999999999999998773

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.81  E-value=7e-10  Score=90.47  Aligned_cols=70  Identities=16%  Similarity=0.014  Sum_probs=55.2

Q ss_pred             EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhhcc
Q 007293          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL  442 (609)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~  442 (609)
                      .++.||.+++|.|||++|++||+|+++|||+|+|...+..     ...+.....|.+.++++|+.+|.+..|.|.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~~tg~~I~Id~d~g~-----v~i~~~~~~~~~~a~~~a~~iI~aI~rGf~   74 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM-----VIVEPEAEGIPPVNLMKAAEVVKAISLGFP   74 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHHHHTEEEEEETTTTE-----EEEEESSTTSCHHHHHHHHHHHHHHHHTCC
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHHHHCCEEEEEcCCCe-----EEEecCCccccHHHHHHHHHHHHHHhCCCC
Confidence            3689999999999999999999999999999999642210     011112236789999999999999877664

>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=4.1e-10  Score=88.63  Aligned_cols=62  Identities=11%  Similarity=0.009  Sum_probs=48.1

Q ss_pred             EEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHhhhc
Q 007293          369 SILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRHN  441 (609)
Q Consensus       369 ~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~~~Lr~~  441 (609)
                      .+.||.+++|.|||++|++||+|+++|||+|.|.+           +..|+|+|. .++++.|+.+|....++.
T Consensus         4 vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~-----------~g~v~I~g~~~~~v~~A~~~I~~i~~ea   66 (69)
T d2je6i3           4 VIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVAN-----------NGRIWATCPSRFSEEILIEAIRKIENES   66 (69)
T ss_dssp             EEECCGGGHHHHHCGGGHHHHHHHTTC---CEECT-----------TSEEEC-----CTTCCTHHHHTTTTTTT
T ss_pred             EEEEChhhccceECCchhHHHHHHHHHCCEEEEcC-----------CCEEEEEeCCHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999999999953           356999996 678999999998766653

>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=4.1e-08  Score=80.03  Aligned_cols=65  Identities=12%  Similarity=0.013  Sum_probs=57.0

Q ss_pred             EEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHHHHhhhccc
Q 007293          368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVVGRLRHNLK  443 (609)
Q Consensus       368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~~~Lr~~~~  443 (609)
                      ..+.||.+++|.|||++|++|+.|++.|||+|.|.+           +-.|.|.|. .+.+..|+.+|....++..+
T Consensus         3 ~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d-----------~G~V~I~g~~~~~~~~A~~~I~~I~~ea~v   68 (87)
T d2z0sa2           3 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR-----------NGRIHLECPNEDLEAIAVMAIKIIDEEAYT   68 (87)
T ss_dssp             EEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEET-----------TTEEEEECSCHHHHHHHHHHHHHHHHCSCC
T ss_pred             EEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECC-----------CcEEEEEeCCHHHHHHHHHHHHHHHHhchh
Confidence            367899999999999999999999999999999953           357999995 88999999999998776543

>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=98.48  E-value=3.6e-08  Score=80.11  Aligned_cols=63  Identities=14%  Similarity=0.214  Sum_probs=53.1

Q ss_pred             EEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEE-----eccHHHHHHHHHHHHHHHhcc
Q 007293          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI-----TGATLAVKKALVAVTTCLQHL  201 (609)
Q Consensus       132 rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I-----~G~~e~V~~A~~~I~~~L~e~  201 (609)
                      .+-||.+.+|.||||+|++|++|+++|||+|+|..+       +..+.+     .|.+.++.+|...|.++.+.+
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            478999999999999999999999999999999663       344554     356899999999999887653

>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=98.46  E-value=2.6e-09  Score=83.91  Aligned_cols=61  Identities=16%  Similarity=0.138  Sum_probs=47.4

Q ss_pred             EEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       132 rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      .+-||.+.+|.||||+|++|++|+++|||+|.|.+        +..|+|+|. .+++.+|..+|..+.++
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        356999996 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=98.38  E-value=1.2e-08  Score=75.72  Aligned_cols=48  Identities=23%  Similarity=0.383  Sum_probs=15.8

Q ss_pred             EEEEEecCCcccceecCCChHHHHHHHHhCceEEEcCCCCCCCceEEEEccCcc
Q 007293           26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGS   79 (609)
Q Consensus        26 ~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~~~~g~~eRvI~I~G~~e   79 (609)
                      ..+|.||.+++|.|||++|++||+|+++|||+|.+.+      +..|.|+|...
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            3567889999999999999999999999999999974      57788888643

>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=98.36  E-value=1.9e-08  Score=74.51  Aligned_cols=46  Identities=20%  Similarity=0.412  Sum_probs=14.5

Q ss_pred             EEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC
Q 007293          367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE  423 (609)
Q Consensus       367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~  423 (609)
                      ..+|.||.+++|.|||++|.+||+|+++|||+|.|.+           +..|+|.|.
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            4578899999999999999999999999999999853           567877775

>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=98.32  E-value=1.8e-07  Score=76.20  Aligned_cols=61  Identities=13%  Similarity=0.120  Sum_probs=54.8

Q ss_pred             EEEeecceeeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEecc-HHHHHHHHHHHHHHHhc
Q 007293          132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH  200 (609)
Q Consensus       132 rllVP~~~vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~-~e~V~~A~~~I~~~L~e  200 (609)
                      -+-||.+.++.|||++|++|+.|+++|||+|.|..        +-.|.|.|. .+.+.+|+.+|..+.++
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            36789999999999999999999999999999965        246899995 89999999999998876

>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=2.9e-07  Score=77.44  Aligned_cols=53  Identities=23%  Similarity=0.304  Sum_probs=47.9

Q ss_pred             cccccccCCCchhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHhhh
Q 007293          376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH  440 (609)
Q Consensus       376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~  440 (609)
                      ..|+|||++|.+|+.|++.|||+|.|..            ..|.|.|++++++.|+.+|..++.+
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            5899999999999999999999999942            3588889999999999999998875

>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=98.21  E-value=2.6e-07  Score=77.73  Aligned_cols=52  Identities=19%  Similarity=0.199  Sum_probs=47.2

Q ss_pred             eeeeeecCcchhhhcccccCcEEEecCCCCCCCCCCceEEEeccHHHHHHHHHHHHHHHhc
Q 007293          140 IGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH  200 (609)
Q Consensus       140 vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~~~~~~dR~V~I~G~~e~V~~A~~~I~~~L~e  200 (609)
                      .|.|||++|.+|+.|++.|||+|.|..         ..|.|.|+++++..|..+|..++.+
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            489999999999999999999999943         4577889999999999999999975

>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=97.78  E-value=1.1e-05  Score=69.71  Aligned_cols=73  Identities=18%  Similarity=0.252  Sum_probs=58.5

Q ss_pred             ceEEEEEeecce------eeeeeecCcchhhhcccccCcEEEecCCCC-------------CC-CCCCceEEEecc-HHH
Q 007293          128 VAYCGLLANTTK------IGVVVGKGGRNVTRMRIESGAKIVMLPPPA-------------CA-AIDDQLIQITGA-TLA  186 (609)
Q Consensus       128 ~vt~rllVP~~~------vG~IIGkgG~~Ik~I~~eSGa~I~I~~~p~-------------~~-~~~dR~V~I~G~-~e~  186 (609)
                      .++.+++||-..      +|.|||.+|+++|+|+++|||+|.|.....             .+ ...+=.|.|+++ .+.
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      899999999999999999999999975300             00 122336778886 889


Q ss_pred             HHHHHHHHHHHHhc
Q 007293          187 VKKALVAVTTCLQH  200 (609)
Q Consensus       187 V~~A~~~I~~~L~e  200 (609)
                      +.+|+.+|..+|..
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=97.77  E-value=3.5e-05  Score=66.43  Aligned_cols=77  Identities=18%  Similarity=0.343  Sum_probs=58.3

Q ss_pred             eEEEEEeccc------cccccccCCCchhHHHHHhhCCeEEecCCCc----------ccccC-CCCCcEEEEcCC-HHHH
Q 007293          366 VAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ----------VLGCA-AQNDVVIQISGE-YKNV  427 (609)
Q Consensus       366 ~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~----------~P~~~-~~~er~V~I~G~-~~~V  427 (609)
                      ++.+|.||-+      ++|.|||.+|.++|+|+++|||+|.|-.+..          .+.+. ....--|.|++. ++.+
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      5999999999999999999999999965322          11111 123345677776 6689


Q ss_pred             HHHHHHHHHHhhhcc
Q 007293          428 QNALSEVVGRLRHNL  442 (609)
Q Consensus       428 ~~A~~~I~~~Lr~~~  442 (609)
                      ..|+.+|...|...+
T Consensus        83 ~~A~~~i~~ll~~~~   97 (122)
T d1k1ga_          83 KKAVEQIRNILKQGI   97 (122)
T ss_dssp             HHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999999997644

>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=97.27  E-value=0.00011  Score=64.05  Aligned_cols=74  Identities=23%  Similarity=0.310  Sum_probs=54.0

Q ss_pred             eEEEEEecc------ccccccccCCCchhHHHHHhhCCeEEecCCCcc------------ccc-CCCCCcEEEEcCCH--
Q 007293          366 VAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV------------LGC-AAQNDVVIQISGEY--  424 (609)
Q Consensus       366 ~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~------------P~~-~~~~er~V~I~G~~--  424 (609)
                      ++.+|.||-      +++|.|||.+|.++|+|+++|||+|.|-.+.-.            |.+ ...++--|.|++..  
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 12345567777652  


Q ss_pred             ----HHHHHHHHHHHHHhh
Q 007293          425 ----KNVQNALSEVVGRLR  439 (609)
Q Consensus       425 ----~~V~~A~~~I~~~Lr  439 (609)
                          ..+.+|..+|...|.
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                357888888887774

>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=97.05  E-value=0.00012  Score=63.74  Aligned_cols=37  Identities=24%  Similarity=0.526  Sum_probs=33.4

Q ss_pred             EEEEEEecCC------cccceecCCChHHHHHHHHhCceEEEc
Q 007293           25 VSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE   61 (609)
Q Consensus        25 v~~RilvP~~------~vG~IIGk~G~~Ik~IreeTga~I~V~   61 (609)
                      +.-+|+||.+      ++|.|||.+|.++|+|+++|||+|.|.
T Consensus         2 l~eKv~IP~~~~P~~NfvG~IiGPrG~t~K~le~eTg~kI~Ir   44 (134)
T d2bl5a1           2 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVR   44 (134)
T ss_dssp             EEEEEECCTTTCSSSCHHHHHTTTTHHHHHHHHHHHSEEEEEE
T ss_pred             cceEEeCCCCCCCCCCeeEEEECCCCchHHHHHHHHCCEEEEE
Confidence            5668899975      799999999999999999999999995

>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=94.02  E-value=0.017  Score=43.78  Aligned_cols=40  Identities=20%  Similarity=0.185  Sum_probs=36.5

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCC
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~  405 (609)
                      -...+.||.++.+.-|||+|.+|+-..+-||.+|.|...+
T Consensus        27 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~idI~s~~   66 (68)
T d1hh2p3          27 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIM   66 (68)
T ss_dssp             TEEEEEECTTSHHHHHCGGGHHHHHHHHHHSCEEEEEECC
T ss_pred             CEEEEEECcccccccccCCcchHHHHHHHHCCEEeeEEcc
Confidence            3688999999999999999999999999999999997643

>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=93.92  E-value=0.017  Score=43.64  Aligned_cols=40  Identities=18%  Similarity=0.168  Sum_probs=36.7

Q ss_pred             eEEEEEeccccccccccCCCchhHHHHHhhCCeEEecCCC
Q 007293          366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE  405 (609)
Q Consensus       366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~  405 (609)
                      ....+.||.++....|||+|.+++-..+-||.+|.|....
T Consensus        26 ~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~~es   65 (67)
T d2asba3          26 RAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIRGDA   65 (67)
T ss_dssp             TEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEEESS
T ss_pred             cEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEEeCC
Confidence            4788999999999999999999999999999999997643

>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=93.55  E-value=0.018  Score=43.47  Aligned_cols=40  Identities=25%  Similarity=0.244  Sum_probs=36.1

Q ss_pred             CCcEEEEEEecCCcccceecCCChHHHHHHHHhCceEEEc
Q 007293           22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE   61 (609)
Q Consensus        22 ~~~v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~   61 (609)
                      ++.-.+.+.||.+..+..|||+|.|+|-..+-||.+|.|.
T Consensus        23 e~~~~~~v~V~~~qls~AIGk~G~NvrLas~Ltg~~IdI~   62 (67)
T d2asba3          23 QTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDIR   62 (67)
T ss_dssp             TTTTEEEEEECGGGHHHHHCGGGHHHHHHHHHHSCEEEEE
T ss_pred             CCCcEEEEEECcccccchhcCCceeHHHHHHHHCCEEEEE
Confidence            3445778999999999999999999999999999999985

>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=93.27  E-value=0.028  Score=42.52  Aligned_cols=38  Identities=18%  Similarity=0.232  Sum_probs=34.9

Q ss_pred             EEEEEEecCCcccceecCCChHHHHHHHHhCceEEEcC
Q 007293           25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG   62 (609)
Q Consensus        25 v~~RilvP~~~vG~IIGk~G~~Ik~IreeTga~I~V~~   62 (609)
                      -.+.+.||.+..+..|||+|.|||-..+-||.+|.|..
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            35778999999999999999999999999999999953

>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=81.62  E-value=1.1  Score=34.88  Aligned_cols=56  Identities=14%  Similarity=0.076  Sum_probs=43.9

Q ss_pred             EEEeccccccccccCCCc-hhHHHHHhhCCeEEecCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHHH
Q 007293          369 SILVGADFVGCLTGSGSS-AVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEVV  435 (609)
Q Consensus       369 ~l~VP~~~vG~IIGkgG~-~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I~  435 (609)
                      -+.|+..++..|||++++ .++.|.+.+++.|-|-.           +-.|=|.|. ++....+...|.
T Consensus         4 v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~-----------NGrIWi~~~~~~~~i~i~~aI~   61 (85)
T d2ja9a2           4 IIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGL-----------NGKIWVKCEELSNTLACYRTIM   61 (85)
T ss_dssp             EEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEET-----------TTEEEEECSSHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEec-----------CcEEEEECCCHHHHHHHHHHHH
Confidence            567999999999999998 89999999999999954           455888885 555554444443