Psyllid ID: psy11433

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-

VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQDALDSRSVSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKEHARAEEEEVPR

cccccccccccHHHHHHHcHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHccccHHHHHHHHHccccEEEEcccccccHHHHHHHccccccccEEEEcccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHccccHHccccccHHHHHHHHHHHHHHccccccccccHHHHHHHcccccccccccEEEEcccccccccccccEEEEEEccccccHHHHHHcccEEEEEcccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHcccccccccEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHccccccccccccccccccccccccccccHHcccccHHHHHHHHccHHHHHHccccccEEEEEccccHHHHHHHHHHcHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccHHHHHHHHHccccEEEEcccccccHHHHHHHccccccccEEEEEccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHccccccHHHHHHHHHHHHHHHHccHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHccc

ccccccccEccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHcccccccccccEcHHHHHHHHccccccHHHHHHHHHHHccEEEEEcHHHccHHHHHHHHHHcccccEEEEEcccccccHEHHHEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHcccHHHHcccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccHEccccHHHHHHHHHHHcccccccccEEcHHHHccccEEEEEEEEEEccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHccccEEEEEccccccccccccEEEEEcccHHHHHHHHHHHccEEEEEccccccccccHHHcccccHEEccccccccccccccEEEEccccEEccccEEEEEccccccHHHHHHHHHHcccccccccEEEEEEccccHHHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHHHHHHHHHHHHHHccccccEEEEEEcccccccccccHcHcccccEEcHHHHHHHccccccccEEEEcccccEEEEccccccccHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHHHHHccHHHHHHHcccEEEccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHcccccccccccEcHHHHHHHHccccccHHHHHHHHHHHccEEEEEcHHHccHHHHHHHHHHcccccEEEEEcccccccHEHHHEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEcccccccHHHHccccccEEEEEEcHHHcHHHHHcccHHHHHHHHcHccccccHHHHHHHHHHHHHHHcccccHccccccEEccHHHHHHHHHHHHHHHcccc

vskerdgkivdgrchsltsssvrdrhkagenipvcdfyekfdavgreaplapgvySITKLKEMgrelglcpYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARssvvvfdeahnidnvcvdslsvrINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDaqsaretdvvlanpvlpdeilqevvpgnirTAEHFVGFLKRFIEYLKTRLRVQQVVQEspatflkdisskpapsmiSEAYRYIFSTEEHLKTRLRVQQVVQespatflkdisskvcierkpLRFCAERLASLLRTLeitnltdfsSLVVITHLATLVSSYTKGFAiivepfsdkaptvpnpvlyfccldsslaikpvfdRFQTVvitsgtlspldmypkilnfqpvimhsfsmtlarpcllpmVRENYAMglmiddlpvffpyeyiypeQYAYMVELKKALDAkghcllempsgtgktTSLLSLIVAYMNahpldvtkllycsrtvpEIEKVVEELARLFDYYIKHNEEINMTGLVLssrknlcihsefetrdDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETqdaldsrsvskerdgkivdgrchsltsssvrdrhkagenipvcdfyekfdavgreaplapgvySITKLKEMgrelglcpYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARssvvvfdeahnidnvcvdslsvrINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDaqsaretdvvlanpvlpdeilqgktdygimifadkrfarsdkrsklPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMaqpftredMLGVALLSLDQLLEKEHARaeeeevpr

vskerdgkivdgrchsltsssvrdrhkagenipVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVvvfdeahnidnvcvdslsvrinrrtiekavgniqtlegtlkeMKEADSAKLREEYARLVEGLrdaqsaretDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVqespatflkdisskpapSMISEAYRYIFSTEEHLKTRLRVQQVVqespatflkdisskvcierkpLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITsgtlspldmYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIetqdaldsrsvskerdgkivdgrchsltsssvrdrhkagenipVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVvvfdeahnidnvcvdslsvrinrrtiekavgniqtlegtlkeMKEADSAKLREEYARLVEGLrdaqsaretdvvlanpvlpdeilqgktdyGIMIFADKrfarsdkrsklPKWIQEYltdnltnlstEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKeharaeeeevpr

*****************************ENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEG******************RLVE*********ETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLK*********MISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQ************************************ENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEG******************RLV**********ETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQL***************

***********GRC**LT**************PVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPF*****TVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQDALDSRSVSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLS*******************

********IVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQD************GKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKE***********

******GKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQDALDSRSVSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKEHAR********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTxxxxxxxxxxxxxxxxxxxxxDSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKRKLLFIETQDALDSRSVSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTxxxxxxxxxxxxxxxxxxxxxDSAKLREEYARLVEGLRDAQSARETDVVLANPVLPDEILQGKTDYGIMIFADKRFARSDKRSKLPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKEHARAEEEEVPR

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		941	2.2.26 [Sep-21-2011]
P18074		760	TFIIH basal transcription	yes	N/A	0.397	0.492	0.586	1e-145
A6QLJ0		760	TFIIH basal transcription	yes	N/A	0.397	0.492	0.578	1e-143
Q60452		760	TFIIH basal transcription	yes	N/A	0.397	0.492	0.576	1e-142
O08811		760	TFIIH basal transcription	yes	N/A	0.397	0.492	0.576	1e-141
P26659		772	DNA repair helicase rad15	yes	N/A	0.397	0.484	0.466	1e-114
Q8W4M7		758	DNA repair helicase UVH6	yes	N/A	0.387	0.481	0.449	1e-102
P06839		778	DNA repair helicase RAD3	yes	N/A	0.456	0.552	0.404	1e-100
Q55G81		776	TFIIH basal transcription	yes	N/A	0.391	0.474	0.399	9e-89
B4PZB4		985	Regulator of telomere elo	N/A	N/A	0.213	0.204	0.260	4e-12
B3NSW1		985	Regulator of telomere elo	N/A	N/A	0.097	0.093	0.365	8e-12

>sp\|P18074\|ERCC2_HUMAN TFIIH basal transcription factor complex helicase XPD subunit OS=Homo sapiens GN=ERCC2 PE=1 SV=1	Back alignment and function desciption

 Score =  514 bits (1325), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 245/418 (58%), Positives = 309/418 (73%), Gaps = 44/418 (10%)

Query: 1   VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKL 60
           V+  R GK VDG+CHSLT+S VR +++   ++P C FYE+FDA GRE PL  G+Y++  L
Sbjct: 121 VTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDL 180

Query: 61  KEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNID 120
           K +GR  G CPYFLAR +I+HA +VVYSYHYLLDPKIA++VSKELAR +VVVFDEAHNID
Sbjct: 181 KALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNID 240

Query: 121 NVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARE 180
           NVC+DS+SV + RRT+++  GN++TL+ T+  +KE D  +LR+EY RLVEGLR+A +ARE
Sbjct: 241 NVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARE 300

Query: 181 TDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKD 240
           TD  LANPVLPDE+LQE VPG+IRTAEHF+GFL+R +EY+K RLRVQ VVQESP  F   
Sbjct: 301 TDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVQHVVQESPPAF--- 357

Query: 241 ISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCA 300
                                                    L  ++ +VCI+RKPLRFCA
Sbjct: 358 -----------------------------------------LSGLAQRVCIQRKPLRFCA 376

Query: 301 ERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFC 360
           ERL SLL TLEIT+L DFS L ++ + ATLVS+Y KGF II+EPF D+ PT+ NP+L+F 
Sbjct: 377 ERLRSLLHTLEITDLADFSPLTLLANFATLVSTYAKGFTIIIEPFDDRTPTIANPILHFS 436

Query: 361 CLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMV 418
           C+D+SLAIKPVF+RFQ+V+ITSGTLSPLD+YPKIL+F PV M +F+MTLAR CL PM+
Sbjct: 437 CMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMATFTMTLARVCLCPMI 494

ATP-dependent 5'-3' DNA helicase, component of the core-TFIIH basal transcription factor. Involved in nucleotide excision repair (NER) of DNA by opening DNA around the damage, and in RNA transcription by RNA polymerase II by anchoring the CDK-activating kinase (CAK) complex, composed of CDK7, cyclin H and MAT1, to the core-TFIIH complex. Involved in the regulation of vitamin-D receptor activity. As part of the mitotic spindle-associated MMXD complex it plays a role in chromosome segregation. Might have a role in aging process and could play a causative role in the generation of skin cancers.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp\|A6QLJ0\|ERCC2_BOVIN TFIIH basal transcription factor complex helicase XPD subunit OS=Bos taurus GN=ERCC2 PE=2 SV=1	Back alignment and function description

>sp\|Q60452\|ERCC2_CRIGR TFIIH basal transcription factor complex helicase XPD subunit OS=Cricetulus griseus GN=ERCC2 PE=1 SV=1	Back alignment and function description

>sp\|O08811\|ERCC2_MOUSE TFIIH basal transcription factor complex helicase XPD subunit OS=Mus musculus GN=Ercc2 PE=2 SV=2	Back alignment and function description

>sp\|P26659\|RAD15_SCHPO DNA repair helicase rad15 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad15 PE=1 SV=2	Back alignment and function description

>sp\|Q8W4M7\|ERCC2_ARATH DNA repair helicase UVH6 OS=Arabidopsis thaliana GN=UVH6 PE=1 SV=1	Back alignment and function description

>sp\|P06839\|RAD3_YEAST DNA repair helicase RAD3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD3 PE=1 SV=1	Back alignment and function description

>sp\|Q55G81\|ERCC2_DICDI TFIIH basal transcription factor complex helicase repD subunit OS=Dictyostelium discoideum GN=repD PE=2 SV=1	Back alignment and function description

>sp\|B4PZB4\|RTEL1_DROYA Regulator of telomere elongation helicase 1 homolog OS=Drosophila yakuba GN=GE16425 PE=3 SV=1	Back alignment and function description

>sp\|B3NSW1\|RTEL1_DROER Regulator of telomere elongation helicase 1 homolog OS=Drosophila erecta GN=GG18780 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		941
350400679		777	PREDICTED: TFIIH basal transcription fac	0.397	0.481	0.677	1e-165
340710930		759	PREDICTED: LOW QUALITY PROTEIN: TFIIH ba	0.397	0.492	0.677	1e-165
332026203		774	TFIIH basal transcription factor complex	0.397	0.483	0.667	1e-164
345480734		759	PREDICTED: TFIIH basal transcription fac	0.397	0.492	0.657	1e-163
328786210		759	PREDICTED: TFIIH basal transcription fac	0.397	0.492	0.657	1e-161
307210249		735	TFIIH basal transcription factor complex	0.397	0.508	0.655	1e-161
380014617		759	PREDICTED: TFIIH basal transcription fac	0.397	0.492	0.655	1e-161
307182232		759	TFIIH basal transcription factor complex	0.397	0.492	0.655	1e-161
383850774		759	PREDICTED: TFIIH basal transcription fac	0.397	0.492	0.655	1e-160
242024030		747	TFIIH basal transcription factor complex	0.397	0.500	0.648	1e-159

>gi\|350400679\|ref\|XP_003485920.1\| PREDICTED: TFIIH basal transcription factor complex helicase XPD subunit-like [Bombus impatiens]	Back alignment and taxonomy information

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 283/418 (67%), Positives = 328/418 (78%), Gaps = 44/418 (10%)

Query: 1   VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKL 60
           VS+ER+GKIVDGRCHSLT+S VR+RH   E+ P+C+FYE FD  G+E  + PG+YSI  L
Sbjct: 139 VSREREGKIVDGRCHSLTASYVRERHNYDESTPICNFYEGFDMEGKEQFMPPGIYSIDDL 198

Query: 61  KEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNID 120
           KE GR+   CPYFLAR  I+HA+IVVYSYHYLLDPKIA  VSKEL++SSVVVFDEAHNID
Sbjct: 199 KEYGRDRNWCPYFLARFTILHAQIVVYSYHYLLDPKIAETVSKELSKSSVVVFDEAHNID 258

Query: 121 NVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARE 180
           NVC+DS+SV+INRRT+EK+  NIQ LE T+ EM+E D  KL+EEY RLVEGL+DA  ARE
Sbjct: 259 NVCIDSMSVKINRRTLEKSSANIQLLEKTVAEMREDDVNKLKEEYERLVEGLKDAHVARE 318

Query: 181 TDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKD 240
           TD++LANPVLPDEILQEVVPGNIR AEHFVGFL+RF+EYLKTRLRVQ VVQESPA FL+D
Sbjct: 319 TDIILANPVLPDEILQEVVPGNIRNAEHFVGFLRRFVEYLKTRLRVQHVVQESPAAFLRD 378

Query: 241 ISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCA 300
                                                       + +KV IERKPLRFCA
Sbjct: 379 --------------------------------------------VQTKVSIERKPLRFCA 394

Query: 301 ERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFC 360
           ERLASLLRT+EIT+LTDFS ++++THLATLVS+YTKGF IIVEPF DK P V NP+L+F 
Sbjct: 395 ERLASLLRTMEITDLTDFSPVILVTHLATLVSTYTKGFTIIVEPFDDKTPNVLNPILHFV 454

Query: 361 CLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMV 418
           CLDSS+AIKP+FDRFQ+VVITSGTLSPLDMYPKILNF PVIM SF+MTLARPCLLPM+
Sbjct: 455 CLDSSIAIKPIFDRFQSVVITSGTLSPLDMYPKILNFHPVIMSSFTMTLARPCLLPMI 512

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|340710930\|ref\|XP_003394036.1\| PREDICTED: LOW QUALITY PROTEIN: TFIIH basal transcription factor complex helicase XPD subunit-like [Bombus terrestris]	Back alignment and taxonomy information

>gi\|332026203\|gb\|EGI66345.1\| TFIIH basal transcription factor complex helicase subunit [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|345480734\|ref\|XP_001605333.2\| PREDICTED: TFIIH basal transcription factor complex helicase XPD subunit-like [Nasonia vitripennis]	Back alignment and taxonomy information

>gi\|328786210\|ref\|XP_396155.4\| PREDICTED: TFIIH basal transcription factor complex helicase XPD subunit [Apis mellifera]	Back alignment and taxonomy information

>gi\|307210249\|gb\|EFN86899.1\| TFIIH basal transcription factor complex helicase subunit [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|380014617\|ref\|XP_003691322.1\| PREDICTED: TFIIH basal transcription factor complex helicase XPD subunit-like [Apis florea]	Back alignment and taxonomy information

>gi\|307182232\|gb\|EFN69563.1\| TFIIH basal transcription factor complex helicase subunit [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|383850774\|ref\|XP_003700951.1\| PREDICTED: TFIIH basal transcription factor complex helicase XPD subunit-like [Megachile rotundata]	Back alignment and taxonomy information

>gi\|242024030\|ref\|XP_002432433.1\| TFIIH basal transcription factor complex helicase subunit, putative [Pediculus humanus corporis] gi\|212517866\|gb\|EEB19695.1\| TFIIH basal transcription factor complex helicase subunit, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		941
ZFIN\|ZDB-GENE-040426-997		760	ercc2 "excision repair cross-c	0.304	0.377	0.588	2.7e-147
UNIPROTKB\|Q91941		760	ERCC2/XPD "ERCC2/XPD protein"	0.304	0.377	0.588	3.9e-146
FB\|FBgn0261850		769	Xpd "Xeroderma pigmentosum D"	0.259	0.317	0.627	6.3e-144
UNIPROTKB\|P18074		760	ERCC2 "TFIIH basal transcripti	0.336	0.417	0.527	3.5e-141
RGD\|1309109		760	Ercc2 "excision repair cross-c	0.336	0.417	0.518	3.1e-140
UNIPROTKB\|Q60452		760	ERCC2 "TFIIH basal transcripti	0.336	0.417	0.518	3.9e-140
UNIPROTKB\|A6QLJ0		760	ERCC2 "TFIIH basal transcripti	0.336	0.417	0.518	5e-140
UNIPROTKB\|F1N2P3		759	ERCC2 "TFIIH basal transcripti	0.336	0.417	0.518	5e-140
MGI\|MGI:95413		760	Ercc2 "excision repair cross-c	0.336	0.417	0.515	4.4e-139
UNIPROTKB\|A8MX75		706	ERCC2 "TFIIH basal transcripti	0.336	0.449	0.527	6.4e-136

ZFIN\|ZDB-GENE-040426-997 ercc2 "excision repair cross-complementing rodent repair deficiency, complementation group 2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

 Score = 890 (318.4 bits), Expect = 2.7e-147, Sum P(3) = 2.7e-147
 Identities = 170/289 (58%), Positives = 215/289 (74%)

Query:     1 VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKL 60
             VS  R GK VDG+CHSLT+S +R +H++  N PVC FYE+FD VGR+ P+ PG+Y++  L
Sbjct:   121 VSSLRFGKEVDGKCHSLTASYIRAQHQSNPNQPVCQFYEEFDNVGRQVPIPPGIYNLDDL 180

Query:    61 KEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNID 120
             K+ GR  G CPYFLAR A++HA IVVYSYHYLLDPKIA++VSKELA+ SVVVFDEAHNID
Sbjct:   181 KDFGRRKGWCPYFLARYALLHANIVVYSYHYLLDPKIADLVSKELAKKSVVVFDEAHNID 240

Query:   121 NVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARE 180
             NVC+DS+SV I RRT+++   N++TL+ T+  +KE D+AKLREEY RLVEGL++A  ARE
Sbjct:   241 NVCIDSMSVNITRRTLDRCQTNVETLQNTISRIKETDAAKLREEYRRLVEGLKEANVARE 300

Query:   181 TDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKD 240
             TD+ L+NPVLPDEILQE VPG+IRTAEHFVGF+KRF+EYLK RLR+  VVQES   FLKD
Sbjct:   301 TDIYLSNPVLPDEILQEAVPGSIRTAEHFVGFMKRFLEYLKARLRIHHVVQESAPQFLKD 360

Query:   241 ISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKV 289
             I  K    +  +  R+       L   L +  +   SP T +   ++ V
Sbjct:   361 IFEKVC--IDRKPLRFCAERLRSLLRTLEIADIADFSPITLISHFATLV 407

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB\|Q91941 ERCC2/XPD "ERCC2/XPD protein" [Xiphophorus maculatus (taxid:8083)]	Back alignment and assigned GO terms

FB\|FBgn0261850 Xpd "Xeroderma pigmentosum D" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|P18074 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

RGD\|1309109 Ercc2 "excision repair cross-complementing rodent repair deficiency, complementation group 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q60452 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Cricetulus griseus (taxid:10029)]	Back alignment and assigned GO terms

UNIPROTKB\|A6QLJ0 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N2P3 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:95413 Ercc2 "excision repair cross-complementing rodent repair deficiency, complementation group 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|A8MX75 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P18074	ERCC2_HUMAN	3, ., 6, ., 4, ., 1, 2	0.5861	0.3974	0.4921	yes	N/A
O08811	ERCC2_MOUSE	3, ., 6, ., 4, ., 1, 2	0.5765	0.3974	0.4921	yes	N/A
A6QLJ0	ERCC2_BOVIN	3, ., 6, ., 4, ., 1, 2	0.5789	0.3974	0.4921	yes	N/A
Q60452	ERCC2_CRIGR	3, ., 6, ., 4, ., 1, 2	0.5765	0.3974	0.4921	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	0.824
3rd Layer	3.6.4	0.766

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		941
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	1e-122
pfam06777		146	pfam06777, DUF1227, Protein of unknown function (D	3e-65
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	1e-57
smart00488		289	smart00488, DEXDc2, DEAD-like helicases superfamil	2e-47
smart00488		289	smart00488, DEXDc2, DEAD-like helicases superfamil	2e-47
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	6e-37
pfam06733		168	pfam06733, DEAD_2, DEAD_2	1e-35
pfam06733		168	pfam06733, DEAD_2, DEAD_2	1e-35
smart00488		289	smart00488, DEXDc2, DEAD-like helicases superfamil	1e-33
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	6e-22
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	8e-18
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	2e-15
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	8e-15
pfam06777		146	pfam06777, DUF1227, Protein of unknown function (D	4e-14
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	4e-11
pfam06733		168	pfam06733, DEAD_2, DEAD_2	3e-09
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	8e-06
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	1e-05
pfam13307		165	pfam13307, Helicase_C_2, Helicase C-terminal domai	3e-05
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	7e-05
pfam13307		165	pfam13307, Helicase_C_2, Helicase C-terminal domai	6e-04
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	7e-04

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

 Score =  388 bits (999), Expect = e-122
 Identities = 181/419 (43%), Positives = 247/419 (58%), Gaps = 49/419 (11%)

Query: 1   VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAV-GREAPLAPGVYSITK 59
           VSKER GK+V+G+C  LT S ++++     N+  C+FYE FD +   E  L   +  I  
Sbjct: 114 VSKERQGKVVNGKCIKLTVSKIKEQRTEKPNVESCEFYENFDELREVEDLLLSEIMDIED 173

Query: 60  LKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNI 119
           L E G  LGLCPYF  R+ +  A IV+  Y YLLDPKI + VS EL   S+V+FDEAHN+
Sbjct: 174 LVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELK-DSIVIFDEAHNL 232

Query: 120 DNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSAR 179
           DNVC+ SLS  ++ R++++    I      ++E KE D+ KL +E  +LVEGL+      
Sbjct: 233 DNVCISSLSSNLSVRSLKRCSKEIAEYFEKIEERKEVDARKLLDELQKLVEGLKQEDLLT 292

Query: 180 ETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLK 239
           + D+ LANPVLP E+L E VPGNIR AE F+  L R++EYLK  L+V  VV E P  FL+
Sbjct: 293 DEDIFLANPVLPKEVLPEAVPGNIRIAEIFLHKLSRYLEYLKDALKVLGVVSELPDAFLE 352

Query: 240 DISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFC 299
            +  K                                              I+R PLRFC
Sbjct: 353 HLKEKT--------------------------------------------FIDR-PLRFC 367

Query: 300 AERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYF 359
           +ERL++LLR LEIT+  DFS+LV++   ATLV +YT GF   +EP+ +K  TVPNP+L F
Sbjct: 368 SERLSNLLRELEITHPEDFSALVLLFTFATLVLTYTNGFLEGIEPYENK--TVPNPILKF 425

Query: 360 CCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMV 418
            CLD S+A+KP+F+R ++V++ SGTLSPLD +P+ L F PV   S +  L R  LL ++
Sbjct: 426 MCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKRENLLTLI 484

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 705

>gnl\|CDD\|191608 pfam06777, DUF1227, Protein of unknown function (DUF1227)	Back alignment and domain information

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

>gnl\|CDD\|214693 smart00488, DEXDc2, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|214693 smart00488, DEXDc2, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

>gnl\|CDD\|219153 pfam06733, DEAD_2, DEAD_2	Back alignment and domain information

>gnl\|CDD\|219153 pfam06733, DEAD_2, DEAD_2	Back alignment and domain information

>gnl\|CDD\|214693 smart00488, DEXDc2, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|191608 pfam06777, DUF1227, Protein of unknown function (DUF1227)	Back alignment and domain information

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

>gnl\|CDD\|219153 pfam06733, DEAD_2, DEAD_2	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		941
KOG1131\|consensus		755		100.0
KOG1133\|consensus		821		100.0
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	100.0
KOG1132\|consensus		945		100.0
KOG1131\|consensus		755		100.0
KOG1133\|consensus		821		100.0
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	100.0
KOG1132\|consensus		945		100.0
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	100.0
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	100.0
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	99.97
PF06777		146	DUF1227: Protein of unknown function (DUF1227); In	99.96
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.93
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	99.93
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	99.93
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	99.92
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	99.91
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.91
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.9
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.89
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	99.88
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	99.88
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	99.86
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.84
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.81
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.81
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	99.6
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.58
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	99.38
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	99.17
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	98.28
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	98.06
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	98.04
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.03
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	98.0
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	97.94
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	97.93
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	97.91
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	97.9
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	97.89
PTZ00424		401	helicase 45; Provisional	97.85
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	97.8
PTZ00110		545	helicase; Provisional	97.78
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	97.76
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	97.73
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	97.62
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.58
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	97.55
smart00487		201	DEXDc DEAD-like helicases superfamily.	97.54
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	97.52
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	97.47
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	97.46
PRK13767		876	ATP-dependent helicase; Provisional	97.46
PRK13766		773	Hef nuclease; Provisional	97.44
KOG0348\|consensus		708		97.4
PRK02362		737	ski2-like helicase; Provisional	97.37
KOG0335\|consensus		482		97.31
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	97.3
KOG0345\|consensus		567		97.29
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	97.28
KOG0331\|consensus		519		97.26
PRK00254		720	ski2-like helicase; Provisional	97.25
PRK01172		674	ski2-like helicase; Provisional	97.24
KOG0344\|consensus		593		97.2
KOG0350\|consensus		620		97.1
KOG0342\|consensus		543		97.07
COG1201		814	Lhr Lhr-like helicases [General function predictio	96.99
KOG0330\|consensus		476		96.93
PRK10689		1147	transcription-repair coupling factor; Provisional	96.8
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	96.72
PHA02558		501	uvsW UvsW helicase; Provisional	96.66
COG4889		1518	Predicted helicase [General function prediction on	96.66
PRK09694		878	helicase Cas3; Provisional	96.54
PRK09401		1176	reverse gyrase; Reviewed	96.52
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	96.51
PF13245		76	AAA_19: Part of AAA domain	96.46
PRK14701		1638	reverse gyrase; Provisional	96.38
PRK05580		679	primosome assembly protein PriA; Validated	96.36
KOG0340\|consensus		442		96.3
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	96.26
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	96.22
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	96.22
COG1205		851	Distinct helicase family with a unique C-terminal	96.18
KOG0346\|consensus		569		96.15
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	96.08
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	96.06
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.03
COG1204		766	Superfamily II helicase [General function predicti	95.97
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	95.89
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.77
KOG0354\|consensus		746		95.55
PHA02653		675	RNA helicase NPH-II; Provisional	95.45
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	95.4
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	95.35
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	95.34
PRK09200		790	preprotein translocase subunit SecA; Reviewed	95.22
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	95.18
KOG0338\|consensus		691		94.93
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	94.93
KOG1802\|consensus		935		94.82
KOG0952\|consensus		1230		94.64
KOG0333\|consensus		673		94.59
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	94.48
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	94.44
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	94.34
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	94.03
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	94.02
KOG0334\|consensus		997		93.94
TIGR00376		637	DNA helicase, putative. The gene product may repre	93.89
PRK04914		956	ATP-dependent helicase HepA; Validated	93.72
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	93.62
PRK12904		830	preprotein translocase subunit SecA; Reviewed	93.55
KOG0343\|consensus		758		93.44
PRK13107		908	preprotein translocase subunit SecA; Reviewed	93.2
TIGR02640		262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.0
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	92.98
KOG0336\|consensus		629		92.84
COG4096		875	HsdR Type I site-specific restriction-modification	92.73
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	92.6
PRK10536		262	hypothetical protein; Provisional	92.6
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	92.3
TIGR00595		505	priA primosomal protein N'. All proteins in this f	91.1
PRK08769		319	DNA polymerase III subunit delta'; Validated	91.01
PRK15483		986	type III restriction-modification system StyLTI en	90.84
COG0714		329	MoxR-like ATPases [General function prediction onl	90.74
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	90.47
KOG1803\|consensus		649		90.03
PHA02244		383	ATPase-like protein	89.64
KOG0328\|consensus		400		89.33
KOG0326\|consensus		459		89.24
PRK13531		498	regulatory ATPase RavA; Provisional	89.22
KOG0339\|consensus		731		88.81
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	88.57
KOG0347\|consensus		731		88.55
KOG0337\|consensus		529		87.95
PRK12326		764	preprotein translocase subunit SecA; Reviewed	87.67
KOG0989\|consensus		346		86.71
PF01695		178	IstB_IS21: IstB-like ATP binding protein; InterPro	86.01
PF05673		249	DUF815: Protein of unknown function (DUF815); Inte	85.56
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309		127	Torsin: Torsin; InterPro: IPR010448 This family co	85.42
KOG0351\|consensus		941		85.42
KOG0389\|consensus		941		85.0
PRK13894		319	conjugal transfer ATPase TrbB; Provisional	84.86
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	84.45
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	84.21
KOG4284\|consensus		980		84.13
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	84.12
PF01078		206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	84.08
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	83.86
PRK06835		329	DNA replication protein DnaC; Validated	83.69
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	83.3
KOG0327\|consensus		397		83.18
PRK13407		334	bchI magnesium chelatase subunit I; Provisional	82.83
smart00382		148	AAA ATPases associated with a variety of cellular	82.44
PRK12402		337	replication factor C small subunit 2; Reviewed	82.39
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	82.34
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	82.23
KOG0991\|consensus		333		82.17
KOG0352\|consensus		641		81.94
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	81.74
CHL00122		870	secA preprotein translocase subunit SecA; Validate	81.74
PF12775		272	AAA_7: P-loop containing dynein motor region D3; P	81.59
PRK11331		459	5-methylcytosine-specific restriction enzyme subun	81.1
PRK07993		334	DNA polymerase III subunit delta'; Validated	80.95
COG1474		366	CDC6 Cdc6-related protein, AAA superfamily ATPase	80.29
PLN03025		319	replication factor C subunit; Provisional	80.21
PRK06871		325	DNA polymerase III subunit delta'; Validated	80.19

>KOG1131\|consensus	Back alignment and domain information

Probab=100.00  E-value=1.9e-139  Score=1147.86  Aligned_cols=625  Identities=57%  Similarity=0.959  Sum_probs=592.7

Q ss_pred             CCCCCchhhHHHHhhhhhhhhhhhhhhcCCCCCCCcCccCcccccccCCCCCCCCCHHHHHHhchhCCCCHHHHHHHHhh
Q psy11433          1 VSKERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMGRELGLCPYFLARQAII   80 (941)
Q Consensus         1 ~~~~~~~~~i~~~C~~L~~~~~~~~~~~~~~~~~C~fy~~~~~~~~~~~l~~~i~diEdL~~~g~~~~~CPY~~aR~~~~   80 (941)
                      |+++++|+.||++|++||++|+|+|...+++.+.|.||+|++.  ....++.|+|++|||+++|++.++||||.+|+++.
T Consensus       121 v~~~r~g~~VD~~Cr~ltas~vr~~~~ed~~~~~C~f~en~~~--~~~~lp~gvy~~~dL~~~g~~k~~CPYflaR~~I~  198 (755)
T KOG1131|consen  121 VLKERNGNVVDAACRKLTASYVRAKLAEDPNVELCDFFENLED--KESLLPVGVYTLEDLKEYGEKKGWCPYFLARRMIP  198 (755)
T ss_pred             HHHHhcCCchhHHHHHHhHHHHHHHHhcCCCcchhhHHhhhhc--ccccCCcccccHHHHHHhhhcCCcChHHHHHHhhh
Confidence            5788999999999999999999999999999999999999976  45678899999999999999999999999999999


Q ss_pred             cCcEEEEccccccChhhhhHhhhhcCCCcEEEEecCccccHHhhhhcccccCHHHHHHHHHHHHHHHHHHHHHhHhhHHH
Q psy11433         81 HAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAK  160 (941)
Q Consensus        81 ~AdIVv~~y~yLl~~~~r~~~~~~l~~~~ivI~DEAHNL~d~~~~~~S~~is~~~l~~a~~~l~~~~~~~~rlk~~~~~~  160 (941)
                      .|+|||++||||+||.+.+.++..+.++++|||||||||+++|++++|+.|+..++++|.+.|..+++.+.|+|+.+.++
T Consensus       199 ~~nvivYsYhYllDPkIa~~VSkels~~svVvFDEAHNIDnvCIeslSv~i~r~~l~ra~~~l~~l~~~v~r~k~~d~~k  278 (755)
T KOG1131|consen  199 FANVIVYSYHYLLDPKIAELVSKELSKESVVVFDEAHNIDNVCIESLSVDITRRTLERASRNLNSLEQLVNRVKETDSQK  278 (755)
T ss_pred             cccEEEEehhhhcChHHHHHHHHhhCcCcEEEecccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhcchhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhcccchhhhcCCCCchhHhhhhcCCCccchhhHHHHHHHHHHHHHHHhhhhhhcccCccccccc
Q psy11433        161 LREEYARLVEGLRDAQSARETDVVLANPVLPDEILQEVVPGNIRTAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFLKD  240 (941)
Q Consensus       161 L~~~~~~l~~~l~~~~~~~~~d~~~~n~~~~~~il~e~~p~ni~~~~~f~~~l~~li~~lk~~~~~~~~~~~~~~~~~~~  240 (941)
                      |+.+|++|++||+.+...+.+|.+++||++|++++.|++|||||+++||+.||++|++|+|+||++.|            
T Consensus       279 l~~eY~klvegL~~~~~~~~~d~~lanPvLP~dvl~EavPGniR~aeHFv~fLkR~~ey~ktrl~~~h------------  346 (755)
T KOG1131|consen  279 LQDEYEKLVEGLKDASAERDEDQFLANPVLPDDVLKEAVPGNIRRAEHFVSFLKRLLEYLKTRLKVHH------------  346 (755)
T ss_pred             HHHHHHHHHHHhhccccccCccchhcCCCCchhhhhhhCCcchhhHHHHHHHHHHHHHHHHHhhhhee------------
Confidence            99999999999999998999999999999999999999999999999999999999999999998765            


Q ss_pred             cCCCCCCcchhhhhhhhhhhhhhhhhhhhhhhhhccchhhHHhhhchhhhhhccchhhhHHHHHHHHHhhhhcccCCCch
Q psy11433        241 ISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRFCAERLASLLRTLEITNLTDFSS  320 (941)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~l~f~~~rl~~l~~tl~~~~~~~~~~  320 (941)
                                                      +++|||.+|++++.+.+||++||+|||++||.++++||++++.+||++
T Consensus       347 --------------------------------v~~Esp~sFl~~i~~~~~IerKplrFCaeRL~~L~~tLeitd~~df~~  394 (755)
T KOG1131|consen  347 --------------------------------VIQESPASFLKSIKSLTFIERKPLRFCAERLSSLVRTLEITDVEDFGA  394 (755)
T ss_pred             --------------------------------eeccCcHHHHHHHHHhhhhhccchHHHHHHHHHHHHHhccCchhhhhH
Confidence                                            889999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhhhcccCCceEEEEccCCCCCCCCCCCEEEEEecCccccchHHhhhccEEEEecCCCCCCCchhhhhccccc
Q psy11433        321 LVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLYFCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPV  400 (941)
Q Consensus       321 ~~~~~~~~~l~~~~~~gf~ii~e~~~~~~~~~~~~~L~~~cLdPs~~fk~I~~~~rSVILtSGTLsPl~~y~~~L~f~p~  400 (941)
                      |..+++|+||+++|++||.+|+||+++..+++++|+|+|.|||+|+|++|||++|+|||+|||||||+++||++|+|.|+
T Consensus       395 l~~v~~faTlVstY~kGF~iIiEPfd~~~~tv~npil~~sClDaSiAikPVf~RFqsViITSGTlspldmyPk~lnf~pv  474 (755)
T KOG1131|consen  395 LKTVADFATLVSTYSKGFSIIIEPFDDRNPTVPNPILRFSCLDASIAIKPVFERFQSVIITSGTLSPLDMYPKILNFGPV  474 (755)
T ss_pred             HHHHHHHHHHHHHHhcCcEEEEcccccCCCCCCCCeeEEeecccchhhhHHHHhhheEEEecCcccccccCchhhccCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccccccccccCCCCchhhhhhcccccCCccccCCCCCCCHHHHHHHHHHHHHHHhcCceeeeCCCCCchhHHHHHHHH
Q psy11433        401 IMHSFSMTLARPCLLPMVRENYAMGLMIDDLPVFFPYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIV  480 (941)
Q Consensus       401 ~~~sf~~~l~~~~l~p~~~~~~~~~~~~~~~~~~FPy~~py~~Q~~~M~~v~~al~~~~~~iiEaPTGTGKTls~L~~al  480 (941)
                      .+.||+|+|+|+|++|++..                                                            
T Consensus       475 ~~~s~~mtLaR~c~~Pmiit------------------------------------------------------------  494 (755)
T KOG1131|consen  475 VGASFTMTLARNCLLPLIIT------------------------------------------------------------  494 (755)
T ss_pred             cchhhheecccccccceeee------------------------------------------------------------
Confidence            99999999999999999981                                                            


Q ss_pred             HHHhcCCCCCceEEEeccccchhHHHHHHHHHHHHHHhhcccccceeeEEecccccccccccccccchhhhhhhcccccc
Q psy11433        481 AYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVIRNYGQLLV  560 (941)
Q Consensus       481 ~~~~~~~~~~~ki~~ct~t~~q~~q~i~el~~~~~~~~~~~~~~~~~~~~l~sr~~lC~~~~~~~~~~~~~~~~~~~~~~  560 (941)
                                                            +|++|+.+                                  
T Consensus       495 --------------------------------------rG~Dqv~i----------------------------------  502 (755)
T KOG1131|consen  495 --------------------------------------RGNDQVAI----------------------------------  502 (755)
T ss_pred             --------------------------------------cCCcchhh----------------------------------
Confidence                                                  33444433                                  


Q ss_pred             ccccccCCCccccccccccccccccccccHHHHHHHhhhHhhhhcccCCceEEeccchHHHHHHHHHHhhcCchhhhhhc
Q psy11433        561 DIACVVPDGVVCFFTSYLYLESVFETRDDISVIRNYGQLLVDIACVVPDGVVCFFTSYLYLESVVASWYDQGIIDNLQKR  640 (941)
Q Consensus       561 ~~~~~~~~g~~~~~~~~~~l~~~~~~r~~~~~l~~lg~~l~~~~~~vp~Gi~~Ff~Sy~~~~~~l~~w~~~gi~~~l~~~  640 (941)
                                          ++.|+.|.++.+.+++|+.+.++++.+|||++||||||.||+++++.|+.+||++++.+.
T Consensus       503 --------------------ss~fe~r~d~~VvrnyG~llve~sk~vpdG~v~ff~sylYmesiv~~w~~~gil~ei~k~  562 (755)
T KOG1131|consen  503 --------------------SSKFEARGDPSVVRNYGNLLVEMSKIVPDGIVCFFPSYLYMESIVSRWYEQGILDEIMKY  562 (755)
T ss_pred             --------------------hhhhhhccChHHHhhcCcceeeecccCCCceEEEEehHHHHHHHHHHHHHHhHHHHHhhC
Confidence                                467889999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccccccchhhhhhhccc-cccCcccccccchhhcccccCCCCCCCCCchhhhhhccCCCCCCCCCCHHHHHHhc
Q psy11433        641 KLLFIETQDALDSRSVSKERDGK-IVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAPGVYSITKLKEMG  719 (941)
Q Consensus       641 K~if~E~~~~~~~~~~~l~~y~~-~~~~~Ga~L~av~~~~rGK~sEGid~C~F~d~~~~~gR~~vi~~~v~diedL~~~g  719 (941)
                      |++|||++|..+++ .++++|.. |.+||||+|++|   .|||+|||||   |.+   ++||+ |+|             
T Consensus       563 KL~fIetpD~~ETs-~al~ny~~aC~~gRGavl~sV---argkVsEgid---F~h---hyGR~-ViM-------------  618 (755)
T KOG1131|consen  563 KLLFIETPDFRETS-LALANYRYACDNGRGAVLLSV---ARGKVSEGID---FDH---HYGRE-VIM-------------  618 (755)
T ss_pred             ceEEEeCCchhhhH-HHHHHHHHHhcCCCCceEEEE---ecCccccCcc---ccc---ccCce-EEE-------------
Confidence            99999999999988 99999987 999999999999   9999999999   999   99999 999             


Q ss_pred             hhcCcCChHHHHHHHHccCEEEeccccccCHHHhhHhhhhccCCcEEEEeCCcCchHHhhhhcccccCHHHHHHHHHHHH
Q psy11433        720 RELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQ  799 (941)
Q Consensus       720 ~~~g~CPY~~~r~~~~~AdiIi~ny~yLld~~~~~~~~~~l~~~~ilIiDEAHNL~d~~~~~~S~~ls~~~l~~a~~~l~  799 (941)
                        .| .||......+..|.                                                             
T Consensus       619 --~g-IP~qytesriLkar-------------------------------------------------------------  634 (755)
T KOG1131|consen  619 --EG-IPYQYTESRILKAR-------------------------------------------------------------  634 (755)
T ss_pred             --Ee-ccchhhHHHHHHHH-------------------------------------------------------------
Confidence              78 88877443332221                                                             


Q ss_pred             HHHhHHHHhhHHhHHHHHHHHHHHHHHHHHhhccccccccccCCC-----ChhhhhhcCCCceEEEechhhhccccccCC
Q psy11433        800 TLEGTLKEMKEADSAKLREEYARLVEGLRDAQSARETDVVLANPV-----LPDEILQGKTDYGIMIFADKRFARSDKRSK  874 (941)
Q Consensus       800 ~~~~~l~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~~~~~-----~igr~ir~~~d~~~~il~d~r~~~~~~~~k  874 (941)
                                              ++||+++++++||+++.+++|     |.||++|+++|||+|||+|+||++.++++|
T Consensus       635 ------------------------le~Lrd~~~irE~dflTFDAmRhaAQC~GrvLr~K~dYg~mI~aDkRf~R~dKR~k  690 (755)
T KOG1131|consen  635 ------------------------LEYLRDQFQIRENDFLTFDAMRHAAQCLGRVLRGKTDYGLMIFADKRFSRGDKRSK  690 (755)
T ss_pred             ------------------------HHHHHHHhcccccceechHhHHHHHHHHHHHHhccccceeeEeeehhhccccchhh
Confidence                                    289999999999999888877     999999999999999999999999999999


Q ss_pred             chHHHHhhhccccCCCCHHHHHHHHHHHHHhcCCCCCccccccccccCHHHHHHHHHHhHh
Q psy11433        875 LPKWIQEYLTDNLTNLSTEEAVQLSKRWLRQMAQPFTREDMLGVALLSLDQLLEKEHARAE  935 (941)
Q Consensus       875 l~~wi~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  935 (941)
                      ||+||++++.+...|+|+++|++..++|+|.|||||+++|++|++|||++||+..+..+.+
T Consensus       691 lp~wi~~~l~~~~~nlstd~a~~varrflR~maQp~~k~dq~G~Sll~~edle~~~~~~~~  751 (755)
T KOG1131|consen  691 LPKWIRNHLFDAKLNLSTDMANQVARRFLRLMAQPFDKEDQLGVSLLSLEDLEKMQEEKLK  751 (755)
T ss_pred             hhHHHHhhhhhhccCCCcchhHHHHHHHHHHhcCCCCcccccccccccHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999977665443

>KOG1133\|consensus	Back alignment and domain information

>TIGR00604 rad3 DNA repair helicase (rad3)	Back alignment and domain information

>KOG1132\|consensus	Back alignment and domain information

>KOG1131\|consensus	Back alignment and domain information

>KOG1133\|consensus	Back alignment and domain information

>TIGR00604 rad3 DNA repair helicase (rad3)	Back alignment and domain information

>KOG1132\|consensus	Back alignment and domain information

>smart00488 DEXDc2 DEAD-like helicases superfamily	Back alignment and domain information

>smart00489 DEXDc3 DEAD-like helicases superfamily	Back alignment and domain information

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional	Back alignment and domain information

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional	Back alignment and domain information

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>smart00488 DEXDc2 DEAD-like helicases superfamily	Back alignment and domain information

>smart00489 DEXDc3 DEAD-like helicases superfamily	Back alignment and domain information

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin	Back alignment and domain information

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A	Back alignment and domain information

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4	Back alignment and domain information

>smart00491 HELICc2 helicase superfamily c-terminal domain	Back alignment and domain information

>smart00492 HELICc3 helicase superfamily c-terminal domain	Back alignment and domain information

>cd00268 DEADc DEAD-box helicases	Back alignment and domain information

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3	Back alignment and domain information

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases	Back alignment and domain information

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase	Back alignment and domain information

>PTZ00110 helicase; Provisional	Back alignment and domain information

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

>smart00487 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>TIGR01389 recQ ATP-dependent DNA helicase RecQ	Back alignment and domain information

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional	Back alignment and domain information

>TIGR00643 recG ATP-dependent DNA helicase RecG	Back alignment and domain information

>PRK13767 ATP-dependent helicase; Provisional	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>KOG0348\|consensus	Back alignment and domain information

>PRK02362 ski2-like helicase; Provisional	Back alignment and domain information

>KOG0335\|consensus	Back alignment and domain information

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype	Back alignment and domain information

>KOG0345\|consensus	Back alignment and domain information

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional	Back alignment and domain information

>KOG0331\|consensus	Back alignment and domain information

>PRK00254 ski2-like helicase; Provisional	Back alignment and domain information

>PRK01172 ski2-like helicase; Provisional	Back alignment and domain information

>KOG0344\|consensus	Back alignment and domain information

>KOG0350\|consensus	Back alignment and domain information

>KOG0342\|consensus	Back alignment and domain information

>COG1201 Lhr Lhr-like helicases [General function prediction only]	Back alignment and domain information

>KOG0330\|consensus	Back alignment and domain information

>PRK10689 transcription-repair coupling factor; Provisional	Back alignment and domain information

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional	Back alignment and domain information

>PHA02558 uvsW UvsW helicase; Provisional	Back alignment and domain information

>COG4889 Predicted helicase [General function prediction only]	Back alignment and domain information

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

>PRK12899 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PF13245 AAA_19: Part of AAA domain	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

>KOG0340\|consensus	Back alignment and domain information

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family	Back alignment and domain information

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>TIGR03714 secA2 accessory Sec system translocase SecA2	Back alignment and domain information

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]	Back alignment and domain information

>KOG0346\|consensus	Back alignment and domain information

>PRK12898 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>cd00046 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A	Back alignment and domain information

>COG1204 Superfamily II helicase [General function prediction only]	Back alignment and domain information

>TIGR01587 cas3_core CRISPR-associated helicase Cas3	Back alignment and domain information

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []	Back alignment and domain information

>KOG0354\|consensus	Back alignment and domain information

>PHA02653 RNA helicase NPH-II; Provisional	Back alignment and domain information

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type	Back alignment and domain information

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK09200 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR00963 secA preprotein translocase, SecA subunit	Back alignment and domain information

>KOG0338\|consensus	Back alignment and domain information

>PRK13104 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG1802\|consensus	Back alignment and domain information

>KOG0952\|consensus	Back alignment and domain information

>KOG0333\|consensus	Back alignment and domain information

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB	Back alignment and domain information

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A	Back alignment and domain information

>KOG0334\|consensus	Back alignment and domain information

>TIGR00376 DNA helicase, putative	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12904 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0343\|consensus	Back alignment and domain information

>PRK13107 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN	Back alignment and domain information

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>KOG0336\|consensus	Back alignment and domain information

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]	Back alignment and domain information

>PRK09751 putative ATP-dependent helicase Lhr; Provisional	Back alignment and domain information

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>PRK08769 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional	Back alignment and domain information

>COG0714 MoxR-like ATPases [General function prediction only]	Back alignment and domain information

>PRK12906 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG1803\|consensus	Back alignment and domain information

>PHA02244 ATPase-like protein	Back alignment and domain information

>KOG0328\|consensus	Back alignment and domain information

>KOG0326\|consensus	Back alignment and domain information

>PRK13531 regulatory ATPase RavA; Provisional	Back alignment and domain information

>KOG0339\|consensus	Back alignment and domain information

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold	Back alignment and domain information

>KOG0347\|consensus	Back alignment and domain information

>KOG0337\|consensus	Back alignment and domain information

>PRK12326 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0989\|consensus	Back alignment and domain information

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif	Back alignment and domain information

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function	Back alignment and domain information

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins	Back alignment and domain information

>KOG0351\|consensus	Back alignment and domain information

>KOG0389\|consensus	Back alignment and domain information

>PRK13894 conjugal transfer ATPase TrbB; Provisional	Back alignment and domain information

>cd00046 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A	Back alignment and domain information

>KOG4284\|consensus	Back alignment and domain information

>PRK13103 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX	Back alignment and domain information

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length	Back alignment and domain information

>PRK06835 DNA replication protein DnaC; Validated	Back alignment and domain information

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3	Back alignment and domain information

>KOG0327\|consensus	Back alignment and domain information

>PRK13407 bchI magnesium chelatase subunit I; Provisional	Back alignment and domain information

>smart00382 AAA ATPases associated with a variety of cellular activities	Back alignment and domain information

>PRK12402 replication factor C small subunit 2; Reviewed	Back alignment and domain information

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane	Back alignment and domain information

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0991\|consensus	Back alignment and domain information

>KOG0352\|consensus	Back alignment and domain information

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]	Back alignment and domain information

>CHL00122 secA preprotein translocase subunit SecA; Validated	Back alignment and domain information

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A	Back alignment and domain information

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional	Back alignment and domain information

>PRK07993 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03025 replication factor C subunit; Provisional	Back alignment and domain information

>PRK06871 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

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	Alignment Graph	Length	Definition	E-value
Query		941
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	3e-53
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	4e-31
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	3e-19
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	3e-08
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	6e-08
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	3e-07
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	3e-25
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	1e-24
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	2e-17
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	3e-09
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	8e-09
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	3e-07
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	5e-07
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	6e-22
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	1e-21
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	4e-17
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	1e-10
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	6e-09
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	7e-08
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	2e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

 Score =  195 bits (498), Expect = 3e-53
 Identities = 66/482 (13%), Positives = 142/482 (29%), Gaps = 127/482 (26%)

Query: 4   ERDGKIVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGREAPLAP-GVYSITKLKE 62
             D   ++    +   +  + R     N   C ++                + +  +  +
Sbjct: 98  VDDLHEINAESLAKFCNMKK-REVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYD 156

Query: 63  MGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARS---SVVVFDEAHNI 119
            G    +CPY   + A+  A IV+  Y Y L+  +A         S    V++ DEAHN+
Sbjct: 157 YGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNL 216

Query: 120 DNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQSAR 179
            ++     S RI+  ++ +A    Q                 +   + L+E +R A    
Sbjct: 217 PDIGRSIGSFRISVESLNRADREAQAYGDP--------ELSQKIHVSDLIEMIRSA---- 264

Query: 180 ETDVVLANPVLPDEILQEVVPGNIR-TAEHFVGFLKRFIEYLKTRLRVQQVVQESPATFL 238
                     L   + +    G++R   + F+ +++   +  +  +R           ++
Sbjct: 265 ----------LQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYV 314

Query: 239 KDISSKPAPSMISEAYRYIFSTEEHLKTRLRVQQVVQESPATFLKDISSKVCIERKPLRF 298
           ++   K                                              + + P  +
Sbjct: 315 ENEKEK----------------------------------------------VGKVPFSY 328

Query: 299 CAERLASLLRTLEITNLTDFSSLVVITHLATLVSSYTKGFAIIVEPFSDKAPTVPNPVLY 358
           C+   + ++   +                        + +A I+ P            + 
Sbjct: 329 CSSVASRIIAFSD---------------------QDEEKYAAILSPEDG-------GYMQ 360

Query: 359 FCCLDSSLAIKPVFDRFQTVVITSGTLSPLDMYPKILNFQPVIMHSFSMTLARPCLLPMV 418
             CLD S  ++ + +     +  SGTL P D Y  I  F+        +       +   
Sbjct: 361 AACLDPSGILEVLKES--KTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYIAYY 418

Query: 419 R----------ENY--AMGLMIDDL----P----VFFP-YEYIYPEQYAYMVELKKALDA 457
                      E     M  +I+D+         V+FP Y  +  ++    V  +   + 
Sbjct: 419 DGVSSKYDTLDEKELDRMATVIEDIILKVKKNTIVYFPSYSLM--DRVENRVSFEHMKEY 476

Query: 458 KG 459
           +G
Sbjct: 477 RG 478

PyMOL of 4a15

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		941
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	100.0
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	100.0
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	100.0
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.96
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.93
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.93
2pl3_A		236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.79
1fuu_A		394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	98.63
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	98.6
2z0m_A		337	337AA long hypothetical ATP-dependent RNA helicase	98.58
3dkp_A		245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.36
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.35
3fe2_A		242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.32
1vec_A		206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.29
1wrb_A		253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.28
3iuy_A		228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.26
1t6n_A		220	Probable ATP-dependent RNA helicase; RECA-like fol	98.26
1q0u_A		219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.25
3ber_A		249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.24
1qde_A		224	EIF4A, translation initiation factor 4A; DEAD box	98.23
2oxc_A		230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.2
2gxq_A		207	Heat resistant RNA dependent ATPase; RNA helicase,	98.16
3bor_A		237	Human initiation factor 4A-II; translation initiat	98.15
3ly5_A		262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.14
3sqw_A		579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.07
2db3_A		434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	98.03
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	98.01
3fmo_B		300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.0
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	97.98
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	97.98
3i5x_A		563	ATP-dependent RNA helicase MSS116; protein-RNA com	97.98
3pey_A		395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	97.97
3fht_A		412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	97.92
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	97.92
3eiq_A		414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	97.89
3oiy_A		414	Reverse gyrase helicase domain; topoisomerase, DNA	97.88
2v1x_A		591	ATP-dependent DNA helicase Q1; DNA strand annealin	97.81
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	97.79
3fmp_B		479	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.75
3b6e_A		216	Interferon-induced helicase C domain-containing P;	97.74
1gm5_A		780	RECG; helicase, replication restart; HET: DNA ADP;	97.69
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	97.64
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	97.63
1oyw_A		523	RECQ helicase, ATP-dependent DNA helicase; winged	97.59
1rif_A		282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.51
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	97.5
2xgj_A		1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	97.44
3fho_A		508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	97.43
4a4z_A		997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	97.38
3l9o_A		1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	97.38
2eyq_A		1151	TRCF, transcription-repair coupling factor; MFD, S	97.36
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	97.35
4gl2_A		699	Interferon-induced helicase C domain-containing P;	97.21
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	97.21
2va8_A		715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	97.2
2zj8_A		720	DNA helicase, putative SKI2-type helicase; RECA fo	97.19
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	97.13
2p6r_A		702	Afuhel308 helicase; protein-DNA complex, SF2 helic	97.08
4ddu_A		1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	97.08
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	97.02
3h1t_A		590	Type I site-specific restriction-modification syst	97.02
1gku_B		1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	97.01
2fz4_A		237	DNA repair protein RAD25; RECA-like domain, DNA da	97.0
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.94
1tf5_A		844	Preprotein translocase SECA subunit; ATPase, helic	96.82
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	96.69
2w00_A		1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	96.65
1yks_A		440	Genome polyprotein [contains: flavivirin protease	96.6
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	96.57
2fsf_A		853	Preprotein translocase SECA subunit; ATPase, DNA-R	96.56
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	96.51
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	96.42
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	96.33
3llm_A		235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	96.33
1nkt_A		922	Preprotein translocase SECA 1 subunit; preprotein	96.31
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	96.11
4b3f_X		646	DNA-binding protein smubp-2; hydrolase, helicase;	95.61
3upu_A		459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.51
2ipc_A		997	Preprotein translocase SECA subunit; nucleotide bi	95.41
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	94.76
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	94.55
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	94.52
2gk6_A		624	Regulator of nonsense transcripts 1; UPF1, helicas	93.77
3jux_A		822	Protein translocase subunit SECA; protein transloc	93.77
3rc3_A		677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	93.09
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	91.75
2xzl_A		802	ATP-dependent helicase NAM7; hydrolase-RNA complex	91.7
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	91.67
2wjy_A		800	Regulator of nonsense transcripts 1; nonsense medi	91.23
1w36_D		608	RECD, exodeoxyribonuclease V alpha chain; recombin	91.05
3lfu_A		647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	90.0
3n70_A		145	Transport activator; sigma-54, ntpase, PSI, MCSG,	88.42
3co5_A		143	Putative two-component system transcriptional RES	88.23
1a5t_A		334	Delta prime, HOLB; zinc finger, DNA replication; 2	88.04
3e1s_A		574	Exodeoxyribonuclease V, subunit RECD; alpha and be	87.97
2r44_A		331	Uncharacterized protein; putative ATPase, structur	87.42
3nbx_X		500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	87.02
2w58_A		202	DNAI, primosome component (helicase loader); ATP-b	86.45
1c4o_A		664	DNA nucleotide excision repair enzyme UVRB; uvrabc	86.28
3b6e_A		216	Interferon-induced helicase C domain-containing P;	84.52
1uaa_A		673	REP helicase, protein (ATP-dependent DNA helicase	83.89
2pl3_A		236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	83.43
1jbk_A		195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	82.89
3hws_A		363	ATP-dependent CLP protease ATP-binding subunit CL;	82.79
1iqp_A		327	RFCS; clamp loader, extended AAA-ATPase domain, co	82.59
1ofh_A		310	ATP-dependent HSL protease ATP-binding subunit HSL	82.35
2gxq_A		207	Heat resistant RNA dependent ATPase; RNA helicase,	82.12
4fcw_A		311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	81.91
2chg_A		226	Replication factor C small subunit; DNA-binding pr	81.89
1njg_A		250	DNA polymerase III subunit gamma; rossman-like fol	81.83
3te6_A		318	Regulatory protein SIR3; heterochromatin, gene sil	81.44
1qde_A		224	EIF4A, translation initiation factor 4A; DEAD box	81.26
2bjv_A		265	PSP operon transcriptional activator; AAA, transcr	81.14
2p65_A		187	Hypothetical protein PF08_0063; CLPB, malaria, str	81.08
3ec2_A		180	DNA replication protein DNAC; helicase loader, rep	80.72
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	80.67

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*	Back alignment and structure

Probab=100.00  E-value=3.7e-48  Score=466.38  Aligned_cols=132  Identities=20%  Similarity=0.339  Sum_probs=108.4

Q ss_pred             hHHH---HhhhhhhhhhhhhhhcCCCCCCCcCccCcccccc-cCCCCCCCCCHHHHHHhchhCCCCHHHHHHHHhhcCcE
Q psy11433          9 IVDG---RCHSLTSSSVRDRHKAGENIPVCDFYEKFDAVGR-EAPLAPGVYSITKLKEMGRELGLCPYFLARQAIIHAKI   84 (941)
Q Consensus         9 ~i~~---~C~~L~~~~~~~~~~~~~~~~~C~fy~~~~~~~~-~~~l~~~i~diEdL~~~g~~~~~CPY~~aR~~~~~AdI   84 (941)
                      ..++   .|.+|++++.      ......|+||.+.+..+. .+.+..+++|+|++++.|++++.||||.+|+.+..|||
T Consensus       105 ~~~~~~~~C~~l~~~~~------~~~~~~C~~~~~~~~~gd~~~~l~~~~~die~l~~~~~~~~~CPy~~aR~~~~~ADv  178 (620)
T 4a15_A          105 NAESLAKFCNMKKREVM------AGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDADI  178 (620)
T ss_dssp             CHHHHHHHHHHHHHHHH------TTCTTSSTTCSGGGGCHHHHHHHHHHCCCHHHHHHHHHHTTCCHHHHHHHHGGGCSE
T ss_pred             hhhhHHHHHHHHHhccc------cCCCCCCCcccccCcccchhHHhccCCCCHHHHHHHhhhcCCCccHHHHHHhhcCCE
Confidence            4554   9999987643      123467999998754221 12234578999999999999999999999999999999


Q ss_pred             EEEccccccChhhhhHhhhh---cCCCcEEEEecCccccHHhhhhcccccCHHHHHHHHHHHHHH
Q psy11433         85 VVYSYHYLLDPKIANVVSKE---LARSSVVVFDEAHNIDNVCVDSLSVRINRRTIEKAVGNIQTL  146 (941)
Q Consensus        85 Vv~~y~yLl~~~~r~~~~~~---l~~~~ivI~DEAHNL~d~~~~~~S~~is~~~l~~a~~~l~~~  146 (941)
                      ||+||||||++.+++.+...   .+++++|||||||||+|+|++++|.+||..+|..+.+++..+
T Consensus       179 VV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d~a~~~~S~~ls~~~l~~~~~~l~~~  243 (620)
T 4a15_A          179 VIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFRISVESLNRADREAQAY  243 (620)
T ss_dssp             EEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHHHHHHHHCEEEEHHHHHHHHHHHHHT
T ss_pred             EEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHHHHHHhhcceeCHHHHHHHHHHHHHH
Confidence            99999999999988753222   257899999999999999999999999999999999998764

PyMOL of 4a15

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}	Back alignment and structure

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}	Back alignment and structure

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*	Back alignment and structure

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}	Back alignment and structure

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}	Back alignment and structure

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A	Back alignment and structure

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19	Back alignment and structure

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}	Back alignment and structure

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19	Back alignment and structure

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}	Back alignment and structure

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A	Back alignment and structure

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*	Back alignment and structure

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A	Back alignment and structure

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*	Back alignment and structure

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}	Back alignment and structure

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}	Back alignment and structure

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}	Back alignment and structure

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}	Back alignment and structure

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}	Back alignment and structure

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A	Back alignment and structure

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A	Back alignment and structure

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A	Back alignment and structure

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*	Back alignment and structure

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B	Back alignment and structure

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A	Back alignment and structure

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}	Back alignment and structure

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*	Back alignment and structure

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*	Back alignment and structure

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}	Back alignment and structure

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}	Back alignment and structure

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}	Back alignment and structure

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19	Back alignment and structure

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*	Back alignment and structure

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*	Back alignment and structure

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*	Back alignment and structure

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23	Back alignment and structure

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}	Back alignment and structure

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A	Back alignment and structure

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}	Back alignment and structure

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1	Back alignment and structure

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}	Back alignment and structure

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}	Back alignment and structure

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}	Back alignment and structure

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}	Back alignment and structure

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*	Back alignment and structure

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B	Back alignment and structure

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A	Back alignment and structure

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A	Back alignment and structure

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B	Back alignment and structure

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}	Back alignment and structure

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*	Back alignment and structure

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19	Back alignment and structure

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*	Back alignment and structure

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A	Back alignment and structure

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A	Back alignment and structure

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*	Back alignment and structure

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*	Back alignment and structure

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}	Back alignment and structure

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*	Back alignment and structure

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A	Back alignment and structure

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A	Back alignment and structure

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A	Back alignment and structure

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}	Back alignment and structure

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A	Back alignment and structure

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A	Back alignment and structure

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A	Back alignment and structure

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}	Back alignment and structure

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}	Back alignment and structure

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}	Back alignment and structure

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}	Back alignment and structure

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A	Back alignment and structure

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*	Back alignment and structure

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A	Back alignment and structure

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*	Back alignment and structure

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}	Back alignment and structure

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...	Back alignment and structure

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A	Back alignment and structure

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*	Back alignment and structure

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*	Back alignment and structure

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}	Back alignment and structure

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}	Back alignment and structure

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*	Back alignment and structure

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*	Back alignment and structure

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}	Back alignment and structure

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}	Back alignment and structure

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}	Back alignment and structure

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*	Back alignment and structure

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}	Back alignment and structure

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}	Back alignment and structure

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20	Back alignment and structure

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A	Back alignment and structure

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20	Back alignment and structure

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*	Back alignment and structure

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A	Back alignment and structure

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*	Back alignment and structure

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}	Back alignment and structure

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*	Back alignment and structure

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A	Back alignment and structure

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*	Back alignment and structure

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}	Back alignment and structure

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*	Back alignment and structure

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		941
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.41
d1t6na_		207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.37
d1veca_		206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.32
d1wrba1		238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.32
d2g9na1		218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.22
d1gkub1		237	Helicase-like "domain" of reverse gyrase {Archaeon	98.16
d1wp9a1		200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.12
d1q0ua_		209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.09
d1qdea_		212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.09
d1oywa2		206	RecQ helicase domain {Escherichia coli [TaxId: 562	98.08
d1s2ma1		206	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.98
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	97.94
d2p6ra3		202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.79
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	97.35
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.31
d1yksa1		140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.26
d1rifa_		282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	97.17
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	96.93
d2fz4a1		206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.84
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	95.37
d1uaaa1		306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.53
d1pjra1		318	DEXX box DNA helicase {Bacillus stearothermophilus	93.16
d1w36d1		359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.87
d1z63a1		230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	92.63
d1fnna2		276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	91.07
d1a5ta2		207	delta prime subunit of DNA polymerase III, N-domai	90.47
d1in4a2		238	Holliday junction helicase RuvB {Thermotoga mariti	89.11
d1ixsb2		239	Holliday junction helicase RuvB {Thermus thermophi	87.67
d1iqpa2		231	Replication factor C {Archaeon Pyrococcus furiosus	87.27
d1t5la1		413	Nucleotide excision repair enzyme UvrB {Bacillus c	86.61
d1sxjc2		227	Replication factor C3 {Baker's yeast (Saccharomyce	85.92
d2i3ba1		189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	85.04
d1w5sa2		287	CDC6-like protein APE0152, N-terminal domain {Aero	84.76
d1ofha_		309	HslU {Haemophilus influenzae [TaxId: 727]}	84.39
d1sxjb2		224	Replication factor C4 {Baker's yeast (Saccharomyce	83.51
d1g8pa_		333	ATPase subunit of magnesium chelatase, BchI {Rhodo	82.26

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.41  E-value=2.8e-07  Score=94.35  Aligned_cols=74  Identities=19%  Similarity=0.144  Sum_probs=60.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHhcCceeeeCCCCCchhHHHHHHHHHHHhcCCCCCceEEEeccccchhHHHHHHHHHHH
Q psy11433        436 PYEYIYPEQYAYMVELKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLF  514 (941)
Q Consensus       436 Py~~py~~Q~~~M~~v~~al~~~~~~iiEaPTGTGKTls~L~~al~~~~~~~~~~~ki~~ct~t~~q~~q~i~el~~~~  514 (941)
                      -|+.|+|+|.+.+    ..+-+|+++++.||||||||+||+.|++..+.... ...+.++.+.|.....|+.++++++.
T Consensus        36 g~~~pt~IQ~~aI----p~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~-~~~~~lil~PtreLa~Qi~~~~~~l~  109 (222)
T d2j0sa1          36 GFEKPSAIQQRAI----KQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV-RETQALILAPTRELAVQIQKGLLALG  109 (222)
T ss_dssp             TCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS-CSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHH----HHHHCCCCeEEEcCcchhhhhhhcccccccccccc-cCceeEEecchHHHHHHHHHHHHHHh
Confidence            3567999996554    44557999999999999999999999998876553 45677888899999999999988873

PyMOL of d2j0sa1

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}	Back information, alignment and structure

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}	Back information, alignment and structure

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}	Back information, alignment and structure

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}	Back information, alignment and structure

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}	Back information, alignment and structure

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}	Back information, alignment and structure

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}	Back information, alignment and structure

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}	Back information, alignment and structure