Psyllid ID: psy3462

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-----
Protein Sequence
MTKKSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQSTKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVRRRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQESTGGTQSQNSTVMPQRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRDSQ
Secondary Structure (PSIPRED)
ccccccccccEEEcccccccccHHHHHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHcccccccccccccccccccccccHHHHccccHHcccccccccHHHHHHHHHHHHHHccccccccccccHHHHHHcccccccccEEEEEccccccccccccccEEEEEEEEEccccccccccccccccccccccEEEccEEEcccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHccccccccccccccccEEEEEEccHHHHHHHHccccccccccEEEcccccccccHHHHHHHHHHHccHHHHHcccccHHHHHHHccccccccEEEEcccccccHHHHHHHHHHHcccccccccccccccccccccEEEEEEEcccccccEEEEcccHHHHHHHHHHHHHcccccccccEEEEEccHHHHHHHHHHHccccHHHHHHccccEEEcccccccHHHHHHHHHHHHccccccEEEEEEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEEEEccccccccccccccHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccEEEEccccccccEEEEEEEEEEEcccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHcccccccccccHHHHHHHHHHHHHHHcccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcEcccccEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccccEEcHHHHHHHHHccccccccccccHHcHHHHHHEEEEccHEEEEcccHHHccccccccccccccccccccEEEEccEEEcccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccEEEEcccccHHHHHHHccccHHHHHHHccccHHHHHcHHHHHHHHHcccccccHHEcccHHHHHHHHcccHHHHHEHHccccHHHHHHHHHHHHHHHcccccccccEEcHcHHHHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHccHHHHHcHHHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHHHHHcccccccccccccHEEEEccccccccEEEHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHcHccccEEEEEccHccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHccccccHHHHHHcHcccccccccccccccHHcccccEEEEEccccccHHHHHEEHHHHHHHccc
Coil and Loop (DISEMBL)
MTKKSSDIFKTylnepnyflkyssckILHLQVIQGCNkakncllesptgsgkTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKtsfvfcgrsdfFLLFRERRIsdtmvkkpatkkkplnevvtrdytIHMHKRlhkvgfkkraPRAIKVVRAFVKKQmgtedvridTRLNKHIWskginnhtlgtAYFDSAAKCHKEMRYRNRVVKLtgfdqligesavlpsvkdklkpsaatsytiggvkvefpvkaypsqisMMNQVSnlfeqpnhflkyssckILHLQVIQGCNkakncllesptgsgkTLALLCSVLAWQRKEKELVQQKMFEQRTQDLqkipfrklkisrlkakdfstnngmEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRqstkktkvdKLKVLNGRSKNLVSSIDFILGLLykgvncedyhvcmessvAFDQLIQLDLMLdehlnpyvlkvkdtpciedleqfstralvspCFQLIQLDLMldehlnpyvlkvkdtpciedlVLKRNIFYDTLMLCdvqtketkhrdsvkqvmgkgnlelckgvfwtrfpntcqysvvyptgllkggdwYQIQAYRALNQALGRCIRHRYDWGAILLVDQRfysknsqqGLSKWVRNQVQNTSSHNTFMENLRNFVRRRMEIQLEEERVKREEanlneeeevmddtdrasssqestggtqsqnstvMPQRWAYLSLLKklsplaptwgpplkiqsvpqvifhkpcdnksIFKLISIKYMLIRDSQ
Flexible Loop (DISEMBL)
MTKKSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRErrisdtmvkkpatkkkplnevvtrdytihmhkrlhkvgfkkrapraIKVVRAFvkkqmgtedvridtrlnkhiwskginnhtlGTAYFDSAAKCHKEMRYRNRVVKLTGfdqligesavlpsvkdklkpsaatsytiggvkveFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEqrtqdlqkipfrklkisrlkakdfstnngmEQQLLTCITTINQqedelrqstkktrvdklkvlngrsknlvsSIDFILGLLYKGIQTCITTINqqedelrqstkktkvdklkvlngrsknlvssIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVqtketkhrdsvkqvmgkgnLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRnqvqntsshntfmenlrNFVRRRMEIQLeeervkreeanlneeeevmddtdrasssqestggtqsqnstvmPQRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKymlirdsq
Low Complexity Region (SEG)
MTKKSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQStkktkvdklkvlNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVRRRMEIQLEEERVKReeanlneeeeVMDDTDRAsssqestggtqsqnstVMPQRWaylsllkklsplapTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRDSQ
Disordered region (IsUnstruct)
*******IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRERRISDTMV*********LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMF******LQKIPFRKLKISRLKAK*F*****MEQQLLTCITTIN*****************LKVLNGRSKNLVSSIDFILGLLYKGIQTCITTIN*****************LKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRN**************LRNFV****************************************************QRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLI****
Disordered Region (DISOPRED)
*********KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE*********************VFCGRSDFFLL*****************KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYF****************VKLTGFDQLIGESAVLPSVKD*LKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR*****************************************MEQQLLTCI***********************************IDFILGLLYKGIQTC***********************************SIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNF**********************************************************************************************IFKLISIKYMLIR***
Disordered Region (DISEMBL)
MTKKSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQSTKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQT**********QVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVRRRMEIQLEEERVKREEANL*****************************VMPQRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRDSQ
Disordered Region (DISPRO)
****SSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRER***************PLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKIS**************QQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQSTKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVRRRMEI*********************************************PQRWA*LSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRD**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTKKSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGESAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQSTKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLDLMLDEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSVKQVMGKGNLELCKGVFWTRFPNTCQYSVVYPTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSSSQESTGGTQSQNSTVMPQRWAYLSLLKKLSPLAPTWGPPLKIQSVPQVIFHKPCDNKSIFKLISIKYMLIRDSQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	795	2.2.26 [Sep-21-2011]
Q5SXJ3	1174	Fanconi anemia group J pr	yes	N/A	0.152	0.103	0.438	3e-22
Q7KF90	124	60S ribosomal protein L31	N/A	N/A	0.083	0.532	0.712	1e-21
Q9GP16	124	60S ribosomal protein L31	N/A	N/A	0.083	0.532	0.712	1e-21
Q9BX63	1249	Fanconi anemia group J pr	yes	N/A	0.101	0.064	0.566	1e-21
Q3YK19	1252	Fanconi anemia group J pr	yes	N/A	0.096	0.061	0.582	3e-21
Q9V597	124	60S ribosomal protein L31	yes	N/A	0.094	0.604	0.64	2e-20
Q5RBR9	125	60S ribosomal protein L31	no	N/A	0.083	0.528	0.681	2e-20
Q9IA76	124	60S ribosomal protein L31	N/A	N/A	0.089	0.572	0.675	2e-20
P62902	125	60S ribosomal protein L31	no	N/A	0.083	0.528	0.681	3e-20
P62901	125	60S ribosomal protein L31	no	N/A	0.083	0.528	0.681	3e-20

>sp|Q5SXJ3|FANCJ_MOUSE Fanconi anemia group J protein homolog OS=Mus musculus GN=Brip1 PE=2 SV=1

 Score =  107 bits (268), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 57/130 (43%), Positives = 83/130 (63%), Gaps = 9/130 (6%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
           GLL G  WY+IQAYRALNQALGRCIRH+ DWGA++LVD RF +  ++   GLSKWVR Q+
Sbjct: 812 GLLPGRQWYEIQAYRALNQALGRCIRHKNDWGALILVDDRFNNNPNRYISGLSKWVRQQI 871

Query: 670 QNTSSHNTFMENLRNFVRRRMEIQLEEERVKREEANLNEEEEVMDDTDRASSSQESTGGT 729
           Q+ SS  + +E+L  F RR  ++     R K++E    + E  ++     +  ++ST  +
Sbjct: 872 QHHSSFASALESLTEFSRRHQKVT---NRSKKDEKCTKDNEPTLE----VACLEDSTFTS 924

Query: 730 QSQNSTVMPQ 739
            S++S   P+
Sbjct: 925 VSESSHQSPE 934

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q7KF90|RL31_SPOFR 60S ribosomal protein L31 OS=Spodoptera frugiperda GN=RpL31 PE=2 SV=1

 Score =  105 bits (263), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 47/66 (71%), Positives = 57/66 (86%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           K  +NEVVTR+YT+++HKRLH VGFKKRAPRAIK +R F +KQMGT DVR+DTRLNK +W
Sbjct: 11  KSAINEVVTREYTVNLHKRLHGVGFKKRAPRAIKEIRKFAEKQMGTPDVRVDTRLNKFLW 70

Query: 177 SKGINN 182
           SKG+ N
Sbjct: 71  SKGVRN 76

Spodoptera frugiperda (taxid: 7108)

>sp|Q9GP16|RL31_HELVI 60S ribosomal protein L31 OS=Heliothis virescens GN=RpL31 PE=2 SV=1

 Score =  105 bits (263), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 47/66 (71%), Positives = 57/66 (86%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           K  +NEVVTR+YT+++HKRLH VGFKKRAPRAIK +R F +KQMGT DVR+DTRLNK +W
Sbjct: 11  KSAINEVVTREYTVNLHKRLHGVGFKKRAPRAIKEIRKFAEKQMGTPDVRVDTRLNKFLW 70

Query: 177 SKGINN 182
           SKG+ N
Sbjct: 71  SKGVRN 76

Heliothis virescens (taxid: 7102)

>sp|Q9BX63|FANCJ_HUMAN Fanconi anemia group J protein OS=Homo sapiens GN=BRIP1 PE=1 SV=1

 Score =  105 bits (263), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 47/83 (56%), Positives = 62/83 (74%), Gaps = 2/83 (2%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
           GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  S+   GLSKWVR Q+
Sbjct: 809 GLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQI 868

Query: 670 QNTSSHNTFMENLRNFVRRRMEI 692
           Q+ S+  + +E+L  F ++  ++
Sbjct: 869 QHHSTFESALESLAEFSKKHQKV 891

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the Fanconi anemia pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3YK19|FANCJ_CHICK Fanconi anemia group J protein homolog OS=Gallus gallus GN=BRIP1 PE=2 SV=1

 Score =  104 bits (259), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 46/79 (58%), Positives = 58/79 (73%), Gaps = 2/79 (2%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
           GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  ++   GLSKW+R QV
Sbjct: 819 GLLPGSQWYEIQAYRALNQALGRCIRHRSDWGALILVDDRFRNNPNKYITGLSKWIRQQV 878

Query: 670 QNTSSHNTFMENLRNFVRR 688
           Q+  +  + +E+L  F  R
Sbjct: 879 QHHENFGSALESLHAFAER 897

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway of DNA repair, after FANCD2 ubiquitination. Probably not involved in the repair of DNA double-strand breaks by homologous recombination.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9V597|RL31_DROME 60S ribosomal protein L31 OS=Drosophila melanogaster GN=RpL31 PE=1 SV=1

 Score =  102 bits (253), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/75 (64%), Positives = 58/75 (77%)

Query: 108 TMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRI 167
           T  K     K  +NEVVTR+ TIH+ KR+H +GFKKRAPRAIK +R F +++MGT DVRI
Sbjct: 2   TKTKGEKINKSAINEVVTRECTIHLAKRVHNIGFKKRAPRAIKEIRKFAEREMGTTDVRI 61

Query: 168 DTRLNKHIWSKGINN 182
           DTRLNKHIWSKGI +
Sbjct: 62  DTRLNKHIWSKGIRS 76

Drosophila melanogaster (taxid: 7227)

>sp|Q5RBR9|RL31_PONAB 60S ribosomal protein L31 OS=Pongo abelii GN=RPL31 PE=2 SV=1

 Score =  102 bits (253), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/66 (68%), Positives = 56/66 (84%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           +  +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F  K+MGT DVRIDTRLNK +W
Sbjct: 14  RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVW 73

Query: 177 SKGINN 182
           +KGI N
Sbjct: 74  AKGIRN 79

Pongo abelii (taxid: 9601)

>sp|Q9IA76|RL31_PAROL 60S ribosomal protein L31 OS=Paralichthys olivaceus GN=rpl31 PE=2 SV=1

 Score =  101 bits (252), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/74 (67%), Positives = 59/74 (79%), Gaps = 3/74 (4%)

Query: 112 KPATKKK---PLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRID 168
           K   KKK    +NEVVTR+YTI++HKR+H VGFKKRAPRAIK +R F  K+MGT DVRID
Sbjct: 5   KKGEKKKGRSAINEVVTREYTINVHKRIHGVGFKKRAPRAIKEIRKFAVKEMGTPDVRID 64

Query: 169 TRLNKHIWSKGINN 182
           TRLNK +WSKG+ N
Sbjct: 65  TRLNKAVWSKGVRN 78

Paralichthys olivaceus (taxid: 8255)

>sp|P62902|RL31_RAT 60S ribosomal protein L31 OS=Rattus norvegicus GN=Rpl31 PE=2 SV=1

 Score =  101 bits (251), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 45/66 (68%), Positives = 56/66 (84%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           +  +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F  K+MGT DVRIDTRLNK +W
Sbjct: 14  RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVW 73

Query: 177 SKGINN 182
           +KGI N
Sbjct: 74  AKGIRN 79

Rattus norvegicus (taxid: 10116)

>sp|P62901|RL31_PIG 60S ribosomal protein L31 OS=Sus scrofa GN=RPL31 PE=2 SV=1

 Score =  101 bits (251), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 45/66 (68%), Positives = 56/66 (84%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           +  +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F  K+MGT DVRIDTRLNK +W
Sbjct: 14  RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVW 73

Query: 177 SKGINN 182
           +KGI N
Sbjct: 74  AKGIRN 79

Sus scrofa (taxid: 9823)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	795
110671500	122	putative ribosomal protein L31e [Diaphor	0.093	0.606	0.959	4e-27
241122570	128	ribosomal protein L31, putative [Ixodes	0.090	0.562	0.708	9e-22
346470041	128	hypothetical protein [Amblyomma maculatu	0.088	0.546	0.728	1e-21
194246091	128	ribosomal protein L31 [Dermacentor varia	0.088	0.546	0.728	1e-21
114153208	128	ribosomal protein L31 [Argas monolakensi	0.083	0.515	0.757	2e-21
328714715	912	PREDICTED: Fanconi anemia group J protei	0.069	0.060	0.628	2e-21
328714717	918	PREDICTED: Fanconi anemia group J protei	0.069	0.059	0.628	2e-21
332019760	123	60S ribosomal protein L31 [Acromyrmex ec	0.083	0.536	0.742	3e-21
264667407	124	ribosomal protein L31 [Chrysomela tremul	0.083	0.532	0.727	3e-21
72153924	124	PREDICTED: 60S ribosomal protein L31-lik	0.093	0.596	0.675	3e-21

>gi|110671500|gb|ABG82001.1| putative ribosomal protein L31e [Diaphorina citri]

 Score =  130 bits (326), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 71/74 (95%), Positives = 72/74 (97%)

Query: 109 MVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRID 168
           MVKKP TKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRID
Sbjct: 1   MVKKPTTKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRID 60

Query: 169 TRLNKHIWSKGINN 182
           TRLNKHIWSKGI +
Sbjct: 61  TRLNKHIWSKGIKS 74

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241122570|ref|XP_002403582.1| ribosomal protein L31, putative [Ixodes scapularis] gi|67084033|gb|AAY66951.1| ribosomal protein L31, partial [Ixodes scapularis] gi|215493472|gb|EEC03113.1| ribosomal protein L31, putative [Ixodes scapularis]

 Score =  112 bits (280), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 51/72 (70%), Positives = 60/72 (83%)

Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
           K+    K  LNEVVTR+Y+IH+HKRLH VGFK+RAPRAIK ++ F +KQMGT DVRIDTR
Sbjct: 9   KREKRGKSTLNEVVTREYSIHLHKRLHGVGFKRRAPRAIKEIKKFAEKQMGTSDVRIDTR 68

Query: 171 LNKHIWSKGINN 182
           LNK+IWSKGI N
Sbjct: 69  LNKYIWSKGIRN 80

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346470041|gb|AEO34865.1| hypothetical protein [Amblyomma maculatum]

 Score =  111 bits (278), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 58/70 (82%)

Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
           K+    K  LNEVVTR+YTIH+HKRLH +GFKKRAPRAIK +R F +KQMGT DVR+DTR
Sbjct: 9   KREKRGKSTLNEVVTREYTIHLHKRLHGIGFKKRAPRAIKEIRKFAEKQMGTSDVRVDTR 68

Query: 171 LNKHIWSKGI 180
           LNK IWSKGI
Sbjct: 69  LNKFIWSKGI 78

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194246091|gb|ACF35537.1| ribosomal protein L31 [Dermacentor variabilis]

 Score =  111 bits (278), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 58/70 (82%)

Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
           K+    K  LNEVVTR+YTIH+HKRLH +GFKKRAPRAIK +R F +KQMGT DVR+DTR
Sbjct: 9   KREKRGKSTLNEVVTREYTIHLHKRLHGIGFKKRAPRAIKEIRKFAEKQMGTSDVRVDTR 68

Query: 171 LNKHIWSKGI 180
           LNK IWSKGI
Sbjct: 69  LNKFIWSKGI 78

Source: Dermacentor variabilis

Species: Dermacentor variabilis

Genus: Dermacentor

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114153208|gb|ABI52770.1| ribosomal protein L31 [Argas monolakensis]

 Score =  111 bits (278), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 57/66 (86%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           K  LNEVVTR+YTIH+HKRLH VGFKK+APRAIK +R F +KQMGT DVR+DTRLNK IW
Sbjct: 15  KSTLNEVVTREYTIHLHKRLHGVGFKKKAPRAIKEIRKFAEKQMGTSDVRVDTRLNKFIW 74

Query: 177 SKGINN 182
           SKG+ N
Sbjct: 75  SKGVRN 80

Source: Argas monolakensis

Species: Argas monolakensis

Genus: Argas

Family: Argasidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328714715|ref|XP_003245432.1| PREDICTED: Fanconi anemia group J protein homolog isoform 2 [Acyrthosiphon pisum]

 Score =  110 bits (276), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 59/78 (75%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQN 671
           GLL G +WYQIQAYRALNQALGRCIRHR DWGAILLVD R+    +  GLSKW+R +V+ 
Sbjct: 825 GLLPGWEWYQIQAYRALNQALGRCIRHRNDWGAILLVDSRYEQPKNLSGLSKWIRGRVER 884

Query: 672 TSSHNTFMENLRNFVRRR 689
            +S +T +  L+NFV  R
Sbjct: 885 NNSWSTIVTKLKNFVETR 902

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328714717|ref|XP_001943091.2| PREDICTED: Fanconi anemia group J protein homolog isoform 1 [Acyrthosiphon pisum]

 Score =  110 bits (276), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 59/78 (75%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQN 671
           GLL G +WYQIQAYRALNQALGRCIRHR DWGAILLVD R+    +  GLSKW+R +V+ 
Sbjct: 831 GLLPGWEWYQIQAYRALNQALGRCIRHRNDWGAILLVDSRYEQPKNLSGLSKWIRGRVER 890

Query: 672 TSSHNTFMENLRNFVRRR 689
            +S +T +  L+NFV  R
Sbjct: 891 NNSWSTIVTKLKNFVETR 908

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332019760|gb|EGI60224.1| 60S ribosomal protein L31 [Acromyrmex echinatior]

 Score =  110 bits (275), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 57/66 (86%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           K  +NEVVTR+YT+++HKRLH VGFKKRAPRAIK +R F +KQMGT DVRIDTRLNK +W
Sbjct: 10  KSAINEVVTREYTVNLHKRLHGVGFKKRAPRAIKEIRKFAEKQMGTPDVRIDTRLNKQLW 69

Query: 177 SKGINN 182
           SKGI N
Sbjct: 70  SKGIRN 75

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|264667407|gb|ACY71289.1| ribosomal protein L31 [Chrysomela tremula]

 Score =  110 bits (275), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 57/66 (86%)

Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           K  +NEVVTR+YT+++HKRLH +GFKKRAPRAIK +R F +KQMGT DVRIDTRLNK +W
Sbjct: 11  KSAINEVVTREYTVNLHKRLHGIGFKKRAPRAIKAIRQFAEKQMGTPDVRIDTRLNKQLW 70

Query: 177 SKGINN 182
           SKGI N
Sbjct: 71  SKGIRN 76

Source: Chrysomela tremula

Species: Chrysomela tremula

Genus: Chrysomela

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|72153924|ref|XP_793832.1| PREDICTED: 60S ribosomal protein L31-like [Strongylocentrotus purpuratus]

 Score =  110 bits (275), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 52/77 (67%), Positives = 63/77 (81%), Gaps = 3/77 (3%)

Query: 109 MVKKPATKKK---PLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDV 165
           MVKK  ++KK    LNEVVTRDYTIH+HKR+H V FK+RAPRAIK +R F  K MGT+D+
Sbjct: 1   MVKKGGSEKKKRSALNEVVTRDYTIHLHKRIHGVSFKRRAPRAIKEIRTFATKMMGTDDI 60

Query: 166 RIDTRLNKHIWSKGINN 182
           RIDTRLNKHIWS+G+ +
Sbjct: 61  RIDTRLNKHIWSQGVRS 77

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	795
UNIPROTKB|J3QSE8	994	BRIP1 "Fanconi anemia group J	0.101	0.081	0.566	8.3e-27
UNIPROTKB|J9NVZ8	1214	BRIP1 "Uncharacterized protein	0.101	0.066	0.566	8.7e-27
UNIPROTKB|E2RHN5	1244	BRIP1 "Uncharacterized protein	0.101	0.065	0.566	9.3e-27
MGI|MGI:2442836	1174	Brip1 "BRCA1 interacting prote	0.101	0.068	0.578	1e-26
UNIPROTKB|E1C1X9	1249	BRIP1 "Fanconi anemia group J	0.100	0.064	0.560	1.3e-26
UNIPROTKB|Q3YK19	1252	BRIP1 "Fanconi anemia group J	0.100	0.063	0.560	1.3e-26
UNIPROTKB|Q9BX63	1249	BRIP1 "Fanconi anemia group J	0.101	0.064	0.566	1.6e-26
ZFIN|ZDB-GENE-081107-11	1217	brip1 "BRCA1 interacting prote	0.108	0.070	0.539	1.2e-25
RGD|1307659	818	Brip1 "BRCA1 interacting prote	0.101	0.099	0.554	2e-25
DICTYBASE|DDB_G0286621	1078	fncJ "DEAD/DEAH box helicase"	0.090	0.066	0.541	3.8e-25

UNIPROTKB|J3QSE8 BRIP1 "Fanconi anemia group J protein" [Homo sapiens (taxid:9606)]

 Score = 253 (94.1 bits), Expect = 8.3e-27, Sum P(2) = 8.3e-27
 Identities = 47/83 (56%), Positives = 62/83 (74%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  S+   GLSKWVR Q+
Sbjct:   809 GLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQI 868

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ S+  + +E+L  F ++  ++
Sbjct:   869 QHHSTFESALESLAEFSKKHQKV 891

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

UNIPROTKB|J9NVZ8 BRIP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 8.7e-27, Sum P(2) = 8.7e-27
 Identities = 47/83 (56%), Positives = 63/83 (75%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRH+ DWGA++LVD RF S  S+   GLSKW+R Q+
Sbjct:   808 GLLPGRQWYEIQAYRALNQALGRCIRHKNDWGALILVDDRFRSNPSRYISGLSKWIRQQI 867

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ S+  + +E+L +F R+  ++
Sbjct:   868 QHHSTFESALESLSDFSRKHQKV 890

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RHN5 BRIP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 9.3e-27, Sum P(2) = 9.3e-27
 Identities = 47/83 (56%), Positives = 63/83 (75%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRH+ DWGA++LVD RF S  S+   GLSKW+R Q+
Sbjct:   809 GLLPGRQWYEIQAYRALNQALGRCIRHKNDWGALILVDDRFRSNPSRYISGLSKWIRQQI 868

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ S+  + +E+L +F R+  ++
Sbjct:   869 QHHSTFESALESLSDFSRKHQKV 891

GO:0031965 "nuclear membrane" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:2442836 Brip1 "BRCA1 interacting protein C-terminal helicase 1" [Mus musculus (taxid:10090)]

 Score = 254 (94.5 bits), Expect = 1.0e-26, Sum P(2) = 1.0e-26
 Identities = 48/83 (57%), Positives = 62/83 (74%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRH+ DWGA++LVD RF +  ++   GLSKWVR Q+
Sbjct:   812 GLLPGRQWYEIQAYRALNQALGRCIRHKNDWGALILVDDRFNNNPNRYISGLSKWVRQQI 871

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ SS  + +E+L  F RR  ++
Sbjct:   872 QHHSSFASALESLTEFSRRHQKV 894

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

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

GO:0006281 "DNA repair" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=IEA

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

GO:0008285 "negative regulation of cell proliferation" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

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:0046872 "metal ion binding" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

UNIPROTKB|E1C1X9 BRIP1 "Fanconi anemia group J protein homolog" [Gallus gallus (taxid:9031)]

 Score = 246 (91.7 bits), Expect = 1.3e-26, Sum P(2) = 1.3e-26
 Identities = 46/82 (56%), Positives = 59/82 (71%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQ--GLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  ++   GLSKW+R QV
Sbjct:   819 GLLPGSQWYEIQAYRALNQALGRCIRHRSDWGALILVDDRFRNNPNKYITGLSKWIRQQV 878

Query:   670 QNTSSHNTFMENLRNFVRRRME 691
             Q+  +  + +E+L  F  R  +
Sbjct:   879 QHHENFGSALESLHAFAERNQK 900

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

UNIPROTKB|Q3YK19 BRIP1 "Fanconi anemia group J protein homolog" [Gallus gallus (taxid:9031)]

 Score = 246 (91.7 bits), Expect = 1.3e-26, Sum P(2) = 1.3e-26
 Identities = 46/82 (56%), Positives = 59/82 (71%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQ--GLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  ++   GLSKW+R QV
Sbjct:   819 GLLPGSQWYEIQAYRALNQALGRCIRHRSDWGALILVDDRFRNNPNKYITGLSKWIRQQV 878

Query:   670 QNTSSHNTFMENLRNFVRRRME 691
             Q+  +  + +E+L  F  R  +
Sbjct:   879 QHHENFGSALESLHAFAERNQK 900

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

UNIPROTKB|Q9BX63 BRIP1 "Fanconi anemia group J protein" [Homo sapiens (taxid:9606)]

 Score = 253 (94.1 bits), Expect = 1.6e-26, Sum P(2) = 1.6e-26
 Identities = 47/83 (56%), Positives = 62/83 (74%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  S+   GLSKWVR Q+
Sbjct:   809 GLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRNNPSRYISGLSKWVRQQI 868

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ S+  + +E+L  F ++  ++
Sbjct:   869 QHHSTFESALESLAEFSKKHQKV 891

GO:0005524 "ATP binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

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

GO:0003677 "DNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0000077 "DNA damage checkpoint" evidence=NAS

GO:0006302 "double-strand break repair" evidence=NAS

GO:0005737 "cytoplasm" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0031965 "nuclear membrane" evidence=IDA

ZFIN|ZDB-GENE-081107-11 brip1 "BRCA1 interacting protein C-terminal helicase 1" [Danio rerio (taxid:7955)]

 Score = 237 (88.5 bits), Expect = 1.2e-25, Sum P(2) = 1.2e-25
 Identities = 48/89 (53%), Positives = 64/89 (71%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQ--GLSKWVRNQV 669
             GLL GG WY+IQAYRALNQALGRCIRHR DWGA++LVD RF +  ++   GLSKWVR  V
Sbjct:   842 GLLPGGRWYEIQAYRALNQALGRCIRHRNDWGALILVDDRFRTNPNKYITGLSKWVRQLV 901

Query:   670 QNTSSHNTFMENLRNFVR-RRMEIQLEEE 697
             ++  +    M++L +F + +R  ++  EE
Sbjct:   902 RHHDTFTGAMQSLESFSQGQRGAVETFEE 930

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

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

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

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

RGD|1307659 Brip1 "BRCA1 interacting protein C-terminal helicase 1" [Rattus norvegicus (taxid:10116)]

 Score = 247 (92.0 bits), Expect = 2.0e-25, Sum P(3) = 2.0e-25
 Identities = 46/83 (55%), Positives = 61/83 (73%)

Query:   612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQ--QGLSKWVRNQV 669
             GLL G  WY+IQAYRALNQALGRCIRH+ DWGA++LVD RF +   +   GLSKWVR Q+
Sbjct:   732 GLLPGRQWYEIQAYRALNQALGRCIRHKNDWGALILVDDRFNNNPDRYISGLSKWVRQQI 791

Query:   670 QNTSSHNTFMENLRNFVRRRMEI 692
             Q+ S+  + +E+L  F +R  ++
Sbjct:   792 QHHSTFASALESLTEFSKRHQKV 814

GO:0003674 "molecular_function" evidence=ND

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=ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0008285 "negative regulation of cell proliferation" evidence=IDA

GO:0031965 "nuclear membrane" evidence=ISO

GO:0071295 "cellular response to vitamin" evidence=IEP

DICTYBASE|DDB_G0286621 fncJ "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 226 (84.6 bits), Expect = 3.8e-25, Sum P(3) = 3.8e-25
 Identities = 39/72 (54%), Positives = 55/72 (76%)

Query:   614 LKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTS 673
             + GGDWY++QAYRALNQALGRCIRH+ D+G+ILL+D+RF    +   LSKW R+ ++N  
Sbjct:  1000 ISGGDWYKLQAYRALNQALGRCIRHKNDYGSILLIDERFTQMGNWNSLSKWTRSCIKNNR 1059

Query:   674 SHNTFMENLRNF 685
             + NT + +L+ F
Sbjct:  1060 NLNTSLSSLKLF 1071

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

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

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

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006302 "double-strand break repair" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;IC

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

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)
Q757D7	RL31_ASHGO	No assigned EC number	0.6393	0.0767	0.5350	yes	N/A
Q9V597	RL31_DROME	No assigned EC number	0.64	0.0943	0.6048	yes	N/A
Q6FWF4	RL31_CANGA	No assigned EC number	0.6065	0.0767	0.5398	yes	N/A
P0C2H8	RL31A_YEAST	No assigned EC number	0.5901	0.0767	0.5398	yes	N/A
Q9STR1	RL312_ARATH	No assigned EC number	0.6119	0.0842	0.5630	yes	N/A
Q9URX6	RL31_SCHPO	No assigned EC number	0.6470	0.0855	0.6017	yes	N/A
P0C2H9	RL31B_YEAST	No assigned EC number	0.6065	0.0767	0.5398	yes	N/A
P51420	RL313_ARATH	No assigned EC number	0.6119	0.0842	0.5630	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	795
pfam01198	83	pfam01198, Ribosomal_L31e, Ribosomal protein L31e	4e-31
cd00463	83	cd00463, Ribosomal_L31e, Eukaryotic/archaeal ribos	2e-27
COG2097	89	COG2097, RPL31A, Ribosomal protein L31E [Translati	6e-21
pfam13307	165	pfam13307, Helicase_C_2, Helicase C-terminal domai	5e-16
PRK01192	89	PRK01192, PRK01192, 50S ribosomal protein L31e; Re	1e-12
PTZ00193	188	PTZ00193, PTZ00193, 60S ribosomal protein L31; Pro	4e-12
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	8e-11
smart00488	289	smart00488, DEXDc2, DEAD-like helicases superfamil	8e-09
smart00488	289	smart00488, DEXDc2, DEAD-like helicases superfamil	1e-08
smart00491	142	smart00491, HELICc2, helicase superfamily c-termin	1e-08
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	2e-07
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	5e-05
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	1e-04
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	3e-04
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	0.002
pfam03133	291	pfam03133, TTL, Tubulin-tyrosine ligase family	0.003

>gnl|CDD|216358 pfam01198, Ribosomal_L31e, Ribosomal protein L31e

 Score =  116 bits (292), Expect = 4e-31
 Identities = 40/62 (64%), Positives = 47/62 (75%), Gaps = 1/62 (1%)

Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
            EVVTR+YTI++ KR   V FKKRAPRAIK +R F  K M T+DVRID +LNK IWS+GI
Sbjct: 1   EEVVTREYTINLRKR-KGVPFKKRAPRAIKEIRKFAAKHMKTDDVRIDPKLNKAIWSRGI 59

Query: 181 NN 182
            N
Sbjct: 60  RN 61

Length = 83

>gnl|CDD|199209 cd00463, Ribosomal_L31e, Eukaryotic/archaeal ribosomal protein L31

 Score =  106 bits (266), Expect = 2e-27
 Identities = 38/62 (61%), Positives = 45/62 (72%), Gaps = 1/62 (1%)

Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
            EVV R+YTI++ KR H V  KKRAPRAIK +R F  K M TEDVRID +LN+ IWS+GI
Sbjct: 2   EEVVEREYTINLRKRKH-VPRKKRAPRAIKEIRKFAAKHMKTEDVRIDPKLNEAIWSRGI 60

Query: 181 NN 182
             
Sbjct: 61  EK 62

Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit. Length = 83

>gnl|CDD|225008 COG2097, RPL31A, Ribosomal protein L31E [Translation, ribosomal structure and biogenesis]

 Score = 87.4 bits (217), Expect = 6e-21
 Identities = 31/61 (50%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 122 EVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGIN 181
            VV R YTI +  R  KV   KRAPRA+K++R FV + M  E+VRID  LN+ IW +GI 
Sbjct: 5   VVVERIYTIPLR-RAKKVPRTKRAPRAVKIIRKFVARHMKAEEVRIDPSLNEKIWERGIE 63

Query: 182 N 182
            
Sbjct: 64  K 64

Length = 89

>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain

 Score = 76.1 bits (188), Expect = 5e-16
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQ 668
           G     ++Y  QA R LNQA+GR IRH  D+G ++L+D+R  +++  + L KW+   
Sbjct: 109 GKDGFREYYLPQAIRKLNQAIGRLIRHEDDYGVVILLDERLLTRSYGKLLLKWLPPG 165

This domain is the second of two tandem AAA domains found in a wide variety of helicase enzymes. Length = 165

>gnl|CDD|234916 PRK01192, PRK01192, 50S ribosomal protein L31e; Reviewed

 Score = 64.2 bits (157), Expect = 1e-12
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTE--DVRIDTRLNKHIWSK 178
            EV  R YTI + + + KV   KRA RA+K+VR F+ +    +   V+ID  +N+ IW +
Sbjct: 3   KEVEERIYTIPL-RDVKKVPRTKRADRAVKLVREFLARHFKADEDKVKIDPSINEKIWER 61

Query: 179 GINN 182
           G   
Sbjct: 62  GREK 65

Length = 89

>gnl|CDD|140220 PTZ00193, PTZ00193, 60S ribosomal protein L31; Provisional

 Score = 65.4 bits (159), Expect = 4e-12
 Identities = 33/66 (50%), Positives = 44/66 (66%), Gaps = 2/66 (3%)

Query: 115 TKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKH 174
           T +KP N  ++ + TIH+ K L K  F KRAP AIK ++AFV + M T+D RID  LN +
Sbjct: 77  TGRKPDN--ISMEATIHLSKLLKKKTFHKRAPIAIKRIKAFVGRLMKTKDNRIDASLNTY 134

Query: 175 IWSKGI 180
           IW KG+
Sbjct: 135 IWHKGV 140

Length = 188

>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3)

 Score = 65.1 bits (159), Expect = 8e-11
 Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 3/67 (4%)

Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNT 677
           D+Y+  A RA+NQA+GR IRH+ D+G+I+L+D+R+   N ++ L KW++       S + 
Sbjct: 641 DFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQ---DTIQSSDL 697

Query: 678 FMENLRN 684
               +  
Sbjct: 698 NGMAISL 704

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|214693 smart00488, DEXDc2, DEAD-like helicases superfamily

 Score = 57.4 bits (139), Expect = 8e-09
 Identities = 29/105 (27%), Positives = 44/105 (41%), Gaps = 33/105 (31%)

Query: 244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSG 303
             FP + YP Q   M ++  + ++                        K  +LESPTG+G
Sbjct: 3   FYFPYEPYPIQYEFMEELKRVLDR-----------------------GKIGILESPTGTG 39

Query: 304 KTLALLCSVLAWQRKEKELVQ----------QKMFEQRTQDLQKI 338
           KTL+LLC  L W R   E +Q              E+R ++L+K+
Sbjct: 40  KTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL 84

Length = 289

>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily

 Score = 56.6 bits (137), Expect = 1e-08
 Identities = 23/58 (39%), Positives = 31/58 (53%), Gaps = 10/58 (17%)

Query: 40 KNCLLESPTGSGKTLALLCSVLAWQRKEKELVQ----------QKMFEQRTQDLQKTS 87
          K  +LESPTG+GKTL+LLC  L W R   E +Q              E+R ++L+K  
Sbjct: 28 KIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM 85

Length = 289

>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain

 Score = 54.2 bits (131), Expect = 1e-08
 Identities = 17/35 (48%), Positives = 26/35 (74%)

Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRF 652
           + Y   A RAL QA+GR IRH+ D+G ++L+D+R+
Sbjct: 106 EVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRY 140

Length = 142

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

 Score = 54.4 bits (131), Expect = 2e-07
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQ 670
           ++Y   A   L QA+GR IR   D G I+L+D+R+ +K   + L   +    +
Sbjct: 584 EFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKLLLDSLPPFPK 636

Length = 654

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

 Score = 46.3 bits (110), Expect = 5e-05
 Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 24/83 (28%)

Query: 239 IGGVKVEFP-VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLE 297
            G + V FP  +  P Q  M   V+   +                         +  L+E
Sbjct: 4   DGYLAVAFPGFEPRPEQREMAEAVAEALK-----------------------GGEGLLIE 40

Query: 298 SPTGSGKTLALLCSVLAWQRKEK 320
           +PTG+GKTLA L   LA+ R+E 
Sbjct: 41  APTGTGKTLAYLLPALAYAREEG 63

Length = 654

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

 Score = 45.6 bits (108), Expect = 1e-04
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 14/75 (18%)

Query: 37  NKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDF 96
              +  L+E+PTG+GKTLA L   LA+ R+E + V   +   RT+ LQ+           
Sbjct: 32  KGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV---IISTRTKALQE----------- 77

Query: 97  FLLFRERRISDTMVK 111
            LL  +  I   + K
Sbjct: 78  QLLEEDLPIHKLLKK 92

Length = 654

>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3)

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)

Query: 41 NCLLESPTGSGKTLALLCSVLAWQRKEKELV-------QQKMFEQRTQDLQKTSFVF 90
            +LE P+G+GKT++LL  +LA+Q+++ E+             EQ T++L+K     
Sbjct: 31 EAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLMSYR 87

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|233047 TIGR00604, rad3, DNA repair helicase (rad3)

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 7/52 (13%)

Query: 293 NCLLESPTGSGKTLALLCSVLAWQRKEKELV-------QQKMFEQRTQDLQK 337
             +LE P+G+GKT++LL  +LA+Q+++ E+             EQ T++L+K
Sbjct: 31  EAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRK 82

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|217380 pfam03133, TTL, Tubulin-tyrosine ligase family

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)

Query: 522 CFQLIQLDLMLDEHLNPYVLKVKDTP-----CIEDLVLKRNIFYDTL 563
           CF+L   D M+DE+L P++L+V  +P        D  LK  +  D L
Sbjct: 233 CFELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQLIDDVL 279

Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain. Length = 291

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	795
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
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.95
PTZ00193	188	60S ribosomal protein L31; Provisional	99.94
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.93
PF01198	83	Ribosomal_L31e: Ribosomal protein L31e; InterPro:	99.93
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.93
PRK01192	89	50S ribosomal protein L31e; Reviewed	99.92
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.92
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.92
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.91
KOG0893|consensus	125		99.91
COG2097	89	RPL31A Ribosomal protein L31E [Translation, riboso	99.89
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	99.88
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.88
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	99.85
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	99.85
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.55
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.55
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.52
KOG1133|consensus	821		99.47
KOG1132|consensus	945		99.36
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.28
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.24
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.08
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.01
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.78
KOG1131|consensus	755		98.73
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	98.64
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.63
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.57
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	98.24
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	98.19
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	98.11
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.07
PTZ00110	545	helicase; Provisional	98.06
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	98.05
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	98.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	97.98
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	97.98
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	97.98
PTZ00424	401	helicase 45; Provisional	97.96
KOG0345|consensus	567		97.93
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.87
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	97.84
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	97.83
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	97.79
KOG0348|consensus	708		97.77
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.71
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	97.66
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	97.62
PRK13767	876	ATP-dependent helicase; Provisional	97.55
COG1201	814	Lhr Lhr-like helicases [General function predictio	97.52
KOG0331|consensus	519		97.52
PRK02362	737	ski2-like helicase; Provisional	97.51
KOG0342|consensus	543		97.46
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.45
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.44
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	97.41
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	97.4
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	97.4
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	97.35
COG1205	851	Distinct helicase family with a unique C-terminal	97.35
KOG0348|consensus	708		97.34
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	97.31
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	97.31
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.3
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.3
KOG0335|consensus	482		97.29
PTZ00424	401	helicase 45; Provisional	97.29
KOG0345|consensus	567		97.23
PRK00254	720	ski2-like helicase; Provisional	97.23
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.23
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	97.23
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.22
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	97.22
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	97.21
PRK01172	674	ski2-like helicase; Provisional	97.19
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	97.14
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	97.09
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	97.08
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	97.05
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	97.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	97.0
PTZ00110	545	helicase; Provisional	96.97
KOG0344|consensus	593		96.95
KOG0331|consensus	519		96.9
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.9
KOG0330|consensus	476		96.85
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.84
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	96.82
KOG0346|consensus	569		96.79
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	96.7
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	96.67
PRK09694	878	helicase Cas3; Provisional	96.67
KOG0333|consensus	673		96.66
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.65
PRK13767	876	ATP-dependent helicase; Provisional	96.6
PRK09401	1176	reverse gyrase; Reviewed	96.49
PRK01172	674	ski2-like helicase; Provisional	96.48
PRK02362	737	ski2-like helicase; Provisional	96.45
KOG0350|consensus	620		96.43
PRK14701	1638	reverse gyrase; Provisional	96.4
COG1201	814	Lhr Lhr-like helicases [General function predictio	96.37
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	96.32
KOG0330|consensus	476		96.32
KOG0338|consensus	691		96.27
KOG0336|consensus	629		96.24
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	96.23
PRK10689	1147	transcription-repair coupling factor; Provisional	96.21
KOG0340|consensus	442		96.1
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	96.04
PRK10689	1147	transcription-repair coupling factor; Provisional	96.04
COG1204	766	Superfamily II helicase [General function predicti	96.03
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	95.98
KOG0343|consensus	758		95.94
KOG0347|consensus	731		95.93
KOG0350|consensus	620		95.92
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	95.92
COG1205	851	Distinct helicase family with a unique C-terminal	95.88
KOG0335|consensus	482		95.86
PRK09694	878	helicase Cas3; Provisional	95.82
PRK00254	720	ski2-like helicase; Provisional	95.81
KOG0334|consensus	997		95.77
PHA02653	675	RNA helicase NPH-II; Provisional	95.75
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	95.72
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	95.7
PRK14701	1638	reverse gyrase; Provisional	95.65
KOG0334|consensus	997		95.61
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	95.5
KOG0344|consensus	593		95.47
PRK09200	790	preprotein translocase subunit SecA; Reviewed	95.45
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	95.41
PRK05580	679	primosome assembly protein PriA; Validated	95.38
KOG0339|consensus	731		95.34
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	95.31
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.21
KOG0342|consensus	543		95.17
PRK05580	679	primosome assembly protein PriA; Validated	95.04
PRK09401	1176	reverse gyrase; Reviewed	95.01
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	94.93
KOG0333|consensus	673		94.92
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	94.91
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	94.73
KOG0346|consensus	569		94.67
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	94.52
PHA02558	501	uvsW UvsW helicase; Provisional	94.49
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.46
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	94.41
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	94.33
KOG0326|consensus	459		94.3
PRK13766	773	Hef nuclease; Provisional	94.28
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	94.13
KOG0337|consensus	529		94.05
PRK12904	830	preprotein translocase subunit SecA; Reviewed	94.05
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	94.04
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	93.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	93.93
PHA02558	501	uvsW UvsW helicase; Provisional	93.85
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	93.64
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	93.53
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	93.41
KOG0352|consensus	641		93.35
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	93.14
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	93.11
KOG0343|consensus	758		93.09
KOG0952|consensus	1230		93.06
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	93.03
PRK13766	773	Hef nuclease; Provisional	92.62
KOG0327|consensus	397		92.54
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	91.94
PRK13107	908	preprotein translocase subunit SecA; Reviewed	91.93
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	91.93
PHA02653	675	RNA helicase NPH-II; Provisional	91.89
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	91.6
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	91.58
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	91.12
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	91.05
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	91.05
PRK15483	986	type III restriction-modification system StyLTI en	91.04
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	90.92
PF13245	76	AAA_19: Part of AAA domain	90.59
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	90.59
PRK09200	790	preprotein translocase subunit SecA; Reviewed	90.33
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.26
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	90.04
COG1204	766	Superfamily II helicase [General function predicti	89.94
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	89.87
PF13245	76	AAA_19: Part of AAA domain	89.84
KOG0354|consensus	746		89.6
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	89.55
KOG0349|consensus	725		89.1
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	88.87
PRK10536	262	hypothetical protein; Provisional	88.75
PRK13531	498	regulatory ATPase RavA; Provisional	88.74
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	88.43
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	88.34
KOG0341|consensus	610		88.32
COG0714	329	MoxR-like ATPases [General function prediction onl	88.01
PRK15483	986	type III restriction-modification system StyLTI en	87.65
KOG0351|consensus	941		87.55
KOG0354|consensus	746		87.41
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	87.06
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	86.71
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	86.26
KOG0353|consensus	695		86.16
KOG0328|consensus	400		86.14
smart00382	148	AAA ATPases associated with a variety of cellular	86.0
PRK06835	329	DNA replication protein DnaC; Validated	85.95
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	85.83
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	85.71
KOG0340|consensus	442		85.71
COG4096	875	HsdR Type I site-specific restriction-modification	85.64
TIGR00376	637	DNA helicase, putative. The gene product may repre	85.42
KOG4284|consensus	980		85.37
PRK13833	323	conjugal transfer protein TrbB; Provisional	85.29
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	85.24
PHA02244	383	ATPase-like protein	85.13
PRK12904	830	preprotein translocase subunit SecA; Reviewed	85.12
COG1484	254	DnaC DNA replication protein [DNA replication, rec	85.11
KOG0952|consensus	1230		85.08
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	85.05
TIGR00595	505	priA primosomal protein N'. All proteins in this f	84.78
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	84.62
PRK08939	306	primosomal protein DnaI; Reviewed	84.62
smart00382	148	AAA ATPases associated with a variety of cellular	84.25
PLN03025	319	replication factor C subunit; Provisional	84.04
PHA02244	383	ATPase-like protein	83.95
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	83.59
PRK12402	337	replication factor C small subunit 2; Reviewed	83.42
COG4889	1518	Predicted helicase [General function prediction on	83.21
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	83.17
PRK08181	269	transposase; Validated	83.08
KOG0920|consensus	924		82.84
PRK09183	259	transposase/IS protein; Provisional	82.8
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	82.61
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	82.4
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	82.34
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	82.3
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	82.21
PRK08181	269	transposase; Validated	82.01
KOG0347|consensus	731		82.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	81.98
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	81.7
COG0714	329	MoxR-like ATPases [General function prediction onl	81.58
PRK13107	908	preprotein translocase subunit SecA; Reviewed	81.57
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	81.44
PRK10536	262	hypothetical protein; Provisional	81.37
PRK06526	254	transposase; Provisional	81.37
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	81.25
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	81.22
PRK06526	254	transposase; Provisional	81.06
KOG0336|consensus	629		81.04
KOG0349|consensus	725		80.98
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	80.97
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	80.65
PRK13851	344	type IV secretion system protein VirB11; Provision	80.34
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	80.18
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	80.13

>KOG1131|consensus

Probab=100.00  E-value=4.2e-56  Score=487.71  Aligned_cols=355  Identities=22%  Similarity=0.349  Sum_probs=309.9

Q ss_pred             cceeeCCeeeccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHH
Q psy3462         235 TSYTIGGVKVEFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       235 ~~~~~~~~~~~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l  313 (795)
                      |+|.|+++.|.|||. .||.|+.+|.+++++|++                       ++|+++|+|+|||||.|+|.-++
T Consensus         1 Mk~~id~l~v~FPY~~iYPEQ~~YM~elKrsLDa-----------------------kGh~llEMPSGTGKTvsLLSli~   57 (755)
T KOG1131|consen    1 MKFYIDDLLVYFPYDYIYPEQYEYMRELKRSLDA-----------------------KGHCLLEMPSGTGKTVSLLSLII   57 (755)
T ss_pred             CeeeecCeeEecCCcccCHHHHHHHHHHHHhhcc-----------------------CCcEEEECCCCCCcchHHHHHHH
Confidence            679999999999997 699999999999999986                       58999999999999999999999


Q ss_pred             HHHHHhhHHHHHHHHhhhhhhhhhcCCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceeeec
Q psy3462         314 AWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLN  393 (795)
Q Consensus       314 ~~~~~~~k~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~l~  393 (795)
                      +|+..++.                                     ...+|+||+||+.++|+.|.+++.        ++.
T Consensus        58 aYq~~~p~-------------------------------------~~~KliYCSRTvpEieK~l~El~~--------l~~   92 (755)
T KOG1131|consen   58 AYQLHYPD-------------------------------------EHRKLIYCSRTVPEIEKALEELKR--------LMD   92 (755)
T ss_pred             HHHHhCCc-------------------------------------ccceEEEecCcchHHHHHHHHHHH--------HHH
Confidence            99988753                                     467899999999999999999997        899


Q ss_pred             ccccccccchhhh-hhccccccceeecccchhhHHhhh-hhcccccccccccccccccccchhhhHhhhcccC---CCCc
Q psy3462         394 GRSKNLVSSIDFI-LGLLYKGIQTCITTINQQEDELRQ-STKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKG---VNCE  468 (795)
Q Consensus       394 sR~~~~~~~~~~~-~~~~~~~~~lCi~~~~~~v~~~~~-~~~~~~c~~l~~~~~~~~~~~~~~~~~~~~~~~~---~~C~  468 (795)
                      .|.|++|..++|+ |||++| |||||   ||+|..+|. ++||++||+|  +++          |+++++..+   ..|+
T Consensus        93 y~~k~~g~~~~flglglssR-KNlCi---~~~v~~~r~g~~VD~~Cr~l--tas----------~vr~~~~ed~~~~~C~  156 (755)
T KOG1131|consen   93 YREKHLGYPEPFLGLGLSSR-KNLCI---HPEVLKERNGNVVDAACRKL--TAS----------YVRAKLAEDPNVELCD  156 (755)
T ss_pred             HHHHhcCCCCceeeeeeccc-ccccc---CHHHHHHhcCCchhHHHHHH--hHH----------HHHHHHhcCCCcchhh
Confidence            9999999999999 999999 99999   779999999 5889999888  444          455555544   3599


Q ss_pred             cchhcccchhhhhhhhhhhhhcccccCccccccCCCCChhHHHHHhhhCCccccchhhhhh-----------HH------
Q psy3462         469 DYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQLD-----------LM------  531 (795)
Q Consensus       469 ~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~~~~~cpyf~~~q~~-----------~~------  531 (795)
                       ||||+++             ....+|+||      |++|||++||++++|||||++|+-=           +.      
T Consensus       157 -f~en~~~-------------~~~~lp~gv------y~~~dL~~~g~~k~~CPYflaR~~I~~~nvivYsYhYllDPkIa  216 (755)
T KOG1131|consen  157 -FFENLED-------------KESLLPVGV------YTLEDLKEYGEKKGWCPYFLARRMIPFANVIVYSYHYLLDPKIA  216 (755)
T ss_pred             -HHhhhhc-------------ccccCCccc------ccHHHHHHhhhcCCcChHHHHHHhhhcccEEEEehhhhcChHHH
Confidence             7788777             123588887      9999999999999999999986410           00      


Q ss_pred             --------------------------------------------------------------HH----------------
Q psy3462         532 --------------------------------------------------------------LD----------------  533 (795)
Q Consensus       532 --------------------------------------------------------------~~----------------  533 (795)
                                                                                    |+                
T Consensus       217 ~~VSkels~~svVvFDEAHNIDnvCIeslSv~i~r~~l~ra~~~l~~l~~~v~r~k~~d~~kl~~eY~klvegL~~~~~~  296 (755)
T KOG1131|consen  217 ELVSKELSKESVVVFDEAHNIDNVCIESLSVDITRRTLERASRNLNSLEQLVNRVKETDSQKLQDEYEKLVEGLKDASAE  296 (755)
T ss_pred             HHHHHhhCcCcEEEecccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhcchhHHHHHHHHHHHHhhccccc
Confidence                                                                          00                


Q ss_pred             --------------------------------------------------------------------------------
Q psy3462         534 --------------------------------------------------------------------------------  533 (795)
Q Consensus       534 --------------------------------------------------------------------------------  533 (795)
                                                                                                      
T Consensus       297 ~~~d~~lanPvLP~dvl~EavPGniR~aeHFv~fLkR~~ey~ktrl~~~hv~~Esp~sFl~~i~~~~~IerKplrFCaeR  376 (755)
T KOG1131|consen  297 RDEDQFLANPVLPDDVLKEAVPGNIRRAEHFVSFLKRLLEYLKTRLKVHHVIQESPASFLKSIKSLTFIERKPLRFCAER  376 (755)
T ss_pred             cCccchhcCCCCchhhhhhhCCcchhhHHHHHHHHHHHHHHHHHhhhheeeeccCcHHHHHHHHHhhhhhccchHHHHHH
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy3462         534 --------------------------------------------------------------------------------  533 (795)
Q Consensus       534 --------------------------------------------------------------------------------  533 (795)
                                                                                                      
T Consensus       377 L~~L~~tLeitd~~df~~l~~v~~faTlVstY~kGF~iIiEPfd~~~~tv~npil~~sClDaSiAikPVf~RFqsViITS  456 (755)
T KOG1131|consen  377 LSSLVRTLEITDVEDFGALKTVADFATLVSTYSKGFSIIIEPFDDRNPTVPNPILRFSCLDASIAIKPVFERFQSVIITS  456 (755)
T ss_pred             HHHHHHHhccCchhhhhHHHHHHHHHHHHHHHhcCcEEEEcccccCCCCCCCCeeEEeecccchhhhHHHHhhheEEEec
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy3462         534 --------------------------------------------------------------------------------  533 (795)
Q Consensus       534 --------------------------------------------------------------------------------  533 (795)
                                                                                                      
T Consensus       457 GTlspldmyPk~lnf~pv~~~s~~mtLaR~c~~PmiitrG~Dqv~iss~fe~r~d~~VvrnyG~llve~sk~vpdG~v~f  536 (755)
T KOG1131|consen  457 GTLSPLDMYPKILNFGPVVGASFTMTLARNCLLPLIITRGNDQVAISSKFEARGDPSVVRNYGNLLVEMSKIVPDGIVCF  536 (755)
T ss_pred             CcccccccCchhhccCcccchhhheecccccccceeeecCCcchhhhhhhhhccChHHHhhcCcceeeecccCCCceEEE
Confidence                                                                                            


Q ss_pred             ----HhhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhcccce--------eEeecCc---------cccceE
Q psy3462         534 ----EHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSV--------KQVMGKG---------NLELCK  592 (795)
Q Consensus       534 ----~~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~ai--------fAV~GGK---------nl~rcV  592 (795)
                          -|||+++++|+++||+++++++|++|+|++|..++.-+|++|+.+|        |+|+|||         ++||||
T Consensus       537 f~sylYmesiv~~w~~~gil~ei~k~KL~fIetpD~~ETs~al~ny~~aC~~gRGavl~sVargkVsEgidF~hhyGR~V  616 (755)
T KOG1131|consen  537 FPSYLYMESIVSRWYEQGILDEIMKYKLLFIETPDFRETSLALANYRYACDNGRGAVLLSVARGKVSEGIDFDHHYGREV  616 (755)
T ss_pred             EehHHHHHHHHHHHHHHhHHHHHhhCceEEEeCCchhhhHHHHHHHHHHhcCCCCceEEEEecCccccCcccccccCceE
Confidence                1556666666677999999999999999999999999999998887        8999998         599999


Q ss_pred             EEEecCCCCCCCccccc------ccccCCcccchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHH
Q psy3462         593 GVFWTRFPNTCQYSVVY------PTGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVR  666 (795)
Q Consensus       593 iVVGIPYPn~~d~~Lk~------~~~~~~G~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr  666 (795)
                      +|.||||.++.+..+++      ....+..++|.+++|||...||+||++|.++|||.+||.|+||...+.+.+||+|++
T Consensus       617 iM~gIP~qytesriLkarle~Lrd~~~irE~dflTFDAmRhaAQC~GrvLr~K~dYg~mI~aDkRf~R~dKR~klp~wi~  696 (755)
T KOG1131|consen  617 IMEGIPYQYTESRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCLGRVLRGKTDYGLMIFADKRFSRGDKRSKLPKWIR  696 (755)
T ss_pred             EEEeccchhhHHHHHHHHHHHHHHHhcccccceechHhHHHHHHHHHHHHhccccceeeEeeehhhccccchhhhhHHHH
Confidence            99999999999888773      345677899999999999999999999999999999999999999999999999999


Q ss_pred             hhcccc---CChhHHHHHHHHHHHHHHHhh
Q psy3462         667 NQVQNT---SSHNTFMENLRNFVRRRMEIQ  693 (795)
Q Consensus       667 ~~l~~~---~sfe~~~~~l~~Ffk~~k~~~  693 (795)
                      +++...   -+.+.+....+.|++.|.+..
T Consensus       697 ~~l~~~~~nlstd~a~~varrflR~maQp~  726 (755)
T KOG1131|consen  697 NHLFDAKLNLSTDMANQVARRFLRLMAQPF  726 (755)
T ss_pred             hhhhhhccCCCcchhHHHHHHHHHHhcCCC
Confidence            998654   378889999999999998865

>KOG1133|consensus

Probab=100.00  E-value=3.1e-54  Score=485.02  Aligned_cols=153  Identities=24%  Similarity=0.379  Sum_probs=133.5

Q ss_pred             hhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhcccce--------eEeecCc---------cccceEEEEec
Q psy3462         535 HLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSV--------KQVMGKG---------NLELCKGVFWT  597 (795)
Q Consensus       535 ~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~ai--------fAV~GGK---------nl~rcViVVGI  597 (795)
                      |+..++..|+..|++.+|..+|+||+|+++.  ++++|+.|+.++        |||+|||         +++|||+|||+
T Consensus       641 yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~--~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGl  718 (821)
T KOG1133|consen  641 YLGQVRKRWEQNGILARIVGKKKVFYEPKDT--VEDVLEGYAEAAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGL  718 (821)
T ss_pred             HHHHHHHHHHhcchHHHhhccchhhccCccc--HHHHHHHHHHHhhcCCCeEEEEEeccccccccccccccccEEEEeec
Confidence            3334455677778999999999999999985  889999997654        9999998         59999999999


Q ss_pred             CCCCCCCcccccc--------cccCCcccchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhc
Q psy3462         598 RFPNTCQYSVVYP--------TGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQV  669 (795)
Q Consensus       598 PYPn~~d~~Lk~~--------~~~~~G~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l  669 (795)
                      ||||+.|.++++.        ...++|++||++.||+||||+|||+|||.+|||+|+|+|.||+.+. ..+||.||+.++
T Consensus       719 PyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkAVNQsIGRAIRH~~DYA~i~LlD~RY~~p~-~RKLp~WI~~~v  797 (821)
T KOG1133|consen  719 PYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKAVNQSIGRAIRHRKDYASIYLLDKRYARPL-SRKLPKWIRKRV  797 (821)
T ss_pred             CCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHhhhccceeEEEehhhhcCch-hhhccHHHHhHh
Confidence            9999999998831        1245689999999999999999999999999999999999999554 459999999988


Q ss_pred             cccCChhHHHHHHHHHHHHHH
Q psy3462         670 QNTSSHNTFMENLRNFVRRRM  690 (795)
Q Consensus       670 ~~~~sfe~~~~~l~~Ffk~~k  690 (795)
                      ....+|++++..++.||+...
T Consensus       798 ~s~~~~G~~ir~~~~ff~~k~  818 (821)
T KOG1133|consen  798 HSKAGFGPAIRATRKFFRAKS  818 (821)
T ss_pred             ccccCccHHHHHHHHHHHHhc
Confidence            888899999999999998764

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=100.00  E-value=1.8e-48  Score=453.31  Aligned_cols=130  Identities=25%  Similarity=0.433  Sum_probs=112.6

Q ss_pred             HhhccCcEEEcCCCcchhhHHhhhccc-------ce-eEeecCc---------cccceEEEEecCCCCCCCcccccc---
Q psy3462         551 DLVLKRNIFYDTLMLCDVQTKETKHRD-------SV-KQVMGKG---------NLELCKGVFWTRFPNTCQYSVVYP---  610 (795)
Q Consensus       551 ~I~~~K~IFiE~kd~~e~~~~L~~Y~~-------ai-fAV~GGK---------nl~rcViVVGIPYPn~~d~~Lk~~---  610 (795)
                      +|...|+||+|++++.+.+.+|++|++       +| |||+||+         +.+|||||||||||++.|+.++..   
T Consensus       550 ~i~~~k~i~~E~~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~  629 (705)
T TIGR00604       550 NIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF  629 (705)
T ss_pred             HHhcCCCEEEeCCCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHH
Confidence            455578999999988788899999953       34 9999997         589999999999999999988731   


Q ss_pred             ---cccCCcc-cchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhccccCChhHHHH
Q psy3462         611 ---TGLLKGG-DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFME  680 (795)
Q Consensus       611 ---~~~~~G~-ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l~~~~sfe~~~~  680 (795)
                         .....|+ .||.++||++||||+||+|||++|||+|+|+|+||.+.++++.||+|+++++...+++++++.
T Consensus       630 ~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G~iillD~R~~~~~~~~~lp~W~~~~~~~~~~~~~~i~  703 (705)
T TIGR00604       630 LRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMAIS  703 (705)
T ss_pred             HHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceEEEEEEehhcCCcchhhhcCHHHHhhccccCCCcchhc
Confidence               1123566 899999999999999999999999999999999999999999999999999998888876653

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).

>KOG1132|consensus

Probab=100.00  E-value=1.4e-47  Score=440.13  Aligned_cols=206  Identities=30%  Similarity=0.445  Sum_probs=152.4

Q ss_pred             eeeC-CeeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         237 YTIG-GVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       237 ~~~~-~~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      ..|+ |++|.|||+|||.|..||..|.++|++                       +.++++|+||||||||++||++|+|
T Consensus         8 ~~i~~Gv~V~fP~qpY~~Q~a~M~rvl~~L~~-----------------------~q~~llESPTGTGKSLsLLCS~LAW   64 (945)
T KOG1132|consen    8 IVINIGVPVEFPFQPYPTQLAFMTRVLSCLDR-----------------------KQNGLLESPTGTGKSLSLLCSTLAW   64 (945)
T ss_pred             eEeccCceeeccCCcchHHHHHHHHHHHHHHH-----------------------hhhhhccCCCCCCccHHHHHHHHHH
Confidence            4455 999999999999999999999999986                       4679999999999999999999999


Q ss_pred             HHHhhHHHHHHHHhhhh----hhhhhcCCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceee
Q psy3462         316 QRKEKELVQQKMFEQRT----QDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKV  391 (795)
Q Consensus       316 ~~~~~k~LQ~Ql~~kdi----p~l~~i~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~  391 (795)
                      ++..+...+.+.+..+.    |.-....+.+.  ...++..-.+.- -.-+++|++|||+|+.|..+++++..++++.+|
T Consensus        65 ~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~--s~e~~e~~~~~~-~ipkIyyaSRTHsQltQvvrElrrT~Y~vkmtV  141 (945)
T KOG1132|consen   65 QQHLKSRKPKGKISERKAGFIPTQPSDSGGEK--SEEAGEPIACYT-GIPKIYYASRTHSQLTQVVRELRRTGYRVKMTV  141 (945)
T ss_pred             HHHhhccccccchhhhhccccCCCCccCCCCc--hhhhcCcccccc-CCceEEEecchHHHHHHHHHHHhhcCCCCceEE
Confidence            99887666666554433    21111111111  111111100001 145799999999999999999999977799999


Q ss_pred             ecccccccccchhhhhhccccccceeecccchhhHHhhhh-hcccccccccccccccccccchhhhHhhhcccCCCCccc
Q psy3462         392 LNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQS-TKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDY  470 (795)
Q Consensus       392 l~sR~~~~~~~~~~~~~~~~~~~~lCi~~~~~~v~~~~~~-~~~~~c~~l~~~~~~~~~~~~~~~~~~~~~~~~~~C~~y  470 (795)
                      ||||.                  |+||   ||+|.+++++ ...+.|+++.                     ....|.||
T Consensus       142 LgSRe------------------q~Ci---npev~k~~~~~~~~~~C~k~~---------------------~~~~C~f~  179 (945)
T KOG1132|consen  142 LGSRE------------------QLCI---NPEVKKLEGNALQNHVCKKLV---------------------KSRSCHFY  179 (945)
T ss_pred             eecch------------------hhcc---CHHHhhhhcchhhhhHHHhhc---------------------cccccccc
Confidence            99999                  9999   8899999984 5677787761                     11349987


Q ss_pred             hhcccchhhhhhhhhhhhhcccccCccccccCCCCChhHHHHHhhhCCccccchhhhh
Q psy3462         471 HVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQL  528 (795)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~~~~~cpyf~~~q~  528 (795)
                      +-+-+.+                ++|-.  ...++|||||+..|++...||||.+|++
T Consensus       180 ~~~~~~s----------------l~~~l--~~~i~DIEDLVk~Gk~~~~CPYfaSR~l  219 (945)
T KOG1132|consen  180 KIVEEKS----------------LQPRL--HDEIFDIEDLVKIGKKSRGCPYFASREL  219 (945)
T ss_pred             ccccccc----------------ccccc--CCCcccHHHHHHhCccCcCCcchhhhhh
Confidence            6333331                12211  1125999999999999999999998875

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

Probab=99.95  E-value=1.9e-26  Score=265.88  Aligned_cols=139  Identities=21%  Similarity=0.123  Sum_probs=111.5

Q ss_pred             HHhhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhcccc---eeEeecCc---------cccceEEEEecCCC
Q psy3462         533 DEHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDS---VKQVMGKG---------NLELCKGVFWTRFP  600 (795)
Q Consensus       533 ~~~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~a---ifAV~GGK---------nl~rcViVVGIPYP  600 (795)
                      .+||+.++..|......        +.++..+..+.+..|++|...   .++|+||+         +.+++|+|+|||||
T Consensus       489 y~~l~~~~~~~~~~~~~--------~~v~~q~~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp  560 (654)
T COG1199         489 YEYLKRVAERLKDERST--------LPVLTQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFP  560 (654)
T ss_pred             HHHHHHHHHHHhhcCcc--------ceeeecCCCcHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCCC
Confidence            47888888888776554        445555555677899999766   48999996         58899999999999


Q ss_pred             CCCCcccccc-----cccCCc-ccchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhccccCC
Q psy3462         601 NTCQYSVVYP-----TGLLKG-GDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSS  674 (795)
Q Consensus       601 n~~d~~Lk~~-----~~~~~G-~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l~~~~s  674 (795)
                      +++|+.++..     +...++ ..||.++||++|+||+||+|||++|||+|+|+|.||.+.+++..||+|+.........
T Consensus       561 ~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~R~~~~~y~~~l~~~l~~~~~~~~~  640 (654)
T COG1199         561 NPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDKRYATKRYGKLLLDSLPPFPKSKDL  640 (654)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecccchhhhHHHHHHHhCCCCcccccc
Confidence            9999988732     112223 4568999999999999999999999999999999999999999999999987766554


Q ss_pred             hhHHH
Q psy3462         675 HNTFM  679 (795)
Q Consensus       675 fe~~~  679 (795)
                      .....
T Consensus       641 ~~~~~  645 (654)
T COG1199         641 NPSAI  645 (654)
T ss_pred             hhhHH
Confidence            44443

>PTZ00193 60S ribosomal protein L31; Provisional

Probab=99.94  E-value=1.4e-27  Score=233.82  Aligned_cols=79  Identities=37%  Similarity=0.517  Sum_probs=75.2

Q ss_pred             CCCCCcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         116 KKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       116 ~~s~~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      .++++.|++||||||||||++||++|+||||+||++||+||+|||||+||+|||+||++||++||+|||++|||+.+..
T Consensus        76 ~~~~~~e~VTREyTINLHKriHgv~fKKRAPrAIKeIRkFA~K~MgT~DVRIDtrLNkaIWsrGIRnvP~RIRVRlsRK  154 (188)
T PTZ00193         76 RTGRKPDNISMEATIHLSKLLKKKTFHKRAPIAIKRIKAFVGRLMKTKDNRIDASLNTYIWHKGVKGVPGRVRVLVERK  154 (188)
T ss_pred             hhccCCCcceeEEEEeeeehhcCCCccccCHHHHHHHHHHHHHhcCCCcEEECHHHHHHHHHccCcCCCceEEEEEEee
Confidence            3456789999999999999999999999999999999999999999999999999999999999999999999998765

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.93  E-value=2e-25  Score=260.94  Aligned_cols=102  Identities=21%  Similarity=0.299  Sum_probs=86.8

Q ss_pred             eeeccC-CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         242 VKVEFP-VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       242 ~~~~fp-y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      +.-.+| |++||.|.+||.+|+++|.+..                  ...++++++|||||||||+|||+|++.|+...+
T Consensus        17 l~~~~~~~e~R~~Q~~M~~~V~~al~~~~------------------~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~   78 (697)
T PRK11747         17 LQEQLPGFIPRAGQRQMIAEVAKTLAGEY------------------LKDGRILVIEAGTGVGKTLSYLLAGIPIARAEK   78 (697)
T ss_pred             HHHhCCCCCcCHHHHHHHHHHHHHHhccc------------------ccccceEEEECCCCcchhHHHHHHHHHHHHHcC
Confidence            444567 9999999999999999997510                  012478999999999999999999999988654


Q ss_pred             H---------HHHHHHHhhhhhhhhhcCCCCceEEEecccc-cccccchhh
Q psy3462         321 E---------LVQQKMFEQRTQDLQKIPFRKLKISRLKAKD-FSTNNGMEQ  361 (795)
Q Consensus       321 k---------~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr~-~~~~~~~~~  361 (795)
                      +         .||+||+.||+|.|+++++.+++++++|||. |.|.+...+
T Consensus        79 k~vVIST~T~~LQeQL~~kDlP~l~~~l~~~~~~~llKGr~nYlCl~r~~~  129 (697)
T PRK11747         79 KKLVISTATVALQEQLVSKDLPLLLKISGLDFKFTLAKGRGRYVCPRKLAA  129 (697)
T ss_pred             CeEEEEcCCHHHHHHHHhhhhhHHHHHcCCCceEEEEcCccccccHHHHHH
Confidence            4         7999999999999999999999999999997 777666554

>PF01198 Ribosomal_L31e: Ribosomal protein L31e; InterPro: IPR000054 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.93  E-value=1.2e-26  Score=205.54  Aligned_cols=74  Identities=53%  Similarity=0.775  Sum_probs=67.9

Q ss_pred             cccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEecccc
Q psy3462         121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAK  195 (795)
Q Consensus       121 ~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~~  195 (795)
                      .+++||||||||||+ |+++|++|||+||++||+||+|||||+||+|||+||++||++|++|||++|+|+++...
T Consensus         1 ~~~v~re~TInL~k~-~~~~~~kRA~rAvk~Ir~f~~k~mkt~dV~iD~~lN~~IWsrGi~~pP~rIRVr~~r~~   74 (83)
T PF01198_consen    1 KEVVTREYTINLRKV-HGVPFKKRAPRAVKEIRKFAQKHMKTEDVKIDPELNKAIWSRGIRKPPRRIRVRVSRKE   74 (83)
T ss_dssp             TSSEEEEEEEECHHH-CCSSGGGHHHHHHHHHHHHHHHHHTTSCEEE-HHHHHHHHTTTSSS--SEEEEEEEEET
T ss_pred             CCceeEEEEEechhh-cCCCCcccCHHHHHHHHHHHHHHhCCCceEEchHHHHHHHhcccCCCCceEEEEEEEcc
Confidence            378999999999997 99999999999999999999999999999999999999999999999999999987764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of: Yeast L34 Archaeal L31 [] Plants L31 Mammalian L31 [] ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3G6E_X 3I56_X 1YIT_X 1NJI_Y 3CC4_X 1VQM_X 1KC8_Y 1VQ9_X 1VQN_X 1M1K_Y ....

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.93  E-value=1.7e-24  Score=259.83  Aligned_cols=130  Identities=12%  Similarity=0.136  Sum_probs=93.1

Q ss_pred             cEEEcCCCcchhhHHhhhcc---cce-eEeec---Cc----cccceEEEEecCCCCCCCcccccccc---cCCcccchH-
Q psy3462         557 NIFYDTLMLCDVQTKETKHR---DSV-KQVMG---KG----NLELCKGVFWTRFPNTCQYSVVYPTG---LLKGGDWYQ-  621 (795)
Q Consensus       557 ~IFiE~kd~~e~~~~L~~Y~---~ai-fAV~G---GK----nl~rcViVVGIPYPn~~d~~Lk~~~~---~~~G~ewY~-  621 (795)
                      .++....+..+...+++.|+   ++| |++..   |-    +..+||||+++|||++.|+.++....   ...++.||. 
T Consensus       782 ~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~  861 (928)
T PRK08074        782 VLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQEL  861 (928)
T ss_pred             eEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhh
Confidence            45554322234456666664   345 44311   21    57899999999999999998873211   112455644 


Q ss_pred             --HHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhccccCChhHHHHHHHHHH
Q psy3462         622 --IQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFV  686 (795)
Q Consensus       622 --~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l~~~~sfe~~~~~l~~Ff  686 (795)
                        ..|+.+++|++||.||+++|+|+|+++|+|+..++|...+...+-..-....+++++...+..|+
T Consensus       862 ~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R~~~k~Yg~~~l~sLP~~~~~~~~~~~~~~~~~~~~  928 (928)
T PRK08074        862 SLPQAVLRFKQGFGRLIRTETDRGTVFVLDRRLTTTSYGKYFLESLPTVPVYEGTLEELLEEVEEFL  928 (928)
T ss_pred             hhHHHHHHHHhhhhhhcccCCceEEEEEecCccccchHHHHHHHhCCCCCcccCCHHHHHHHHHhhC
Confidence              36999999999999999999999999999999999999988877652223458888888888874

>PRK01192 50S ribosomal protein L31e; Reviewed

Probab=99.92  E-value=6.6e-26  Score=203.06  Aligned_cols=73  Identities=33%  Similarity=0.513  Sum_probs=69.1

Q ss_pred             cccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCC--CeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTE--DVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       121 ~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~--dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      .+++||+|||||||+ |+++|+||||+||++||+||+|||||+  ||+|||+||++||++|++|||++|||+++..
T Consensus         3 ~~~~~r~yTInLrk~-~~~~~~kRA~rAik~Ir~f~~k~mkt~~~~V~iD~~lN~~IW~rGi~~~P~riRVr~~rk   77 (89)
T PRK01192          3 KEVEERIYTIPLRDV-KKVPRTKRADRAVKLVREFLARHFKADEDKVKIDPSINEKIWERGREKPPSKVRVRVAKK   77 (89)
T ss_pred             CcceEEEEEEeCeec-cCCCccccCHHHHHHHHHHHHHHhCCCCCcEEEChHHHHHHHHccCCCCCceEEEEEEEe
Confidence            467899999999996 999999999999999999999999998  9999999999999999999999999997554

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.92  E-value=4.7e-25  Score=233.46  Aligned_cols=195  Identities=26%  Similarity=0.352  Sum_probs=135.6

Q ss_pred             eeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH-
Q psy3462         243 KVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE-  321 (795)
Q Consensus       243 ~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k-  321 (795)
                      .|.|||+|||+|.+||+.|++++++                       ++++++|||||||||+|||+|+|+|+..++. 
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~-----------------------~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~   58 (289)
T smart00488        2 LFYFPYEPYPIQYEFMEELKRVLDR-----------------------GKIGILESPTGTGKTLSLLCLTLTWLRSFPER   58 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHc-----------------------CCcEEEECCCCcchhHHHHHHHHHHHHhCccc
Confidence            5789999999999999999999975                       5799999999999999999999999876432 


Q ss_pred             ----HH-----HHHHHhhhhhhhhhcCCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceeee
Q psy3462         322 ----LV-----QQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVL  392 (795)
Q Consensus       322 ----~L-----Q~Ql~~kdip~l~~i~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~l  392 (795)
                          .+     ...+.++.+|.++++..                    ..++++.||++|+.|-++++++.....+..++
T Consensus        59 ~~~~kvi~~t~T~~~~~q~i~~l~~~~~--------------------~~~~~~~~t~sq~~q~~~el~~~~~~~~~~~l  118 (289)
T smart00488       59 IQKIKLIYLSRTVSEIEKRLEELRKLMQ--------------------KVEYESDEESEKQAQLLHELGREKPKVLGLSL  118 (289)
T ss_pred             ccccceeEEeccHHHHHHHHHHHHhccc--------------------ccceecccchhHHHHHHHHHhccCCCcceeEe
Confidence                10     11123333555554321                    12678999999999999999864445667888


Q ss_pred             cccccccccchhhhhhccccccceeecccchhhHHhhhh--hcccccccccccccccccccchhhhHhhhcccCCCCccc
Q psy3462         393 NGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQS--TKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDY  470 (795)
Q Consensus       393 ~sR~~~~~~~~~~~~~~~~~~~~lCi~~~~~~v~~~~~~--~~~~~c~~l~~~~~~~~~~~~~~~~~~~~~~~~~~C~~y  470 (795)
                      +||+                  |+||   |+.|..+...  ..+..|++|.. .+++..-...        .+...|+||
T Consensus       119 ~sR~------------------~lCi---n~~v~~~~~~~~~~~~~C~~l~~-~~~~~~~~~~--------~~~~~c~~~  168 (289)
T smart00488      119 TSRK------------------NLCL---NPEVRTLKQNGLVVDEVCRSLTA-SKARKYRYEN--------PKVERCPFY  168 (289)
T ss_pred             echh------------------hcCC---ChHHhhcccccchHHHHHHHHHh-hccccccccc--------cCCCCCCcc
Confidence            9999                  8999   7788865542  34578988742 2222110000        112359965


Q ss_pred             hhcccchhhhhhhhhhhhhcccccCccccccCCCCChhHHHHHhhhCCccccchhhhh
Q psy3462         471 HVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQL  528 (795)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~~~~~cpyf~~~q~  528 (795)
                      . +...           ......+..+      ++++|||..+|++++.||||.++..
T Consensus       169 ~-~~~~-----------~~~~~~~~~~------~~d~e~l~~~~~~~~~CpY~~~r~~  208 (289)
T smart00488      169 E-NTEF-----------LLVRDLLPAE------VYDIEDLLELGKRLGGCPYFASRKA  208 (289)
T ss_pred             c-hhhh-----------hhhhhhcccC------CCCHHHHHHhcccCCCChhHHHHHH
Confidence            4 2211           0001123333      4999999999999999999999754

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.92  E-value=4.7e-25  Score=233.46  Aligned_cols=195  Identities=26%  Similarity=0.352  Sum_probs=135.6

Q ss_pred             eeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH-
Q psy3462         243 KVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE-  321 (795)
Q Consensus       243 ~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k-  321 (795)
                      .|.|||+|||+|.+||+.|++++++                       ++++++|||||||||+|||+|+|+|+..++. 
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~-----------------------~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~   58 (289)
T smart00489        2 LFYFPYEPYPIQYEFMEELKRVLDR-----------------------GKIGILESPTGTGKTLSLLCLTLTWLRSFPER   58 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHc-----------------------CCcEEEECCCCcchhHHHHHHHHHHHHhCccc
Confidence            5789999999999999999999975                       5799999999999999999999999876432 


Q ss_pred             ----HH-----HHHHHhhhhhhhhhcCCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceeee
Q psy3462         322 ----LV-----QQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVL  392 (795)
Q Consensus       322 ----~L-----Q~Ql~~kdip~l~~i~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~l  392 (795)
                          .+     ...+.++.+|.++++..                    ..++++.||++|+.|-++++++.....+..++
T Consensus        59 ~~~~kvi~~t~T~~~~~q~i~~l~~~~~--------------------~~~~~~~~t~sq~~q~~~el~~~~~~~~~~~l  118 (289)
T smart00489       59 IQKIKLIYLSRTVSEIEKRLEELRKLMQ--------------------KVEYESDEESEKQAQLLHELGREKPKVLGLSL  118 (289)
T ss_pred             ccccceeEEeccHHHHHHHHHHHHhccc--------------------ccceecccchhHHHHHHHHHhccCCCcceeEe
Confidence                10     11123333555554321                    12678999999999999999864445667888


Q ss_pred             cccccccccchhhhhhccccccceeecccchhhHHhhhh--hcccccccccccccccccccchhhhHhhhcccCCCCccc
Q psy3462         393 NGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQS--TKKTKVDKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDY  470 (795)
Q Consensus       393 ~sR~~~~~~~~~~~~~~~~~~~~lCi~~~~~~v~~~~~~--~~~~~c~~l~~~~~~~~~~~~~~~~~~~~~~~~~~C~~y  470 (795)
                      +||+                  |+||   |+.|..+...  ..+..|++|.. .+++..-...        .+...|+||
T Consensus       119 ~sR~------------------~lCi---n~~v~~~~~~~~~~~~~C~~l~~-~~~~~~~~~~--------~~~~~c~~~  168 (289)
T smart00489      119 TSRK------------------NLCL---NPEVRTLKQNGLVVDEVCRSLTA-SKARKYRYEN--------PKVERCPFY  168 (289)
T ss_pred             echh------------------hcCC---ChHHhhcccccchHHHHHHHHHh-hccccccccc--------cCCCCCCcc
Confidence            9999                  8999   7788865542  34578988742 2222110000        112359965


Q ss_pred             hhcccchhhhhhhhhhhhhcccccCccccccCCCCChhHHHHHhhhCCccccchhhhh
Q psy3462         471 HVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRALVSPCFQLIQL  528 (795)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~~~~~cpyf~~~q~  528 (795)
                      . +...           ......+..+      ++++|||..+|++++.||||.++..
T Consensus       169 ~-~~~~-----------~~~~~~~~~~------~~d~e~l~~~~~~~~~CpY~~~r~~  208 (289)
T smart00489      169 E-NTEF-----------LLVRDLLPAE------VYDIEDLLELGKRLGGCPYFASRKA  208 (289)
T ss_pred             c-hhhh-----------hhhhhhcccC------CCCHHHHHHhcccCCCChhHHHHHH
Confidence            4 2211           0001123333      4999999999999999999999754

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.91  E-value=9.7e-24  Score=251.29  Aligned_cols=130  Identities=18%  Similarity=0.213  Sum_probs=96.8

Q ss_pred             CcEEEcCCCcchhhHHhhhccc---ce-eEe---ecCc----cccceEEEEecCCCCCCCcccccccc---cCCcccchH
Q psy3462         556 RNIFYDTLMLCDVQTKETKHRD---SV-KQV---MGKG----NLELCKGVFWTRFPNTCQYSVVYPTG---LLKGGDWYQ  621 (795)
Q Consensus       556 K~IFiE~kd~~e~~~~L~~Y~~---ai-fAV---~GGK----nl~rcViVVGIPYPn~~d~~Lk~~~~---~~~G~ewY~  621 (795)
                      .+++.+..+ .+...+++.|+.   +| +++   ..|-    +..++|||+|+|||++.|+.++....   ...++.||.
T Consensus       703 ~~~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~  781 (850)
T TIGR01407       703 YEVLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYD  781 (850)
T ss_pred             ceEEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHH
Confidence            467777655 355667777753   34 332   1121    57789999999999999998873211   112344543


Q ss_pred             ---HHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhcccc-CChhHHHHHHHHHH
Q psy3462         622 ---IQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNT-SSHNTFMENLRNFV  686 (795)
Q Consensus       622 ---~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l~~~-~sfe~~~~~l~~Ff  686 (795)
                         .+|+.+++|++||+||+++|+|+|+++|.||...+|...+++++.+..... .+++++...+..|+
T Consensus       782 ~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R~~~~~Yg~~~~~sLp~~~~~~~~~~~~~~~~~~~~~  850 (850)
T TIGR01407       782 YVLPMAIIRLRQALGRLIRRENDRGSIVILDRRLVGKRYGKRFEKSLPEYLQVKGDILGELLEAIKEFL  850 (850)
T ss_pred             hhHHHHHHHHHHhhccccccCCceEEEEEEccccccchHHHHHHHhCCCccccccCCHHHHHHHHHhhC
Confidence               469999999999999999999999999999999999999999987654433 35889999888875

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>KOG0893|consensus

Probab=99.91  E-value=2e-25  Score=210.55  Aligned_cols=82  Identities=52%  Similarity=0.803  Sum_probs=79.3

Q ss_pred             CCCCCCCCcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEec
Q psy3462         113 PATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDS  192 (795)
Q Consensus       113 ~k~~~s~~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s  192 (795)
                      +++++|+++|+||||||||+||++|+++|+|+||+|++||++||+|+|||+||++|++||++||+|||+|+|++++|+.+
T Consensus         9 ~~k~~s~ine~vtre~tinihk~~h~v~fkK~ap~alkeI~kFA~keMgt~dv~~Dt~lnkavwakgirnv~~~irvrls   88 (125)
T KOG0893|consen    9 KKKGHSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIWKFAMKEMGTPDVHVDTRLNKAVWEKGIRNVPYRIRVRLS   88 (125)
T ss_pred             cccCccchhhhhhhheecccccchhccchhhhhHHHHHHHHHHHHHHhCCccceecchhhHHHHHhcccCCcchhhcccc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q psy3462         193 AA  194 (795)
Q Consensus       193 ~~  194 (795)
                      ..
T Consensus        89 rk   90 (125)
T KOG0893|consen   89 RK   90 (125)
T ss_pred             cc
Confidence            66

>COG2097 RPL31A Ribosomal protein L31E [Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=2.1e-23  Score=185.73  Aligned_cols=72  Identities=43%  Similarity=0.639  Sum_probs=69.1

Q ss_pred             ccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         122 EVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       122 e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      ++.|++||||||+ ++++++++|||+||++||+|++|||++++|+|||+||++||+||+++||++|||++++-
T Consensus         5 ~~~er~ytI~LR~-~~~v~r~kRA~rAVk~ir~fv~rHmk~e~V~id~~lNe~iW~rG~ekpP~klRVrv~k~   76 (89)
T COG2097           5 VVVERIYTIPLRR-AKKVPRTKRAPRAVKIIRKFVARHMKAEEVRIDPSLNEKIWERGIEKPPSKLRVRVSKF   76 (89)
T ss_pred             ccceEEEEEEchh-hccCCccccchHHHHHHHHHHHHHhCCceEEECHHHhHHHHHhhccCCCceEEEEEEEe
Confidence            5689999999995 89999999999999999999999999999999999999999999999999999998775

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=99.88  E-value=3.8e-23  Score=198.86  Aligned_cols=118  Identities=24%  Similarity=0.313  Sum_probs=100.7

Q ss_pred             HhhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhccc------ce-eEeecCc---------cccceEEEEec
Q psy3462         534 EHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRD------SV-KQVMGKG---------NLELCKGVFWT  597 (795)
Q Consensus       534 ~~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~------ai-fAV~GGK---------nl~rcViVVGI  597 (795)
                      ++|+.++..|++++.+   ...|+||+|++++.+.+.++++|++      +| |+|+||+         +.++||+|+|+
T Consensus         2 ~~m~~v~~~~~~~~~~---~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~gl   78 (142)
T smart00491        2 RYLEQVVEYWKENGIL---EINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGI   78 (142)
T ss_pred             hHHHHHHHHHHhcCcc---ccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEec
Confidence            5899999999998887   5578999999998778899999965      34 9999997         57899999999


Q ss_pred             CCCCCCCcccccc------cc-cCCcccchHHHHHHHHHhccCccccccCceeEEEEeecccCC
Q psy3462         598 RFPNTCQYSVVYP------TG-LLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYS  654 (795)
Q Consensus       598 PYPn~~d~~Lk~~------~~-~~~G~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~  654 (795)
                      |||++.|+.++..      .. ......||..+|+++++||+||+|||++|||+|+|+|+||.+
T Consensus        79 Pfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~D~g~i~l~D~R~~~  142 (142)
T smart00491       79 PFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRYAR  142 (142)
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCccceEEEEEEeccccC
Confidence            9999999886621      11 223456799999999999999999999999999999999964

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.88  E-value=1.4e-21  Score=232.29  Aligned_cols=99  Identities=16%  Similarity=0.212  Sum_probs=81.3

Q ss_pred             ccceEEEEecCCCCCCCcccccccc---cCCcccchH---HHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhH
Q psy3462         588 LELCKGVFWTRFPNTCQYSVVYPTG---LLKGGDWYQ---IQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGL  661 (795)
Q Consensus       588 l~rcViVVGIPYPn~~d~~Lk~~~~---~~~G~ewY~---~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~L  661 (795)
                      ...+|||++||||+|.||.++....   ...++.||.   ..|+.++.|++||.||+++|+|+|+++|+|+.+++|.+.+
T Consensus       714 ~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R~~~k~Yg~~~  793 (820)
T PRK07246        714 DRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRRILTKSYGKQI  793 (820)
T ss_pred             CeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCcccccHHHHHH
Confidence            4567889999999999998773211   112345543   5599999999999999999999999999999999999999


Q ss_pred             hHHHHhhcc-ccCChhHHHHHHHHHH
Q psy3462         662 SKWVRNQVQ-NTSSHNTFMENLRNFV  686 (795)
Q Consensus       662 P~WIr~~l~-~~~sfe~~~~~l~~Ff  686 (795)
                      .+|+-+.+. ...+++++.+.++.||
T Consensus       794 l~sLP~~~~~~~~~~~~~~~~~~~f~  819 (820)
T PRK07246        794 LASLAEEFLISQQNFSDVLVEIDRFL  819 (820)
T ss_pred             HHhCCCCCccccCCHHHHHHHHHHhh
Confidence            999987543 2468999999999998

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

Probab=99.85  E-value=4.9e-22  Score=194.43  Aligned_cols=129  Identities=26%  Similarity=0.329  Sum_probs=92.1

Q ss_pred             HhhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhccc---ce-eEeecCc---------cccceEEEEecCCC
Q psy3462         534 EHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRD---SV-KQVMGKG---------NLELCKGVFWTRFP  600 (795)
Q Consensus       534 ~~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~---ai-fAV~GGK---------nl~rcViVVGIPYP  600 (795)
                      ++|+.+...|+..+.    ...+++|.|.  ..+...++++|++   +| +||+||+         +..+||+|+|+|||
T Consensus        20 ~~l~~~~~~~~~~~~----~~~~~v~~q~--~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vii~glPfp   93 (167)
T PF13307_consen   20 RRLEKVYERLKERLE----EKGIPVFVQG--SKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVIIVGLPFP   93 (167)
T ss_dssp             HHHHHHHTT-TSS-E-----ETSCEEEST--CCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEEEES----
T ss_pred             HHHHHHHHHHHhhcc----cccceeeecC--cchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheeeecCCCCC
Confidence            578888889988763    3345899995  3467888888854   34 8999997         47889999999999


Q ss_pred             CCCCcccccc------cccCCcccchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhh
Q psy3462         601 NTCQYSVVYP------TGLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQ  668 (795)
Q Consensus       601 n~~d~~Lk~~------~~~~~G~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~  668 (795)
                      ++.|+.++..      .....+..||..+|+++++||+||+|||++|||+|+|+|+||..+.+...||+|++++
T Consensus        94 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~R~~~~~y~~~l~~~l~~~  167 (167)
T PF13307_consen   94 PPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDSRFLSKRYGKYLPKWLPPY  167 (167)
T ss_dssp             -TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESGGGGGHHHHHH-T------
T ss_pred             CCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcCccccchhhhcCccccccC
Confidence            9999987621      2334457889999999999999999999999999999999999999999999999863

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=99.85  E-value=1.8e-21  Score=187.25  Aligned_cols=120  Identities=17%  Similarity=0.133  Sum_probs=100.5

Q ss_pred             HhhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhcccc----e-eEeec---Cc----cccceEEEEecCCCC
Q psy3462         534 EHLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDS----V-KQVMG---KG----NLELCKGVFWTRFPN  601 (795)
Q Consensus       534 ~~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~a----i-fAV~G---GK----nl~rcViVVGIPYPn  601 (795)
                      .||+.++..|+.+|.+++|.++|+||+|+++..+.+.++++|++.    | |||++   |-    +..+||+|+|||||+
T Consensus         2 ~~m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~   81 (141)
T smart00492        2 QYMESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPY   81 (141)
T ss_pred             HHHHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCC
Confidence            589999999999999999999999999999887889999999643    4 66665   32    688999999999999


Q ss_pred             CCCcccccc----ccc--CCccc-chHHHHHHHHHhccCccccccCceeEEEEeecccC
Q psy3462         602 TCQYSVVYP----TGL--LKGGD-WYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFY  653 (795)
Q Consensus       602 ~~d~~Lk~~----~~~--~~G~e-wY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~  653 (795)
                      +.|+.++..    +..  ..+.. +|..+|+++++||+||+|||++|||+|+|+|.||.
T Consensus        82 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D~R~~  140 (141)
T smart00492       82 PDSPILKARLELLRDKGQIRPFDFVSLPDAMRTLAQCVGRLIRGANDYGVVVIADKRFA  140 (141)
T ss_pred             CCCHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHhCccccCcCceEEEEEEecccc
Confidence            999987731    111  12222 35689999999999999999999999999999986

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.55  E-value=6.9e-15  Score=156.32  Aligned_cols=54  Identities=35%  Similarity=0.483  Sum_probs=50.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE   69 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~   69 (795)
                      .++|.|||+|.+||+.|++++.++.++++|||||||||+|||+|+|.|+...+.
T Consensus         4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00488        4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            467789999999999999999999999999999999999999999999886554

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.55  E-value=6.9e-15  Score=156.32  Aligned_cols=54  Identities=35%  Similarity=0.483  Sum_probs=50.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE   69 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~   69 (795)
                      .++|.|||+|.+||+.|++++.++.++++|||||||||+|||+|+|.|+...+.
T Consensus         4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00489        4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            467789999999999999999999999999999999999999999999886554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.52  E-value=1.3e-14  Score=170.58  Aligned_cols=68  Identities=24%  Similarity=0.449  Sum_probs=60.8

Q ss_pred             CCCCC-CHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccc
Q psy3462          17 NYFLK-YSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSD   95 (795)
Q Consensus        17 ~~~~p-~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth   95 (795)
                      ++|.| ||+|.+||+.|++++.+++++++|||||||||+|.|+|+|+|+...+               ..+++|||||||
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~---------------~~~kIiy~sRTh   70 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP---------------EVRKIIYASRTH   70 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc---------------ccccEEEEcccc
Confidence            34445 89999999999999999999999999999999999999999987643               347999999999


Q ss_pred             cccc
Q psy3462          96 FFLL   99 (795)
Q Consensus        96 ~~l~   99 (795)
                      +|+.
T Consensus        71 sQl~   74 (705)
T TIGR00604        71 SQLE   74 (705)
T ss_pred             hHHH
Confidence            9996

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).

>KOG1133|consensus

Probab=99.47  E-value=6.5e-14  Score=160.51  Aligned_cols=54  Identities=31%  Similarity=0.540  Sum_probs=51.3

Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          14 NEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        14 ~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .++++|.||.+|.++|+++++.|+.|+.+|+||||||||||+++|++|.|+.+.
T Consensus         9 ~F~fPy~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen    9 EFPFPYTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             ccCCCCCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            456688999999999999999999999999999999999999999999999877

>KOG1132|consensus

Probab=99.36  E-value=4.2e-13  Score=157.08  Aligned_cols=154  Identities=25%  Similarity=0.384  Sum_probs=129.0

Q ss_pred             hhhHHHHHhccccchHHhhccCcEEEcCCCcchhhHHhhhcccce----------eEeecCc---------cccceEEEE
Q psy3462         535 HLNPYVLKVKDTPCIEDLVLKRNIFYDTLMLCDVQTKETKHRDSV----------KQVMGKG---------NLELCKGVF  595 (795)
Q Consensus       535 ~me~iv~~W~~tgil~~I~~~K~IFiE~kd~~e~~~~L~~Y~~ai----------fAV~GGK---------nl~rcViVV  595 (795)
                      -|+.++..|...|.|+++...|++++||+...+...++..|..+|          |||+|||         +.+|+||++
T Consensus       573 vmdk~~tfw~~~~~we~~~~vk~l~vEPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGlDFsD~~~RaVI~t  652 (945)
T KOG1132|consen  573 VMDKLITFWQNRGLWERMEKVKKLVVEPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGLDFSDDNGRAVIIT  652 (945)
T ss_pred             HHHHHHHHHHcchHHHHhhcccCceeccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCCCCccccCCceeEEe
Confidence            578889999999999999999999999998778888888886554          8999998         589999999


Q ss_pred             ecCCCCCCCccccc-------cc-------ccCCcccchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhH
Q psy3462         596 WTRFPNTCQYSVVY-------PT-------GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGL  661 (795)
Q Consensus       596 GIPYPn~~d~~Lk~-------~~-------~~~~G~ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~L  661 (795)
                      |||||+..|+.|+.       .+       ....|.+||+.+|+|||||||||||||++|||+++|+|.||...+-+..+
T Consensus       653 GlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQAiGRviRHR~D~Gav~l~D~Rfe~~~~~~~l  732 (945)
T KOG1132|consen  653 GLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQAIGRVIRHRNDYGAVILCDDRFENADARSQL  732 (945)
T ss_pred             cCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHHHHHHHHhhhcccceeeEeechhhcCcccccc
Confidence            99999999999882       11       14568999999999999999999999999999999999999999888889


Q ss_pred             hHHHHhhccccCChhHHHHHHHHHHHHH
Q psy3462         662 SKWVRNQVQNTSSHNTFMENLRNFVRRR  689 (795)
Q Consensus       662 P~WIr~~l~~~~sfe~~~~~l~~Ffk~~  689 (795)
                      |+|++... .....-+.+..+..+++.+
T Consensus       733 skw~r~~~-~~~~~~~~~~~~~r~~r~~  759 (945)
T KOG1132|consen  733 SKWIRSVK-CDSRYCEVISSLARKFRTH  759 (945)
T ss_pred             chhhhccc-cccccccccchhhhhhhcc
Confidence            99999832 2233334444555555544

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

Probab=99.28  E-value=2.7e-12  Score=149.09  Aligned_cols=91  Identities=30%  Similarity=0.464  Sum_probs=74.6

Q ss_pred             eeeccC-CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         242 VKVEFP-VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       242 ~~~~fp-y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      ....|| |+|||.|.+||..|..++++                       ++++++|||||||||+|||+|++.|++..+
T Consensus         7 ~~~~~~~~~~r~~Q~~~~~~v~~a~~~-----------------------~~~~~iEapTGtGKTl~yL~~al~~~~~~~   63 (654)
T COG1199           7 LAVAFPGFEPRPEQREMAEAVAEALKG-----------------------GEGLLIEAPTGTGKTLAYLLPALAYAREEG   63 (654)
T ss_pred             HHhhCCCCCCCHHHHHHHHHHHHHHcC-----------------------CCcEEEECCCCccHHHHHHHHHHHHHHHcC
Confidence            345677 79999999999999988875                       467999999999999999999999998764


Q ss_pred             H---------HHHHHHHhhhhhhhhhcCCCCceEEEecccc-ccc
Q psy3462         321 E---------LVQQKMFEQRTQDLQKIPFRKLKISRLKAKD-FST  355 (795)
Q Consensus       321 k---------~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr~-~~~  355 (795)
                      +         .+|+|++++|.|..........++..+|||. |.+
T Consensus        64 ~~viist~t~~lq~q~~~~~~~~~~~~~~~~~~~~~~kgr~n~~~  108 (654)
T COG1199          64 KKVIISTRTKALQEQLLEEDLPIHKLLKKLGGKFALLKGRSNYLC  108 (654)
T ss_pred             CcEEEECCCHHHHHHHHHhhcchhhhhhhhhhHHHHHhccccccc
Confidence            3         7999999999998444433333778889996 444

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.24  E-value=7.1e-12  Score=147.70  Aligned_cols=67  Identities=21%  Similarity=0.273  Sum_probs=61.1

Q ss_pred             hhHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhc-----CCcEEEECCCCCchHHHHHHHHHHHHHHhhHH
Q psy3462           4 KSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNK-----AKNCLLESPTGSGKTLALLCSVLAWQRKEKEL   70 (795)
Q Consensus         4 ~~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~-----~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~   70 (795)
                      ..++.|..+...++.|.+|++|.+||.+|+++|.+     ++++++|||||||||||||+|++.|+...++.
T Consensus         9 ~i~~~~~~l~~~~~~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~   80 (697)
T PRK11747          9 QIRQAYKALQEQLPGFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKK   80 (697)
T ss_pred             HHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCCe
Confidence            36788999999999999999999999999999988     47899999999999999999999999866543

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=99.08  E-value=2e-10  Score=134.11  Aligned_cols=84  Identities=17%  Similarity=0.255  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh--h--------HH
Q psy3462         253 SQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE--K--------EL  322 (795)
Q Consensus       253 ~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~--~--------k~  322 (795)
                      .|.+||..|+++|++                       ++++++|||||||||+|||+|++.|+...  +        +.
T Consensus         1 ~Q~~~~~~i~~al~~-----------------------~~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~   57 (636)
T TIGR03117         1 EQALFYLNCLTSLRQ-----------------------KRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLA   57 (636)
T ss_pred             CHHHHHHHHHHHHhc-----------------------CCeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHH
Confidence            499999999999974                       57899999999999999999999998742  2        27


Q ss_pred             HHHHHHhhhhhhhh-hcCCCCceEEEecccc-cccccchh
Q psy3462         323 VQQKMFEQRTQDLQ-KIPFRKLKISRLKAKD-FSTNNGME  360 (795)
Q Consensus       323 LQ~Ql~~kdip~l~-~i~~~~l~~~~~KGr~-~~~~~~~~  360 (795)
                      ||+|+++ |+|.+. +.++.+++++++||+. |.|.+...
T Consensus        58 Lq~Ql~~-~l~~l~~~~l~~~i~~~~lkGr~nYlCl~rl~   96 (636)
T TIGR03117        58 LMGQLWS-ELERLTAEGLAGPVQAGFFPGSQEFVSPGALQ   96 (636)
T ss_pred             HHHHHHH-HHHHHHHhhcCCCeeEEEEECCcccccHHHHH
Confidence            9999996 999999 7888999999999996 76644443

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.01  E-value=2.7e-10  Score=138.25  Aligned_cols=58  Identities=21%  Similarity=0.274  Sum_probs=53.2

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      .+...++.|.+||+|.+||++|++++.++.++++|||||||||+|||+|++.|+...+
T Consensus       248 ~l~~~~~~~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~  305 (928)
T PRK08074        248 KLSLAMPKYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKE  305 (928)
T ss_pred             HHHHhCCCCcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccC
Confidence            3667788999999999999999999999999999999999999999999999987543

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=98.78  E-value=7.6e-09  Score=124.72  Aligned_cols=57  Identities=25%  Similarity=0.334  Sum_probs=50.7

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .|+..+.. ++|.+||+|.+||++|++++.+++++++|||||||||+|||+|++.++.
T Consensus       234 ~~~~~~~~-~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~  290 (850)
T TIGR01407       234 LFSKNIDR-LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI  290 (850)
T ss_pred             HHHHhhhh-cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            44555544 6789999999999999999999999999999999999999999999875

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>KOG1131|consensus

Probab=98.73  E-value=1e-08  Score=115.70  Aligned_cols=71  Identities=24%  Similarity=0.533  Sum_probs=61.7

Q ss_pred             HHhCCCCCCCC----HHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCce
Q psy3462          12 YLNEPNYFLKY----SSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTS   87 (795)
Q Consensus        12 ~~~~~~~~~p~----~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~   87 (795)
                      ++++++.+|||    |.|.++|.++.++|..+.|+++|.|+|||||.|+|.-.++|......              .-.+
T Consensus         4 ~id~l~v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~--------------~~~K   69 (755)
T KOG1131|consen    4 YIDDLLVYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPD--------------EHRK   69 (755)
T ss_pred             eecCeeEecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCc--------------ccce
Confidence            34666777776    99999999999999999999999999999999999999999877654              2468


Q ss_pred             eEEeccccc
Q psy3462          88 FVFCGRSDF   96 (795)
Q Consensus        88 ~~yc~rth~   96 (795)
                      ++||+||-.
T Consensus        70 liYCSRTvp   78 (755)
T KOG1131|consen   70 LIYCSRTVP   78 (755)
T ss_pred             EEEecCcch
Confidence            999999954

>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

Probab=98.64  E-value=4.7e-09  Score=103.20  Aligned_cols=115  Identities=23%  Similarity=0.262  Sum_probs=73.7

Q ss_pred             HHHhHHHHHHHHHHHHhhccc------ccceeeecccccccccchhhhhhccccccceeecccchhhHHhhh-hhccccc
Q psy3462         365 TCITTINQQEDELRQSTKKTR------VDKLKVLNGRSKNLVSSIDFILGLLYKGIQTCITTINQQEDELRQ-STKKTKV  437 (795)
Q Consensus       365 ~~~rt~~q~e~el~~~~~~~~------~~~~~~l~sR~~~~~~~~~~~~~~~~~~~~lCi~~~~~~v~~~~~-~~~~~~c  437 (795)
                      ||+||++|+++-++++++-..      ..+..+|+||+                  ++|+   |+.|..+.. ...+..|
T Consensus         1 y~~RThsQl~q~i~El~~~~~~~~~~~~~~~~~l~gR~------------------~~C~---~~~v~~~~~~~~~~~~C   59 (174)
T PF06733_consen    1 YASRTHSQLSQVIRELKKINKYRPKGESIKAVILKGRQ------------------NLCI---NSKVKRLANNEDINEFC   59 (174)
T ss_dssp             EEESSHHHHHHHHHHHCCHCCCS-------EEEE--CC------------------CC-T---TCHHHTT-SHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHHHHHHHhhcccccceeeeEecccc------------------cccc---CchhhhhhhhhhHHHHH
Confidence            588999999999999997633      24789999999                  9999   778887765 4667778


Q ss_pred             ccccccccccccccchhhhHhhhcccCCCCccchhcccchhhhhhhhhhhhhcccccCccccccCCCCChhHHHHHhhhC
Q psy3462         438 DKLKVLNGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPCIEDLEQFSTRA  517 (795)
Q Consensus       438 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~C~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~~~~  517 (795)
                      +.+.          +..       .....|+||. +.....      ..    .....+.+      +++|||.++|.++
T Consensus        60 ~~l~----------~~~-------~~~~~C~~~~-~~~~~~------~~----~~~~~~~~------~d~~~l~~~~~~~  105 (174)
T PF06733_consen   60 RELR----------KSG-------KRKESCPYYN-NFDEIE------EL----SDLSNEEV------WDIEELVEIGKKH  105 (174)
T ss_dssp             HHHH----------HHH-------HCTCCSTTTT-GGGG-H------HH----HHHHCHCH------HHHHHHHHHHHHC
T ss_pred             HHhh----------ccc-------ccccccchhH-HHHhHH------Hh----hhhccccc------ccHHHHHHhcCCC
Confidence            7761          110       0113699665 321100      00    22344455      9999999999999


Q ss_pred             CccccchhhhhhHHHHH
Q psy3462         518 LVSPCFQLIQLDLMLDE  534 (795)
Q Consensus       518 ~~cpyf~~~q~~~~~~~  534 (795)
                      +.||||.++..-...|.
T Consensus       106 ~~CPY~~~r~~~~~adi  122 (174)
T PF06733_consen  106 GVCPYYLARELAKNADI  122 (174)
T ss_dssp             T--HHHHHHHCGGG-SE
T ss_pred             CCChhHHHHHhcccCCE
Confidence            99999999887766654

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.63  E-value=3.2e-08  Score=119.08  Aligned_cols=50  Identities=20%  Similarity=0.159  Sum_probs=46.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+.|++|+.|.+||++|++++.++.++++|||||||||+|||+|++.++
T Consensus       240 ~~~~~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~  289 (820)
T PRK07246        240 ALLGLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS  289 (820)
T ss_pred             ccCCCccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc
Confidence            45678999999999999999999999999999999999999999988764

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=98.57  E-value=7.3e-08  Score=113.00  Aligned_cols=103  Identities=17%  Similarity=0.081  Sum_probs=69.2

Q ss_pred             CcEEEcCCCcchhhHHhhhcccc-------e-eEeec---Cc------------cccceEEEEecCCCCCCCccccccc-
Q psy3462         556 RNIFYDTLMLCDVQTKETKHRDS-------V-KQVMG---KG------------NLELCKGVFWTRFPNTCQYSVVYPT-  611 (795)
Q Consensus       556 K~IFiE~kd~~e~~~~L~~Y~~a-------i-fAV~G---GK------------nl~rcViVVGIPYPn~~d~~Lk~~~-  611 (795)
                      -+++++... .....+++.|++.       | |+..+   |-            +...||||.=+|||. .|+...... 
T Consensus       496 ~~~l~qg~~-~~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~~G~~Ls~ViI~kLPF~~-~dp~a~~~~~  573 (636)
T TIGR03117       496 AEIVIQSEK-NRLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPDKDNLLTDLIITCAPFGL-NRSLSMLKRI  573 (636)
T ss_pred             CCEEEeCCC-ccHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCCCCCcccEEEEEeCCCCc-CChHHHHHHH
Confidence            568887643 2345677777643       3 43322   21            347788888899996 577533211 


Q ss_pred             ccCCcccc-hHHHHHHHHHhccCccccccCc--eeEEEEeecccCChhhhhhH
Q psy3462         612 GLLKGGDW-YQIQAYRALNQALGRCIRHRYD--WGAILLVDQRFYSKNSQQGL  661 (795)
Q Consensus       612 ~~~~G~ew-Y~~~AmRaVNQAIGRvIRHknD--yGaIiLlD~Rf~~~~~~~~L  661 (795)
                      ....++.| ....|..++.|.+||.||+++|  +|+|.++|+| ....|...+
T Consensus       574 ~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R-~~~~yg~~~  625 (636)
T TIGR03117       574 RKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR-IHWPYMESW  625 (636)
T ss_pred             HhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC-CCchhHHHH
Confidence            11123444 4588999999999999999999  9999999999 555555443

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>cd00268 DEADc DEAD-box helicases

Probab=98.24  E-value=4.2e-06  Score=82.64  Aligned_cols=72  Identities=14%  Similarity=0.139  Sum_probs=52.9

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCc
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKT   86 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~   86 (795)
                      ..++.+.. .++..|++.|.    ++++.+.++++++++||||+|||++|++|++..+....             ..+++
T Consensus         9 ~i~~~l~~-~~~~~~~~~Q~----~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~-------------~~~~~   70 (203)
T cd00268           9 ELLRGIYA-LGFEKPTPIQA----RAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP-------------KKDGP   70 (203)
T ss_pred             HHHHHHHH-cCCCCCCHHHH----HHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc-------------ccCCc
Confidence            45555555 46667999995    44555555899999999999999999999987665442             12467


Q ss_pred             eeEEeccccc
Q psy3462          87 SFVFCGRSDF   96 (795)
Q Consensus        87 ~~~yc~rth~   96 (795)
                      ++++.+.|..
T Consensus        71 ~viii~p~~~   80 (203)
T cd00268          71 QALILAPTRE   80 (203)
T ss_pred             eEEEEcCCHH
Confidence            7888886643

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=98.19  E-value=4.1e-06  Score=93.15  Aligned_cols=71  Identities=18%  Similarity=0.188  Sum_probs=52.9

Q ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeE
Q psy3462          10 KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFV   89 (795)
Q Consensus        10 ~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~   89 (795)
                      .+.++..++..|++.|    .+++.++.+++++++.||||+|||+||++|+|.++.....           ...+.++++
T Consensus        13 ~~~l~~~g~~~p~~iQ----~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~-----------~~~~~~~~l   77 (434)
T PRK11192         13 LEALQDKGYTRPTAIQ----AEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR-----------RKSGPPRIL   77 (434)
T ss_pred             HHHHHHCCCCCCCHHH----HHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-----------cCCCCceEE
Confidence            3445556888999999    5566666678899999999999999999999988764211           122456788


Q ss_pred             Eecccc
Q psy3462          90 FCGRSD   95 (795)
Q Consensus        90 yc~rth   95 (795)
                      +++.|.
T Consensus        78 il~Pt~   83 (434)
T PRK11192         78 ILTPTR   83 (434)
T ss_pred             EECCcH
Confidence            887553

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.11  E-value=4.8e-06  Score=92.52  Aligned_cols=53  Identities=13%  Similarity=0.152  Sum_probs=43.9

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+.+. ..++..|+|+|    .+++..+.+++++++.||||||||+||++|++..+..
T Consensus        20 ~~~l~-~~g~~~pt~iQ----~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~   72 (423)
T PRK04837         20 VEALE-KKGFHNCTPIQ----ALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLS   72 (423)
T ss_pred             HHHHH-HCCCCCCCHHH----HHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHh
Confidence            34443 45788999999    6667778889999999999999999999999987753

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.07  E-value=6.5e-06  Score=92.77  Aligned_cols=52  Identities=19%  Similarity=0.203  Sum_probs=42.7

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +.+....+..|+|.|    .+++.++.+++++|+.||||||||+||++|++..+..
T Consensus        14 ~~l~~~g~~~pt~iQ----~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~   65 (456)
T PRK10590         14 RAVAEQGYREPTPIQ----QQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLIT   65 (456)
T ss_pred             HHHHHCCCCCCCHHH----HHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhh
Confidence            334455888999999    5556667778999999999999999999999887643

>PTZ00110 helicase; Provisional

Probab=98.06  E-value=9.1e-06  Score=94.03  Aligned_cols=52  Identities=21%  Similarity=0.172  Sum_probs=43.4

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +.+....+..|+|+|    .+++..+.+++++|+.||||||||+||++|++..+..
T Consensus       143 ~~l~~~g~~~pt~iQ----~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~  194 (545)
T PTZ00110        143 KSLKNAGFTEPTPIQ----VQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINA  194 (545)
T ss_pred             HHHHHCCCCCCCHHH----HHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHh
Confidence            344455778899999    6677778889999999999999999999999887653

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=98.05  E-value=6.2e-06  Score=94.68  Aligned_cols=49  Identities=24%  Similarity=0.357  Sum_probs=40.8

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +...++..|+|+|    ..++.++..++++++.||||||||+||++|+|..+.
T Consensus       136 L~~~g~~~ptpiQ----~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~  184 (518)
T PLN00206        136 LETAGYEFPTPIQ----MQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCC  184 (518)
T ss_pred             HHHcCCCCCCHHH----HHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHH
Confidence            3445778999999    455566668899999999999999999999988765

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=98.00  E-value=7.3e-06  Score=92.07  Aligned_cols=49  Identities=29%  Similarity=0.243  Sum_probs=41.8

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +...++-.|+|.|    .+++..+.+++++++.||||||||+||++|++..+.
T Consensus        19 l~~~g~~~~t~iQ----~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~   67 (460)
T PRK11776         19 LNELGYTEMTPIQ----AQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLD   67 (460)
T ss_pred             HHHCCCCCCCHHH----HHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhh
Confidence            3445777899999    666677778999999999999999999999998764

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.98  E-value=1.6e-05  Score=92.68  Aligned_cols=52  Identities=19%  Similarity=0.153  Sum_probs=43.7

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +.+...++..|+|+|    ..++..+.+++++|+.||||||||+|||+|++..+..
T Consensus        22 ~~L~~~g~~~ptpiQ----~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~   73 (572)
T PRK04537         22 AGLESAGFTRCTPIQ----ALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLS   73 (572)
T ss_pred             HHHHHCCCCCCCHHH----HHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence            344555888999999    6666777889999999999999999999999987654

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=97.98  E-value=1.1e-05  Score=96.61  Aligned_cols=53  Identities=17%  Similarity=0.190  Sum_probs=45.4

Q ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          10 KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        10 ~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+.+...++..||++|    .+++.++.+|+++|+.||||||||+||++|+|..+..
T Consensus        26 ~~~L~~~g~~~p~~~Q----~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~   78 (742)
T TIGR03817        26 VAALEAAGIHRPWQHQ----ARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD   78 (742)
T ss_pred             HHHHHHcCCCcCCHHH----HHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhh
Confidence            4445556777899999    7777788899999999999999999999999988754

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.98  E-value=1.3e-05  Score=90.71  Aligned_cols=53  Identities=19%  Similarity=0.177  Sum_probs=44.3

Q ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          10 KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        10 ~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+.+...++-.|+++|    .+++..+.+|+++|+.||||||||+||++|++..+..
T Consensus        99 ~~~l~~~g~~~~~~iQ----~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~  151 (475)
T PRK01297         99 MHAIHDLGFPYCTPIQ----AQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQ  151 (475)
T ss_pred             HHHHHHCCCCCCCHHH----HHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            3445556788899999    6677778889999999999999999999999887653

>PTZ00424 helicase 45; Provisional

Probab=97.96  E-value=1.5e-05  Score=87.05  Aligned_cols=54  Identities=13%  Similarity=0.166  Sum_probs=43.5

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ..++.+... ++..|+|.|    .+++..+.++.++++.||||||||++|++|++..+.
T Consensus        38 ~~~~~l~~~-~~~~~~~~Q----~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~   91 (401)
T PTZ00424         38 DLLRGIYSY-GFEKPSAIQ----QRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLID   91 (401)
T ss_pred             HHHHHHHHc-CCCCCCHHH----HHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhc
Confidence            344555443 667899999    677777788899999999999999999999987653

>KOG0345|consensus

Probab=97.93  E-value=1.1e-05  Score=91.13  Aligned_cols=58  Identities=28%  Similarity=0.267  Sum_probs=49.6

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      .+..+.++..+|-..+|.|    .+.+..|.+++++++|||||||||||||+|.|..+....
T Consensus        15 ~~l~~~l~~~GF~~mTpVQ----a~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~   72 (567)
T KOG0345|consen   15 PWLLEALDESGFEKMTPVQ----AATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRRE   72 (567)
T ss_pred             HHHHHHHHhcCCcccCHHH----HhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhc
Confidence            4556667776777888999    889999999999999999999999999999999884433

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

Probab=97.87  E-value=2.5e-05  Score=89.96  Aligned_cols=57  Identities=23%  Similarity=0.230  Sum_probs=47.9

Q ss_pred             hHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           5 SSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         5 ~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +..+.+++.+ .+|-.|.|+|    ..++..+..+.+++..|+||||||+||++|+|..+..
T Consensus        37 ~~~ll~~l~~-~gf~~pt~IQ----~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~   93 (513)
T COG0513          37 SPELLQALKD-LGFEEPTPIQ----LAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILK   93 (513)
T ss_pred             CHHHHHHHHH-cCCCCCCHHH----HHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhc
Confidence            3455556666 6888999999    7778888888999999999999999999999988653

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=97.84  E-value=1.9e-05  Score=89.38  Aligned_cols=43  Identities=26%  Similarity=0.350  Sum_probs=36.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      .++..|+|.|    .+++.++.+++++++.||||+|||++|++|++.
T Consensus         7 ~g~~~~r~~Q----~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~   49 (470)
T TIGR00614         7 FGLSSFRPVQ----LEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC   49 (470)
T ss_pred             cCCCCCCHHH----HHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH
Confidence            4566899999    666667777889999999999999999999873

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=97.83  E-value=2.5e-05  Score=74.17  Aligned_cols=42  Identities=31%  Similarity=0.325  Sum_probs=33.0

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          22 YSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .|.|.+.+.    .+.+++++++.||||+|||++|++|++..+...
T Consensus         1 t~~Q~~~~~----~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~   42 (169)
T PF00270_consen    1 TPLQQEAIE----AIISGKNVLISAPTGSGKTLAYILPALNRLQEG   42 (169)
T ss_dssp             -HHHHHHHH----HHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHH----HHHcCCCEEEECCCCCccHHHHHHHHHhhhccC
Confidence            367855544    444778999999999999999999999876554

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=97.79  E-value=3.2e-05  Score=91.27  Aligned_cols=54  Identities=24%  Similarity=0.208  Sum_probs=43.7

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ...+++ ...++..|+|.|    .+++..+..++++|+.||||||||+||++|++..+.
T Consensus        16 ~ll~al-~~~G~~~ptpiQ----~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~   69 (629)
T PRK11634         16 PILEAL-NDLGYEKPSPIQ----AECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLD   69 (629)
T ss_pred             HHHHHH-HHCCCCCCCHHH----HHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhh
Confidence            344444 445888999999    556677778899999999999999999999987754

>KOG0348|consensus

Probab=97.77  E-value=1.9e-05  Score=90.35  Aligned_cols=58  Identities=24%  Similarity=0.206  Sum_probs=47.3

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQ   72 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq   72 (795)
                      .+.+-+..-.|..+|    ...+..|.++++++++|+||||||||||+|++..++.....+|
T Consensus       150 ~L~~~m~i~~pTsVQ----kq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~  207 (708)
T KOG0348|consen  150 HLNTKMKISAPTSVQ----KQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQ  207 (708)
T ss_pred             HHHHHhccCccchHh----hcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccc
Confidence            344455566799999    5566677779999999999999999999999999887776655

>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

Probab=97.71  E-value=5e-05  Score=72.44  Aligned_cols=45  Identities=27%  Similarity=0.392  Sum_probs=37.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC---CcEEEECCCCCchHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKA---KNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~---~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      +.+|+.|.+.++.+.+.+...   .++++.+|||+|||..++..+...
T Consensus         2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l   49 (184)
T PF04851_consen    2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILEL   49 (184)
T ss_dssp             -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcc
Confidence            568999999999999999876   889999999999998888543333

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=97.66  E-value=5.8e-05  Score=87.81  Aligned_cols=43  Identities=23%  Similarity=0.265  Sum_probs=36.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      .++-.++|.|    .+++.++.+++++++.||||+|||++|++|++.
T Consensus         9 fg~~~fr~~Q----~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~   51 (591)
T TIGR01389         9 FGYDDFRPGQ----EEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL   51 (591)
T ss_pred             cCCCCCCHHH----HHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHH
Confidence            4455789999    666667778899999999999999999999873

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=97.62  E-value=8.2e-05  Score=87.26  Aligned_cols=42  Identities=26%  Similarity=0.455  Sum_probs=35.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      ++-.++|.|    .+++.++.+++++++.+|||+|||++|++|+|.
T Consensus        22 G~~~~r~~Q----~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~   63 (607)
T PRK11057         22 GYQQFRPGQ----QEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALV   63 (607)
T ss_pred             CCCCCCHHH----HHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHH
Confidence            445799999    566666678899999999999999999999874

>PRK13767 ATP-dependent helicase; Provisional

Probab=97.55  E-value=0.00013  Score=88.95  Aligned_cols=45  Identities=31%  Similarity=0.317  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +..|+|.|    .++++.+.+++++++.||||||||+||++|++..+..
T Consensus        30 ~~~~tpiQ----~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~   74 (876)
T PRK13767         30 FGTFTPPQ----RYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFR   74 (876)
T ss_pred             cCCCCHHH----HHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            44699999    5556667788999999999999999999999987653

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=97.52  E-value=0.00014  Score=87.85  Aligned_cols=47  Identities=26%  Similarity=0.213  Sum_probs=41.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      +-.|+|.|    ..++..+.+|+|+++.||||+|||+|.++|+|.-+...+
T Consensus        20 ~~~~t~~Q----~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~   66 (814)
T COG1201          20 FTSLTPPQ----RYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG   66 (814)
T ss_pred             cCCCCHHH----HHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc
Confidence            66799999    666677779999999999999999999999999888773

>KOG0331|consensus

Probab=97.52  E-value=6.7e-05  Score=86.42  Aligned_cols=49  Identities=24%  Similarity=0.158  Sum_probs=44.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .-.+-.|.|+|    ...+..+..|+++|..|-||||||||||+|++.++...
T Consensus       108 ~~g~~~PtpIQ----aq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~  156 (519)
T KOG0331|consen  108 EQGFEKPTPIQ----AQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNE  156 (519)
T ss_pred             hcCCCCCchhh----hcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhc
Confidence            34777899999    77888888999999999999999999999999998764

>PRK02362 ski2-like helicase; Provisional

Probab=97.51  E-value=0.0002  Score=85.77  Aligned_cols=51  Identities=25%  Similarity=0.174  Sum_probs=39.9

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.....++..|||.|.+.+..   .+.+++++++.||||+|||++|++|++..+
T Consensus        14 ~~l~~~g~~~l~p~Q~~ai~~---~~~~g~nvlv~APTGSGKTlia~lail~~l   64 (737)
T PRK02362         14 EFYEAEGIEELYPPQAEAVEA---GLLDGKNLLAAIPTASGKTLIAELAMLKAI   64 (737)
T ss_pred             HHHHhCCCCcCCHHHHHHHHH---HHhCCCcEEEECCCcchHHHHHHHHHHHHH
Confidence            334445677899999544432   267789999999999999999999988765

>KOG0342|consensus

Probab=97.46  E-value=7.6e-05  Score=84.80  Aligned_cols=72  Identities=24%  Similarity=0.181  Sum_probs=57.0

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCc
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKT   86 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~   86 (795)
                      ..++++. .+++....+.|    +..+..+..+++++.-|-||||||||||+|++.+.......           ..+++
T Consensus        92 ~t~kAi~-~~GF~~MT~VQ----~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~-----------~r~~~  155 (543)
T KOG0342|consen   92 LTLKAIK-EMGFETMTPVQ----QKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFK-----------PRNGT  155 (543)
T ss_pred             HHHHHHH-hcCccchhHHH----HhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccC-----------CCCCe
Confidence            3444544 44777888999    78888888899999999999999999999999998876532           22677


Q ss_pred             eeEEeccc
Q psy3462          87 SFVFCGRS   94 (795)
Q Consensus        87 ~~~yc~rt   94 (795)
                      +++-||.|
T Consensus       156 ~vlIi~PT  163 (543)
T KOG0342|consen  156 GVLIICPT  163 (543)
T ss_pred             eEEEeccc
Confidence            77777754

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.45  E-value=0.00024  Score=84.50  Aligned_cols=86  Identities=21%  Similarity=0.297  Sum_probs=61.8

Q ss_pred             eeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         242 VKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       242 ~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      ....+||++++.|...+..|.+-++++                     ...+.|+.||||||||++|++|++..+....+
T Consensus       254 ~~~~l~f~lt~~Q~~ai~~I~~d~~~~---------------------~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q  312 (681)
T PRK10917        254 FLASLPFELTGAQKRVVAEILADLASP---------------------KPMNRLLQGDVGSGKTVVAALAALAAIEAGYQ  312 (681)
T ss_pred             HHHhCCCCCCHHHHHHHHHHHHhhhcc---------------------CCceEEEECCCCCcHHHHHHHHHHHHHHcCCe
Confidence            334689999999999999998877642                     23579999999999999999999887765433


Q ss_pred             --------HHHHHHHhhhhhhhhhcC-CCCceEEEecccc
Q psy3462         322 --------LVQQKMFEQRTQDLQKIP-FRKLKISRLKAKD  352 (795)
Q Consensus       322 --------~LQ~Ql~~kdip~l~~i~-~~~l~~~~~KGr~  352 (795)
                              .|-.|..+.    +++.. +..+++.++-|..
T Consensus       313 ~lilaPT~~LA~Q~~~~----l~~l~~~~~i~v~ll~G~~  348 (681)
T PRK10917        313 AALMAPTEILAEQHYEN----LKKLLEPLGIRVALLTGSL  348 (681)
T ss_pred             EEEEeccHHHHHHHHHH----HHHHHhhcCcEEEEEcCCC
Confidence                    455555543    33322 2346677776653

>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

Probab=97.44  E-value=0.00014  Score=69.33  Aligned_cols=44  Identities=34%  Similarity=0.508  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCS  311 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~  311 (795)
                      |++||.|.+.+..+.+.++..                    ...+++++.+|||||||+.++..
T Consensus         2 ~~lr~~Q~~ai~~i~~~~~~~--------------------~~~~~~ll~~~tGsGKT~~~~~~   45 (184)
T PF04851_consen    2 YKLRPYQQEAIARIINSLENK--------------------KEERRVLLNAPTGSGKTIIALAL   45 (184)
T ss_dssp             -EE-HHHHHHHHHHHHHHHTT--------------------SGCSEEEEEESTTSSHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHhc--------------------CCCCCEEEEECCCCCcChhhhhh
Confidence            678999999999999998751                    12578999999999999988753

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>cd00268 DEADc DEAD-box helicases

Probab=97.41  E-value=0.00026  Score=69.98  Aligned_cols=47  Identities=23%  Similarity=0.333  Sum_probs=38.1

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ++|+ |++.|.+.+..+.+                           ++++++++|||+|||++|+++++..+...
T Consensus        17 ~~~~~~~~~Q~~~~~~~~~---------------------------~~~~li~~~TG~GKT~~~~~~~l~~~~~~   64 (203)
T cd00268          17 LGFEKPTPIQARAIPPLLS---------------------------GRDVIGQAQTGSGKTAAFLIPILEKLDPS   64 (203)
T ss_pred             cCCCCCCHHHHHHHHHHhc---------------------------CCcEEEECCCCCcHHHHHHHHHHHHHHhh
Confidence            4554 89999999888653                           47899999999999999999988765543

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.40  E-value=0.0002  Score=79.74  Aligned_cols=45  Identities=20%  Similarity=0.268  Sum_probs=36.3

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| .|.|+|.+.+..+.                           +++++++.||||||||++|++|++..+.
T Consensus        26 ~g~~~pt~iQ~~aip~il---------------------------~g~dvi~~ApTGsGKTla~llp~l~~l~   71 (423)
T PRK04837         26 KGFHNCTPIQALALPLTL---------------------------AGRDVAGQAQTGTGKTMAFLTATFHYLL   71 (423)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCcEEEECCCCchHHHHHHHHHHHHHH
Confidence            566 47888887766542                           3678999999999999999999987664

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=97.40  E-value=0.0002  Score=88.68  Aligned_cols=48  Identities=17%  Similarity=0.154  Sum_probs=38.6

Q ss_pred             HHHhCCC-CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          11 TYLNEPN-YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        11 ~~~~~~~-~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      .++...+ +..+||.|    .+++.++..++++++.+|||+||||||++|+|.
T Consensus       450 ~~lk~~FG~~sFRp~Q----~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~  498 (1195)
T PLN03137        450 VNNKKVFGNHSFRPNQ----REIINATMSGYDVFVLMPTGGGKSLTYQLPALI  498 (1195)
T ss_pred             HHHHHHcCCCCCCHHH----HHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHH
Confidence            3444444 55789999    556667778999999999999999999999975

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

Probab=97.35  E-value=0.0002  Score=68.09  Aligned_cols=29  Identities=45%  Similarity=0.660  Sum_probs=25.5

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ++++++.||||+|||++|+.+++..+...
T Consensus        14 ~~~~li~aptGsGKT~~~~~~~l~~~~~~   42 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILPALNRLQEG   42 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCCEEEECCCCCccHHHHHHHHHhhhccC
Confidence            57899999999999999999998877554

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

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

Probab=97.35  E-value=0.00026  Score=86.33  Aligned_cols=56  Identities=20%  Similarity=0.273  Sum_probs=47.2

Q ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHH
Q psy3462          10 KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKEL   70 (795)
Q Consensus        10 ~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~   70 (795)
                      ..+.+..+. .+|++|    .++++.+.+|+++|+-+|||+|||+||++|+|..+......
T Consensus        61 ~~l~~~g~~-~lY~HQ----~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a  116 (851)
T COG1205          61 SALVKAGIE-RLYSHQ----VDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA  116 (851)
T ss_pred             HHHHHhccc-cccHHH----HHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc
Confidence            344444333 499999    88999999999999999999999999999999998877665

>KOG0348|consensus

Probab=97.34  E-value=9.7e-05  Score=84.73  Aligned_cols=40  Identities=30%  Similarity=0.363  Sum_probs=34.4

Q ss_pred             HHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         282 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       282 ~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      .+.||.+.+++.++++|+||||||||||+|++.-+.....
T Consensus       165 kq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~  204 (708)
T KOG0348|consen  165 KQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEP  204 (708)
T ss_pred             hcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCc
Confidence            3567788889999999999999999999999988876543

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=97.31  E-value=0.00026  Score=81.58  Aligned_cols=45  Identities=22%  Similarity=0.296  Sum_probs=37.1

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ..| .|+|+|.+.+..+.                           .++++++.||||||||++|++|+|..+.
T Consensus       139 ~g~~~ptpiQ~~aip~il---------------------------~g~dviv~ApTGSGKTlayllPil~~l~  184 (518)
T PLN00206        139 AGYEFPTPIQMQAIPAAL---------------------------SGRSLLVSADTGSGKTASFLVPIISRCC  184 (518)
T ss_pred             cCCCCCCHHHHHHHHHHh---------------------------cCCCEEEEecCCCCccHHHHHHHHHHHH
Confidence            456 58999988876643                           2578999999999999999999987664

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=97.31  E-value=0.00024  Score=80.60  Aligned_cols=44  Identities=30%  Similarity=0.551  Sum_probs=36.4

Q ss_pred             eccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         244 VEFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       244 ~~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      -.|.| .+||.|.+.+..+.                           +++++++.||||+|||++|++|++.
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l---------------------------~g~dvlv~apTGsGKTl~y~lp~l~   49 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVL---------------------------LGRDCFVVMPTGGGKSLCYQLPALC   49 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCCcHhHHHHHHHHH
Confidence            35787 48999998877753                           2568999999999999999999874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.30  E-value=0.00036  Score=65.95  Aligned_cols=48  Identities=29%  Similarity=0.335  Sum_probs=37.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .++..|++.|.+++..+....   .++++.+|||||||.+++.+++.....
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~---~~~~i~~~~GsGKT~~~~~~~~~~~~~   51 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKR   51 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCC---CcEEEECCCCCchhHHHHHHHHHHhcc
Confidence            356789999976665544332   899999999999999999887776543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.30  E-value=0.00074  Score=79.72  Aligned_cols=83  Identities=19%  Similarity=0.289  Sum_probs=59.5

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH--
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE--  321 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k--  321 (795)
                      ..+||++++.|...+.+|.+-+..+                     ...+.++.||||||||++|++|++..+....+  
T Consensus       230 ~~lpf~lt~~Q~~ai~~I~~~~~~~---------------------~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvl  288 (630)
T TIGR00643       230 ASLPFKLTRAQKRVVKEILQDLKSD---------------------VPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVA  288 (630)
T ss_pred             HhCCCCCCHHHHHHHHHHHHHhccC---------------------CCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEE
Confidence            3689999999999999998877532                     13468999999999999999998877665433  


Q ss_pred             ------HHHHHHHhhhhhhhhhcC-CCCceEEEeccc
Q psy3462         322 ------LVQQKMFEQRTQDLQKIP-FRKLKISRLKAK  351 (795)
Q Consensus       322 ------~LQ~Ql~~kdip~l~~i~-~~~l~~~~~KGr  351 (795)
                            .|-+|..+.    +++.+ +..++++++-|.
T Consensus       289 ilaPT~~LA~Q~~~~----~~~l~~~~gi~v~lltg~  321 (630)
T TIGR00643       289 LMAPTEILAEQHYNS----LRNLLAPLGIEVALLTGS  321 (630)
T ss_pred             EECCHHHHHHHHHHH----HHHHhcccCcEEEEEecC
Confidence                  455555433    22322 235667777665

>KOG0335|consensus

Probab=97.29  E-value=0.00012  Score=83.60  Aligned_cols=54  Identities=20%  Similarity=0.227  Sum_probs=47.4

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKEL   70 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~   70 (795)
                      .+-..+-.|.|+|    +..+..+.++.+++..|+||+|||.|||+|++.++.+.+..
T Consensus        89 i~~~~~~~ptpvQ----k~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~  142 (482)
T KOG0335|consen   89 IKRSGYTKPTPVQ----KYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPE  142 (482)
T ss_pred             cccccccCCCcce----eeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcc
Confidence            3444577899999    88889999999999999999999999999999999887653

>PTZ00424 helicase 45; Provisional

Probab=97.29  E-value=0.00031  Score=76.84  Aligned_cols=46  Identities=15%  Similarity=0.239  Sum_probs=37.5

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      .+.| .|+|.|.+.+..+.                           ++.++++.||||||||++|++|++..+.
T Consensus        45 ~~~~~~~~~~Q~~ai~~i~---------------------------~~~d~ii~apTGsGKT~~~~l~~l~~~~   91 (401)
T PTZ00424         45 SYGFEKPSAIQQRGIKPIL---------------------------DGYDTIGQAQSGTGKTATFVIAALQLID   91 (401)
T ss_pred             HcCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCChHHHHHHHHHHHHhc
Confidence            3566 48999998887764                           2467899999999999999999988764

>KOG0345|consensus

Probab=97.23  E-value=0.00053  Score=77.95  Aligned_cols=56  Identities=30%  Similarity=0.350  Sum_probs=42.5

Q ss_pred             HHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH-hhH---------------HHHHHHHhhhhhhhhhc
Q psy3462         283 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK-EKE---------------LVQQKMFEQRTQDLQKI  338 (795)
Q Consensus       283 ~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~-~~k---------------~LQ~Ql~~kdip~l~~i  338 (795)
                      ..||-+.+++.+++|||||||||||||+|++..+.+ +.+               .|-.|+.+--.|+++..
T Consensus        35 ~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l  106 (567)
T KOG0345|consen   35 ATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHL  106 (567)
T ss_pred             hhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHhh
Confidence            345555667899999999999999999999998833 221               57777777666777664

>PRK00254 ski2-like helicase; Provisional

Probab=97.23  E-value=0.00053  Score=81.93  Aligned_cols=56  Identities=27%  Similarity=0.201  Sum_probs=43.3

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +...+.+...++..|+|.|.+-+..   .+.+++++++.||||+|||++|++|++..+.
T Consensus        10 ~~~~~~l~~~g~~~l~~~Q~~ai~~---~~~~g~nvlv~apTGsGKT~~~~l~il~~l~   65 (720)
T PRK00254         10 ERIKRVLKERGIEELYPPQAEALKS---GVLEGKNLVLAIPTASGKTLVAEIVMVNKLL   65 (720)
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHH---HHhCCCcEEEECCCCcHHHHHHHHHHHHHHH
Confidence            3445566666778899999544332   3678899999999999999999999886543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.23  E-value=0.00068  Score=80.00  Aligned_cols=58  Identities=24%  Similarity=0.311  Sum_probs=47.5

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ....++.+.+|| .|++.|++-+.+|...+...  .+.++.||||||||++|++|++....
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~  282 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE  282 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH
Confidence            445677777665 89999999999988887654  36899999999999999999887643

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=97.23  E-value=0.00068  Score=81.64  Aligned_cols=47  Identities=19%  Similarity=0.278  Sum_probs=38.2

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ..| +|||.|.+.+..+.                           +++++++.||||||||+||++|+|..+...
T Consensus        32 ~g~~~p~~~Q~~ai~~il---------------------------~G~nvvv~apTGSGKTla~~LPiL~~l~~~   79 (742)
T TIGR03817        32 AGIHRPWQHQARAAELAH---------------------------AGRHVVVATGTASGKSLAYQLPVLSALADD   79 (742)
T ss_pred             cCCCcCCHHHHHHHHHHH---------------------------CCCCEEEECCCCCcHHHHHHHHHHHHHhhC
Confidence            345 48999988777652                           368999999999999999999999887653

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.22  E-value=0.0007  Score=80.65  Aligned_cols=58  Identities=24%  Similarity=0.291  Sum_probs=46.9

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ...+++.+.+ +|.|++.|++.+.+|..-+..+  .+.|+.||||||||++|++|++..+.
T Consensus       249 ~~~~~~~~~l-~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~  308 (681)
T PRK10917        249 ELLKKFLASL-PFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE  308 (681)
T ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH
Confidence            3445666664 4589999999999888888654  47999999999999999999987653

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=97.22  E-value=0.001  Score=81.94  Aligned_cols=56  Identities=21%  Similarity=0.366  Sum_probs=47.4

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      .|||+|.|.|...+..|.+.++.+                     ...+.++.||||+|||++++.+++..+....+
T Consensus       447 ~~~f~~T~~Q~~aI~~I~~d~~~~---------------------~~~d~Ll~adTGsGKT~val~a~l~al~~g~q  502 (926)
T TIGR00580       447 SFPFEETPDQLKAIEEIKADMESP---------------------RPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQ  502 (926)
T ss_pred             hCCCCCCHHHHHHHHHHHhhhccc---------------------CcCCEEEECCCCccHHHHHHHHHHHHHHhCCe
Confidence            689999999999999999888643                     24679999999999999999998877765543

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=97.21  E-value=0.00038  Score=78.64  Aligned_cols=46  Identities=20%  Similarity=0.245  Sum_probs=37.2

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| +|+|.|.+.+..+.                           +++++++.||||||||++|++|++..+..
T Consensus        19 ~g~~~pt~iQ~~ai~~il---------------------------~g~dvlv~apTGsGKTla~~lpil~~l~~   65 (456)
T PRK10590         19 QGYREPTPIQQQAIPAVL---------------------------EGRDLMASAQTGTGKTAGFTLPLLQHLIT   65 (456)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCCcHHHHHHHHHHHHhhh
Confidence            344 58999988877653                           35789999999999999999999877643

>PRK01172 ski2-like helicase; Provisional

Probab=97.19  E-value=0.0005  Score=81.37  Aligned_cols=49  Identities=24%  Similarity=0.362  Sum_probs=38.3

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.... .+|.+|+.|.    ++++++.+++++++.||||+|||++++++++...
T Consensus        14 ~~~~~-~~~~l~~~Q~----~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l   62 (674)
T PRK01172         14 NLFTG-NDFELYDHQR----MAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETF   62 (674)
T ss_pred             HHHhh-CCCCCCHHHH----HHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHH
Confidence            33333 3567999994    4555678889999999999999999999987654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=97.14  E-value=0.00053  Score=76.51  Aligned_cols=46  Identities=24%  Similarity=0.274  Sum_probs=37.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ..| +|+|.|.+.+..+.                           +++++++.||||||||++|++|++.++.+
T Consensus        19 ~g~~~p~~iQ~~ai~~~~---------------------------~g~d~l~~apTGsGKT~~~~lp~l~~l~~   65 (434)
T PRK11192         19 KGYTRPTAIQAEAIPPAL---------------------------DGRDVLGSAPTGTGKTAAFLLPALQHLLD   65 (434)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCChHHHHHHHHHHHHHhh
Confidence            455 48899988877753                           25679999999999999999999987754

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.09  E-value=0.00068  Score=76.89  Aligned_cols=46  Identities=22%  Similarity=0.297  Sum_probs=36.4

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| .++|.|.+.+..+.                           .++++++.||||||||++|++|++.-+..
T Consensus       105 ~g~~~~~~iQ~~ai~~~~---------------------------~G~dvi~~apTGSGKTlay~lpil~~l~~  151 (475)
T PRK01297        105 LGFPYCTPIQAQVLGYTL---------------------------AGHDAIGRAQTGTGKTAAFLISIINQLLQ  151 (475)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            455 37888887776543                           36789999999999999999999876543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=97.08  E-value=0.00057  Score=79.70  Aligned_cols=43  Identities=28%  Similarity=0.468  Sum_probs=36.5

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .|+|+ +||.|.+.+..+.                           +++++++.||||+|||++|++|++.
T Consensus         8 ~fg~~~fr~~Q~~~i~~il---------------------------~g~dvlv~~PTG~GKTl~y~lpal~   51 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVL---------------------------DGRDVLVVMPTGGGKSLCYQVPALL   51 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCccHhHHHHHHHHH
Confidence            58885 8999999888764                           2568999999999999999999873

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=97.05  E-value=0.00069  Score=76.34  Aligned_cols=45  Identities=24%  Similarity=0.282  Sum_probs=36.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ..| +|.|.|.+.+..+.                           +++++++.||||||||++|++|++..+.
T Consensus        22 ~g~~~~t~iQ~~ai~~~l---------------------------~g~dvi~~a~TGsGKT~a~~lpil~~l~   67 (460)
T PRK11776         22 LGYTEMTPIQAQSLPAIL---------------------------AGKDVIAQAKTGSGKTAAFGLGLLQKLD   67 (460)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------cCCCEEEECCCCCcHHHHHHHHHHHHhh
Confidence            456 38899987777653                           3578999999999999999999987764

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=97.00  E-value=0.00071  Score=79.54  Aligned_cols=43  Identities=30%  Similarity=0.568  Sum_probs=36.1

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .|.|+ +||.|.+.+..+.                           +++++++.||||+|||++|++|++.
T Consensus        20 ~fG~~~~r~~Q~~ai~~il---------------------------~g~dvlv~apTGsGKTl~y~lpal~   63 (607)
T PRK11057         20 TFGYQQFRPGQQEIIDAVL---------------------------SGRDCLVVMPTGGGKSLCYQIPALV   63 (607)
T ss_pred             HcCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCchHHHHHHHHHHH
Confidence            58884 8999998888753                           2578999999999999999999874

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.00  E-value=0.00085  Score=78.51  Aligned_cols=45  Identities=24%  Similarity=0.267  Sum_probs=36.2

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| +|+|+|.+.+..+.                           +++++++.||||||||++||+|++..+.
T Consensus        27 ~g~~~ptpiQ~~~ip~~l---------------------------~G~Dvi~~ApTGSGKTlafllpil~~l~   72 (572)
T PRK04537         27 AGFTRCTPIQALTLPVAL---------------------------PGGDVAGQAQTGTGKTLAFLVAVMNRLL   72 (572)
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            456 48888888776542                           3678999999999999999999987654

>PTZ00110 helicase; Provisional

Probab=96.97  E-value=0.00088  Score=77.87  Aligned_cols=45  Identities=24%  Similarity=0.252  Sum_probs=35.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ..| +|+|+|.+.+..+                           ..++++++.||||||||++|++|++..+.
T Consensus       148 ~g~~~pt~iQ~~aip~~---------------------------l~G~dvI~~ApTGSGKTlaylLP~l~~i~  193 (545)
T PTZ00110        148 AGFTEPTPIQVQGWPIA---------------------------LSGRDMIGIAETGSGKTLAFLLPAIVHIN  193 (545)
T ss_pred             CCCCCCCHHHHHHHHHH---------------------------hcCCCEEEEeCCCChHHHHHHHHHHHHHH
Confidence            456 4899998776553                           23678999999999999999999987654

>KOG0344|consensus

Probab=96.95  E-value=0.00076  Score=78.18  Aligned_cols=52  Identities=29%  Similarity=0.273  Sum_probs=44.0

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      +...++-.|.|+|    ..++..+....+++..||||+||||||++|.|..+....
T Consensus       151 l~~~~F~~Pt~iq----~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~  202 (593)
T KOG0344|consen  151 LQELGFDEPTPIQ----KQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLS  202 (593)
T ss_pred             HhhCCCCCCCccc----chhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhh
Confidence            3445677899999    477788888999999999999999999999888877654

>KOG0331|consensus

Probab=96.90  E-value=0.00042  Score=80.01  Aligned_cols=35  Identities=29%  Similarity=0.269  Sum_probs=30.2

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ++.+..++.++.-|-||||||||||+|++.++..+
T Consensus       122 wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~  156 (519)
T KOG0331|consen  122 WPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNE  156 (519)
T ss_pred             cceeccCCceEEEeccCCcchhhhhhHHHHHHHhc
Confidence            34456789999999999999999999999988764

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.90  E-value=0.0019  Score=79.52  Aligned_cols=58  Identities=10%  Similarity=0.012  Sum_probs=47.0

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+++++.+.. +|.|++.|.+.+.+|.+.+.++  .+.++.||||+|||++|+.|++..+
T Consensus       438 ~~~~~~~~~~~-~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al  497 (926)
T TIGR00580       438 LEWQQEFEDSF-PFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAV  497 (926)
T ss_pred             HHHHHHHHHhC-CCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHH
Confidence            34566666664 4589999999999998888765  5799999999999999999987654

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>KOG0330|consensus

Probab=96.85  E-value=0.00078  Score=75.22  Aligned_cols=48  Identities=21%  Similarity=0.115  Sum_probs=41.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      ....-.|.++|    .+++....+++++|..|-||+|||+||++|+|..+..
T Consensus        78 ~l~~~~PT~IQ----~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~  125 (476)
T KOG0330|consen   78 ELGWKKPTKIQ----SEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQ  125 (476)
T ss_pred             HhCcCCCchhh----hhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHc
Confidence            34567899999    7788889999999999999999999999999887654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.84  E-value=0.0019  Score=76.50  Aligned_cols=46  Identities=26%  Similarity=0.274  Sum_probs=37.1

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| +|+|.|.+.+..+.                           +++.+|+.||||||||++|++|++..+..
T Consensus        24 ~G~~~ptpiQ~~ai~~ll---------------------------~g~dvl~~ApTGsGKT~af~lpll~~l~~   70 (629)
T PRK11634         24 LGYEKPSPIQAECIPHLL---------------------------NGRDVLGMAQTGSGKTAAFSLPLLHNLDP   70 (629)
T ss_pred             CCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCCcHHHHHHHHHHHHhhh
Confidence            456 58999988776653                           25789999999999999999999876643

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=96.82  E-value=0.0018  Score=79.10  Aligned_cols=46  Identities=20%  Similarity=0.169  Sum_probs=34.9

Q ss_pred             CCCCCC---CHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          16 PNYFLK---YSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        16 ~~~~~p---~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .++-.|   +|.|.|.|    ..+..+.++|.+|+||||||+||++|++..+.
T Consensus        85 ~G~~~p~~~tp~qvQ~I----~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL  133 (970)
T PRK12899         85 SGYHQQWDMVPYDVQIL----GAIAMHKGFITEMQTGEGKTLTAVMPLYLNAL  133 (970)
T ss_pred             ccccCCCCCChHHHHHh----hhhhcCCCeEEEeCCCCChHHHHHHHHHHHHh
Confidence            345556   67774444    44555678999999999999999999997653

>KOG0346|consensus

Probab=96.79  E-value=0.0016  Score=73.69  Aligned_cols=54  Identities=26%  Similarity=0.164  Sum_probs=43.4

Q ss_pred             HHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          10 KTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        10 ~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      +++.+ .+.-.|.-+|    ..++.-...++++|.-|-||+|||+|||+|+|+.+...+
T Consensus        32 kAi~~-lG~ekpTlIQ----s~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k   85 (569)
T KOG0346|consen   32 KAITK-LGWEKPTLIQ----SSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEK   85 (569)
T ss_pred             HHHHH-hCcCCcchhh----hcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhh
Confidence            34433 4666799999    777777778899999999999999999999988766544

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=96.70  E-value=0.0014  Score=79.72  Aligned_cols=50  Identities=20%  Similarity=0.204  Sum_probs=34.3

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCC-cEEEECCCCCchHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAK-NCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~-~~llEAPTGTGKTLAyL~paL~   62 (795)
                      |.+.-.+.-+|.|+|+|.+.+..    +..|+ ++++.||||||||.++.++.+.
T Consensus         4 f~~ff~~~~G~~PtpiQ~~~i~~----il~G~~~v~~~apTGSGKTaa~aafll~   54 (844)
T TIGR02621         4 FDEWYQGLHGYSPFPWQLSLAER----FVAGQPPESCSTPTGLGKTSIIAAWLLA   54 (844)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHH----HHcCCCcceEecCCCCcccHHHHHhhcc
Confidence            33333343456799999665554    44555 6888999999999977655553

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=96.67  E-value=0.0019  Score=80.50  Aligned_cols=33  Identities=24%  Similarity=0.395  Sum_probs=27.4

Q ss_pred             HHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         282 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       282 ~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .++|+++..++++++-||||+|||++|++|+|.
T Consensus       466 ~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~  498 (1195)
T PLN03137        466 REIINATMSGYDVFVLMPTGGGKSLTYQLPALI  498 (1195)
T ss_pred             HHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHH
Confidence            345555556889999999999999999999874

>PRK09694 helicase Cas3; Provisional

Probab=96.67  E-value=0.0023  Score=78.39  Aligned_cols=58  Identities=21%  Similarity=0.158  Sum_probs=40.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccc
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSD   95 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth   95 (795)
                      .+.|||.|..+.+    ...+...+|||||||+|||.|.|..+...+.                .....++||+..|-
T Consensus       284 ~~~p~p~Q~~~~~----~~~~pgl~ileApTGsGKTEAAL~~A~~l~~----------------~~~~~gi~~aLPT~  341 (878)
T PRK09694        284 GYQPRQLQTLVDA----LPLQPGLTIIEAPTGSGKTEAALAYAWRLID----------------QGLADSIIFALPTQ  341 (878)
T ss_pred             CCCChHHHHHHHh----hccCCCeEEEEeCCCCCHHHHHHHHHHHHHH----------------hCCCCeEEEECcHH
Confidence            6789999965532    2234567999999999999998877553221                12346889987543

>KOG0333|consensus

Probab=96.66  E-value=0.0015  Score=75.19  Aligned_cols=57  Identities=25%  Similarity=0.315  Sum_probs=48.4

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      +.++ ++..++|..|.|+|    ..++.......+.|.-|-||+|||+||++|+|.|+....
T Consensus       255 e~l~-~I~~~~y~eptpIq----R~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP  311 (673)
T KOG0333|consen  255 ELLS-VIKKPGYKEPTPIQ----RQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLP  311 (673)
T ss_pred             HHHH-HHHhcCCCCCchHH----HhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCC
Confidence            4455 77788999999999    555667777889999999999999999999999987665

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.65  E-value=0.003  Score=59.66  Aligned_cols=47  Identities=30%  Similarity=0.349  Sum_probs=37.2

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      .+++++|.|.+++..+.+..                          +++++.+|||||||.+++.+++..+..
T Consensus         5 ~~~~~~~~Q~~~~~~~~~~~--------------------------~~~~i~~~~GsGKT~~~~~~~~~~~~~   51 (201)
T smart00487        5 GFEPLRPYQKEAIEALLSGL--------------------------RDVILAAPTGSGKTLAALLPALEALKR   51 (201)
T ss_pred             CCCCCCHHHHHHHHHHHcCC--------------------------CcEEEECCCCCchhHHHHHHHHHHhcc
Confidence            45689999999988765211                          579999999999999998887766554

>PRK13767 ATP-dependent helicase; Provisional

Probab=96.60  E-value=0.0026  Score=78.07  Aligned_cols=42  Identities=36%  Similarity=0.453  Sum_probs=35.5

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      .|+|.|.+.+..+.                           +++++++.||||||||++|++|++..+.
T Consensus        32 ~~tpiQ~~Ai~~il---------------------------~g~nvli~APTGSGKTlaa~Lpil~~l~   73 (876)
T PRK13767         32 TFTPPQRYAIPLIH---------------------------EGKNVLISSPTGSGKTLAAFLAIIDELF   73 (876)
T ss_pred             CCCHHHHHHHHHHH---------------------------cCCCEEEECCCCCcHHHHHHHHHHHHHH
Confidence            48999998887652                           2578999999999999999999987664

>PRK09401 reverse gyrase; Reviewed

Probab=96.49  E-value=0.0043  Score=78.33  Aligned_cols=50  Identities=14%  Similarity=0.125  Sum_probs=37.0

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ++.....++.|++.|.    .+++.+..++++++.||||+|||. |++|++.+..
T Consensus        71 ~~f~~~~G~~pt~iQ~----~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~  120 (1176)
T PRK09401         71 KFFKKKTGSKPWSLQR----TWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLA  120 (1176)
T ss_pred             HHHHHhcCCCCcHHHH----HHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHH
Confidence            3444555679999994    555666688999999999999995 5566555543

>PRK01172 ski2-like helicase; Provisional

Probab=96.48  E-value=0.005  Score=73.08  Aligned_cols=49  Identities=22%  Similarity=0.264  Sum_probs=39.3

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      .+|++||.|.+.+..+   +                        +++++++.||||+|||++++.+++......++
T Consensus        19 ~~~~l~~~Q~~ai~~l---~------------------------~~~nvlv~apTGSGKTl~a~lail~~l~~~~k   67 (674)
T PRK01172         19 NDFELYDHQRMAIEQL---R------------------------KGENVIVSVPTAAGKTLIAYSAIYETFLAGLK   67 (674)
T ss_pred             CCCCCCHHHHHHHHHH---h------------------------cCCcEEEECCCCchHHHHHHHHHHHHHHhCCc
Confidence            4678999999988775   2                        25789999999999999999988776655443

>PRK02362 ski2-like helicase; Provisional

Probab=96.45  E-value=0.0072  Score=72.62  Aligned_cols=72  Identities=22%  Similarity=0.300  Sum_probs=48.7

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH-------
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE-------  321 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k-------  321 (795)
                      ++||.|.+.+...   +.                       +++++++.||||+|||++|+++++..+...++       
T Consensus        23 ~l~p~Q~~ai~~~---~~-----------------------~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~   76 (737)
T PRK02362         23 ELYPPQAEAVEAG---LL-----------------------DGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPL   76 (737)
T ss_pred             cCCHHHHHHHHHH---Hh-----------------------CCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeCh
Confidence            5899999988652   22                       35789999999999999999998877765444       


Q ss_pred             -HHHHHHHhhhhhhhhhcCCCCceEEEecc
Q psy3462         322 -LVQQKMFEQRTQDLQKIPFRKLKISRLKA  350 (795)
Q Consensus       322 -~LQ~Ql~~kdip~l~~i~~~~l~~~~~KG  350 (795)
                       .|-+|....    +.+.....+++..+-|
T Consensus        77 raLa~q~~~~----~~~~~~~g~~v~~~tG  102 (737)
T PRK02362         77 RALASEKFEE----FERFEELGVRVGISTG  102 (737)
T ss_pred             HHHHHHHHHH----HHHhhcCCCEEEEEeC
Confidence             455565543    2222222455555555

>KOG0350|consensus

Probab=96.43  E-value=0.0023  Score=73.42  Aligned_cols=51  Identities=18%  Similarity=0.255  Sum_probs=41.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhc-----CCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNK-----AKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~-----~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      ...-..+|.|.+.+-.+.+.+..     ..++.+-||||+||||||-+|+++-+-.
T Consensus       155 ~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~  210 (620)
T KOG0350|consen  155 MAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSS  210 (620)
T ss_pred             hhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHcc
Confidence            34445679998888888888763     5689999999999999999998776543

>PRK14701 reverse gyrase; Provisional

Probab=96.40  E-value=0.0048  Score=79.95  Aligned_cols=52  Identities=19%  Similarity=0.176  Sum_probs=40.1

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      |.++.....+|.|++.|    ..++..+..++++++.||||+|||+.++++++..+
T Consensus        68 ~~~~f~~~~G~~pt~iQ----~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~  119 (1638)
T PRK14701         68 FEEFFEKITGFEFWSIQ----KTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA  119 (1638)
T ss_pred             HHHHHHHhhCCCCCHHH----HHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH
Confidence            44455554456899999    66666677789999999999999997777777654

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=96.37  E-value=0.0043  Score=75.33  Aligned_cols=44  Identities=30%  Similarity=0.345  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      +|+|.|...+..|.                           +|.|+|+-||||+|||+|-++|++.-+...
T Consensus        22 ~~t~~Q~~a~~~i~---------------------------~G~nvLiiAPTGsGKTeAAfLpil~~l~~~   65 (814)
T COG1201          22 SLTPPQRYAIPEIH---------------------------SGENVLIIAPTGSGKTEAAFLPVINELLSL   65 (814)
T ss_pred             CCCHHHHHHHHHHh---------------------------CCCceEEEcCCCCChHHHHHHHHHHHHHhc
Confidence            58888888877764                           478999999999999999999999887765

>TIGR01054 rgy reverse gyrase

Probab=96.32  E-value=0.0047  Score=77.97  Aligned_cols=52  Identities=15%  Similarity=0.166  Sum_probs=39.8

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      |.++.....++.|++.|    ...+..+..++++++.||||+|||+ |++|++.+..
T Consensus        67 f~~~f~~~~g~~p~~iQ----~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~  118 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQ----KMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLA  118 (1171)
T ss_pred             HHHHHHHhcCCCCcHHH----HHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHH
Confidence            44444555677899999    5666677788999999999999997 6677666654

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>KOG0330|consensus

Probab=96.32  E-value=0.005  Score=69.03  Aligned_cols=47  Identities=28%  Similarity=0.261  Sum_probs=37.5

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH-----------HHHHHHHhh
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE-----------LVQQKMFEQ  330 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k-----------~LQ~Ql~~k  330 (795)
                      +||....+++++.-|.||+|||+||++|+|.-+-.+.+           .|-+|+-+.
T Consensus        91 aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~  148 (476)
T KOG0330|consen   91 AIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQ  148 (476)
T ss_pred             hcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHH
Confidence            44555678999999999999999999999988776544           577776654

>KOG0338|consensus

Probab=96.27  E-value=0.0032  Score=72.46  Aligned_cols=54  Identities=24%  Similarity=0.187  Sum_probs=44.9

Q ss_pred             hHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462           5 SSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         5 ~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ||-..+.+.. ++|-.|.|+|    .+.+..-.-|++++..|-||||||.||.+|.|.-
T Consensus       189 SRPlLka~~~-lGy~~PTpIQ----~a~IPvallgkDIca~A~TGsGKTAAF~lPiLER  242 (691)
T KOG0338|consen  189 SRPLLKACST-LGYKKPTPIQ----VATIPVALLGKDICACAATGSGKTAAFALPILER  242 (691)
T ss_pred             chHHHHHHHh-cCCCCCCchh----hhcccHHhhcchhhheecccCCchhhhHHHHHHH
Confidence            5666666654 4888999999    6777766778999999999999999999998865

>KOG0336|consensus

Probab=96.24  E-value=0.0019  Score=72.54  Aligned_cols=62  Identities=16%  Similarity=0.103  Sum_probs=49.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEe
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFC   91 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc   91 (795)
                      ++-.|.|+|    ..++..+..|.+++.-|-||||||||||+|.+.++.....         +..+++.+.++--
T Consensus       239 GFqKPtPIq----SQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~---------~~~qr~~p~~lvl  300 (629)
T KOG0336|consen  239 GFQKPTPIQ----SQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPK---------RREQRNGPGVLVL  300 (629)
T ss_pred             cCCCCCcch----hcccceeecCcceEEEEecCCCcCHHHhccceeeeeccch---------hhhccCCCceEEE
Confidence            566899999    6778999999999999999999999999999988776543         2335555555443

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

Probab=96.23  E-value=0.004  Score=72.12  Aligned_cols=35  Identities=29%  Similarity=0.282  Sum_probs=28.8

Q ss_pred             HHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         283 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       283 ~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      .+||.+..++.++..|+||||||+||++|+|..+.
T Consensus        58 ~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~   92 (513)
T COG0513          58 AAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKIL   92 (513)
T ss_pred             HHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHh
Confidence            34455556789999999999999999999988754

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.21  E-value=0.0092  Score=75.25  Aligned_cols=56  Identities=27%  Similarity=0.302  Sum_probs=45.3

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      -.|||+|.|.|.+.+..|.+-++.+                     ...++++.||||+|||..++.++...+....
T Consensus       595 ~~~~~~~T~~Q~~aI~~il~d~~~~---------------------~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~  650 (1147)
T PRK10689        595 DSFPFETTPDQAQAINAVLSDMCQP---------------------LAMDRLVCGDVGFGKTEVAMRAAFLAVENHK  650 (1147)
T ss_pred             HhCCCCCCHHHHHHHHHHHHHhhcC---------------------CCCCEEEEcCCCcCHHHHHHHHHHHHHHcCC
Confidence            4699999999999999998877642                     2467999999999999999888766554443

>KOG0340|consensus

Probab=96.10  E-value=0.0041  Score=69.05  Aligned_cols=61  Identities=20%  Similarity=0.131  Sum_probs=53.4

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKEL   70 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~   70 (795)
                      +.|.-+-+..+....|.|+|    +.++..+..|.++|-.|-||||||.||-+|.|.-+.++..+
T Consensus        15 ~~Wlve~l~~l~i~~pTpiQ----~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~g   75 (442)
T KOG0340|consen   15 SPWLVEQLKALGIKKPTPIQ----QACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYG   75 (442)
T ss_pred             cHHHHHHHHHhcCCCCCchH----hhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCc
Confidence            45777778888999999999    88999999999999999999999999999999887666543

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=96.04  E-value=0.0063  Score=67.14  Aligned_cols=32  Identities=31%  Similarity=0.478  Sum_probs=26.5

Q ss_pred             HHHHHHHhcCC--cEEEECCCCCchHHHHHHHHH
Q psy3462          30 LQVIQGCNKAK--NCLLESPTGSGKTLALLCSVL   61 (795)
Q Consensus        30 ~~i~~al~~~~--~~llEAPTGTGKTLAyL~paL   61 (795)
                      .++++++.++.  ++++.||||+|||++|++|++
T Consensus         3 ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l   36 (357)
T TIGR03158         3 VATFEALQSKDADIIFNTAPTGAGKTLAWLTPLL   36 (357)
T ss_pred             HHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            45677776665  488999999999999999987

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.04  E-value=0.012  Score=74.18  Aligned_cols=57  Identities=11%  Similarity=0.091  Sum_probs=46.8

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ..++++..+.+|| .|++.|.+-+.++..-+...  .+.++.||||+|||.+|+.+++..
T Consensus       587 ~~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~  645 (1147)
T PRK10689        587 REQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLA  645 (1147)
T ss_pred             HHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHH
Confidence            4678888888655 89999988888887777654  679999999999999999887653

>COG1204 Superfamily II helicase [General function prediction only]

Probab=96.03  E-value=0.0084  Score=72.74  Aligned_cols=60  Identities=25%  Similarity=0.241  Sum_probs=47.0

Q ss_pred             hHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462           5 SSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus         5 ~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      -++.+.++.+..+.-+.++.|++..   ++.+.+++|+|+.||||+|||+-.++.++.-+.+.
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av---~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~   75 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAV---EKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG   75 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHh---hccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc
Confidence            5677888888877668888876544   44444589999999999999998888888777654

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=95.98  E-value=0.0075  Score=73.98  Aligned_cols=47  Identities=19%  Similarity=0.265  Sum_probs=36.6

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +..||..+|.|.+.+-.+.                           .++..+.+|+||||||++|++|++.-+.
T Consensus        87 ~~~p~~~tp~qvQ~I~~i~---------------------------l~~gvIAeaqTGeGKTLAf~LP~l~~aL  133 (970)
T PRK12899         87 YHQQWDMVPYDVQILGAIA---------------------------MHKGFITEMQTGEGKTLTAVMPLYLNAL  133 (970)
T ss_pred             ccCCCCCChHHHHHhhhhh---------------------------cCCCeEEEeCCCCChHHHHHHHHHHHHh
Confidence            4567777888887776653                           1355899999999999999999986553

>KOG0343|consensus

Probab=95.94  E-value=0.0037  Score=72.49  Aligned_cols=57  Identities=25%  Similarity=0.222  Sum_probs=43.1

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      ..+.+.+.++ .|-.|..+|    .+++..-..|.++|--|-||||||||||+|+|..+-..
T Consensus        78 ~~t~kgLke~-~fv~~teiQ----~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~  134 (758)
T KOG0343|consen   78 QKTLKGLKEA-KFVKMTEIQ----RDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRL  134 (758)
T ss_pred             hHHHHhHhhc-CCccHHHHH----HhhcchhccCcccccccccCCCceeeehHHHHHHHHHc
Confidence            3444455544 556777888    55556666788999999999999999999999877644

>KOG0347|consensus

Probab=95.93  E-value=0.0034  Score=72.74  Aligned_cols=59  Identities=19%  Similarity=0.200  Sum_probs=45.0

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC-CcEEEECCCCCchHHHHHHHHHHHHHHhhH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA-KNCLLESPTGSGKTLALLCSVLAWQRKEKE   69 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~-~~~llEAPTGTGKTLAyL~paL~~~~~~~~   69 (795)
                      ..+++++. +.+|-.|.++|    ..++.+.-.| .+++--|-||+||||||-+|.++-+...+.
T Consensus       190 ~~iL~aL~-~~gFs~Pt~IQ----sl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~  249 (731)
T KOG0347|consen  190 MEILRALS-NLGFSRPTEIQ----SLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSD  249 (731)
T ss_pred             HHHHHHHH-hcCCCCCccch----hhcccHhhccchhcccccccCCCceeeecchhhhhhhhccc
Confidence            44555554 44888999999    6666666555 789999999999999999999985544443

>KOG0350|consensus

Probab=95.92  E-value=0.0062  Score=70.01  Aligned_cols=29  Identities=31%  Similarity=0.550  Sum_probs=25.2

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .+.+.+.||||+||||||-+|++.-+-..
T Consensus       183 ~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R  211 (620)
T KOG0350|consen  183 PRDICVNAPTGSGKTLAYVIPIVQLLSSR  211 (620)
T ss_pred             CCceEEecCCCCCceeeehhHHHHHHccC
Confidence            56788999999999999999998877554

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=95.92  E-value=0.0082  Score=71.57  Aligned_cols=44  Identities=20%  Similarity=0.001  Sum_probs=35.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .-+..||+.|    ....-++..|+  |.|+.||+|||++|++|++..+.
T Consensus        99 ~lg~~p~~VQ----~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al  142 (656)
T PRK12898         99 VLGQRHFDVQ----LMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL  142 (656)
T ss_pred             HhCCCCChHH----HHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh
Confidence            3466899999    44555556666  99999999999999999987654

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

Probab=95.88  E-value=0.019  Score=70.49  Aligned_cols=73  Identities=21%  Similarity=0.335  Sum_probs=50.8

Q ss_pred             CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH--------
Q psy3462         250 AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE--------  321 (795)
Q Consensus       250 ~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k--------  321 (795)
                      +|+.|.+.++.+.                           +|+++|+-.|||||||++|++|++.-+....+        
T Consensus        71 lY~HQ~~A~~~~~---------------------------~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYP  123 (851)
T COG1205          71 LYSHQVDALRLIR---------------------------EGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYP  123 (851)
T ss_pred             ccHHHHHHHHHHH---------------------------CCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEec
Confidence            7888888777764                           47899999999999999999999988766543        


Q ss_pred             ---HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 ---LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 ---~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                         ..++|+- + +-.+.+..+.++.+...-|.
T Consensus       124 tnALa~DQ~~-r-l~~~~~~~~~~v~~~~y~Gd  154 (851)
T COG1205         124 TNALANDQAE-R-LRELISDLPGKVTFGRYTGD  154 (851)
T ss_pred             hhhhHhhHHH-H-HHHHHHhCCCcceeeeecCC
Confidence               3556653 2 12222233336677665554

>KOG0335|consensus

Probab=95.86  E-value=0.0057  Score=70.22  Aligned_cols=36  Identities=28%  Similarity=0.388  Sum_probs=31.0

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      |+.+..++.++.+||||+|||.|||+|++.++.+.+
T Consensus       105 ip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~  140 (482)
T KOG0335|consen  105 IPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEG  140 (482)
T ss_pred             cceeecCCceEEEccCCCcchHHHHHHHHHHHHhcC
Confidence            344556888999999999999999999999998764

>PRK09694 helicase Cas3; Provisional

Probab=95.82  E-value=0.022  Score=70.15  Aligned_cols=79  Identities=16%  Similarity=0.081  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh------
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK------  320 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~------  320 (795)
                      .|.|||.|..+++.     ..                      +.++.+||||||+|||.+.|..+...+...+      
T Consensus       284 ~~~p~p~Q~~~~~~-----~~----------------------~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~  336 (878)
T PRK09694        284 GYQPRQLQTLVDAL-----PL----------------------QPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIF  336 (878)
T ss_pred             CCCChHHHHHHHhh-----cc----------------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEE
Confidence            37899999977432     11                      2478999999999999999887665444331      


Q ss_pred             ----HHHHHHHHhhhhhhhhhcCCCCceEEEeccccc
Q psy3462         321 ----ELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDF  353 (795)
Q Consensus       321 ----k~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr~~  353 (795)
                          ..+-+||.++=...++++.+ +..+.++-|+.+
T Consensus       337 aLPT~Atan~m~~Rl~~~~~~~f~-~~~v~L~Hg~a~  372 (878)
T PRK09694        337 ALPTQATANAMLSRLEALASKLFP-SPNLILAHGNSR  372 (878)
T ss_pred             ECcHHHHHHHHHHHHHHHHHHhcC-CCceEeecCcch
Confidence                14556777653333444444 345667777653

>PRK00254 ski2-like helicase; Provisional

Probab=95.81  E-value=0.022  Score=68.43  Aligned_cols=47  Identities=28%  Similarity=0.327  Sum_probs=36.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ..| +++|.|.+.+...   +                       .+++++++.||||+|||++|++|++..+..
T Consensus        19 ~g~~~l~~~Q~~ai~~~---~-----------------------~~g~nvlv~apTGsGKT~~~~l~il~~l~~   66 (720)
T PRK00254         19 RGIEELYPPQAEALKSG---V-----------------------LEGKNLVLAIPTASGKTLVAEIVMVNKLLR   66 (720)
T ss_pred             CCCCCCCHHHHHHHHHH---H-----------------------hCCCcEEEECCCCcHHHHHHHHHHHHHHHh
Confidence            345 5899999877652   1                       136789999999999999999998876543

>KOG0334|consensus

Probab=95.77  E-value=0.0064  Score=74.49  Aligned_cols=55  Identities=27%  Similarity=0.315  Sum_probs=45.7

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ..+...+ +-+.|-.|+|+|    ..++.++..|.++|..|-||+|||+|||+|.+.+..
T Consensus       374 ~~il~tl-kkl~y~k~~~IQ----~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~  428 (997)
T KOG0334|consen  374 SKILETL-KKLGYEKPTPIQ----AQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIK  428 (997)
T ss_pred             HHHHHHH-HHhcCCCCcchh----hhhcchhccCcceEEeeccCCccchhhhcchhhhhh
Confidence            3455555 566788999999    777889999999999999999999999999984443

>PHA02653 RNA helicase NPH-II; Provisional

Probab=95.75  E-value=0.011  Score=70.97  Aligned_cols=54  Identities=24%  Similarity=0.223  Sum_probs=41.9

Q ss_pred             HHhCCCCCC---CCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHH---------HHHHHHHHHH
Q psy3462          12 YLNEPNYFL---KYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLA---------LLCSVLAWQR   65 (795)
Q Consensus        12 ~~~~~~~~~---p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLA---------yL~paL~~~~   65 (795)
                      +..++.+|.   .++-|.++=+++.+.+.+++++|+.|+||+|||.+         ||.|++.++.
T Consensus       149 ~~~n~~~~~~~~l~~~~~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~  214 (675)
T PHA02653        149 ILGNPEPFSKIPLASLQPDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLD  214 (675)
T ss_pred             ccCCCCccccccCCchhHHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhh
Confidence            344444443   23667777789999999999999999999999997         7778877764

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=95.72  E-value=0.0092  Score=70.31  Aligned_cols=42  Identities=26%  Similarity=0.332  Sum_probs=37.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      +-.-|++|    .+|++++.+++++++-.|||.||||+|-+|+|-.
T Consensus        15 y~~FR~gQ----~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~   56 (590)
T COG0514          15 YASFRPGQ----QEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL   56 (590)
T ss_pred             ccccCCCH----HHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc
Confidence            44567899    6888888899999999999999999999998876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=95.70  E-value=0.011  Score=71.59  Aligned_cols=42  Identities=19%  Similarity=0.160  Sum_probs=29.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +.+||+.|  ++..+  ++..|  .|+|++||+||||+|++|++..+.
T Consensus        68 glrpydVQ--lig~l--~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL  109 (762)
T TIGR03714        68 GMFPYDVQ--VLGAI--VLHQG--NIAEMKTGEGKTLTATMPLYLNAL  109 (762)
T ss_pred             CCCccHHH--HHHHH--HhcCC--ceeEecCCcchHHHHHHHHHHHhh
Confidence            34566666  44433  34444  699999999999999999765443

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PRK14701 reverse gyrase; Provisional

Probab=95.65  E-value=0.026  Score=73.42  Aligned_cols=78  Identities=15%  Similarity=0.186  Sum_probs=49.8

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH----
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE----  321 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k----  321 (795)
                      ++|+|+|.|.+.+..+.                           .++.+++-||||||||+.++.+++.......+    
T Consensus        76 ~G~~pt~iQ~~~i~~il---------------------------~G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl  128 (1638)
T PRK14701         76 TGFEFWSIQKTWAKRIL---------------------------RGKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYII  128 (1638)
T ss_pred             hCCCCCHHHHHHHHHHH---------------------------cCCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            67889999998887754                           25678999999999999767666554433322    


Q ss_pred             ----HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 ----LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 ----~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                          .|-.|..++ +..+.+..+..+.+..+-|.
T Consensus       129 ~PTreLa~Qi~~~-l~~l~~~~~~~v~v~~~~g~  161 (1638)
T PRK14701        129 LPTTLLVKQTVEK-IESFCEKANLDVRLVYYHSN  161 (1638)
T ss_pred             ECHHHHHHHHHHH-HHHHHhhcCCceeEEEEeCC
Confidence                455555543 22333334445555554443

>KOG0334|consensus

Probab=95.61  E-value=0.77  Score=57.13  Aligned_cols=32  Identities=34%  Similarity=0.463  Sum_probs=29.8

Q ss_pred             HHHHhhccccCcEEEeCCCCCChhHHHHHHHH
Q psy3462         282 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       282 ~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l  313 (795)
                      .++||++..++.+|--|-||+|||+|||+|.+
T Consensus       393 ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmi  424 (997)
T KOG0334|consen  393 AQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMI  424 (997)
T ss_pred             hhhcchhccCcceEEeeccCCccchhhhcchh
Confidence            46888999999999999999999999999988

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=95.50  E-value=0.015  Score=71.06  Aligned_cols=37  Identities=27%  Similarity=0.408  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ..+.+|.+++.++.++|+.||||||||.+|.+|+|..
T Consensus         8 ~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~   44 (812)
T PRK11664          8 AVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQH   44 (812)
T ss_pred             HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHc
Confidence            4567899999999999999999999999999998864

>KOG0344|consensus

Probab=95.47  E-value=0.018  Score=67.29  Aligned_cols=38  Identities=34%  Similarity=0.410  Sum_probs=33.2

Q ss_pred             HHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         283 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       283 ~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      ++++.+.++++++..||||+||||||++|+|..++.+.
T Consensus       165 ~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~  202 (593)
T KOG0344|consen  165 QAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLS  202 (593)
T ss_pred             hhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhh
Confidence            56677778899999999999999999999988887665

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=95.45  E-value=0.017  Score=70.35  Aligned_cols=42  Identities=19%  Similarity=0.073  Sum_probs=31.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +..||+.|.  +.  .-++..|.  |.|+.||+|||+++++|++..+.
T Consensus        76 g~~p~~vQl--~~--~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al  117 (790)
T PRK09200         76 GMRPYDVQL--IG--ALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL  117 (790)
T ss_pred             CCCCchHHH--Hh--HHHHcCCc--eeeecCCCcchHHHHHHHHHHHH
Confidence            568999992  22  22555554  99999999999999999885544

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=95.41  E-value=0.013  Score=63.63  Aligned_cols=23  Identities=43%  Similarity=0.428  Sum_probs=20.7

Q ss_pred             cEEEECCCCCchHHHHHHHHHHH
Q psy3462          41 NCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        41 ~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ++++.||||+|||++|++|++..
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~   23 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHS   23 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHH
Confidence            47999999999999999998854

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.38  E-value=0.024  Score=68.00  Aligned_cols=46  Identities=20%  Similarity=0.047  Sum_probs=35.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+.+++.|++.++.+.+.+ ...+.++.||||+|||.+|+.++...+
T Consensus       142 ~~~Lt~~Q~~ai~~i~~~~-~~~~~Ll~~~TGSGKT~v~l~~i~~~l  187 (679)
T PRK05580        142 PPTLNPEQAAAVEAIRAAA-GFSPFLLDGVTGSGKTEVYLQAIAEVL  187 (679)
T ss_pred             CCCCCHHHHHHHHHHHhcc-CCCcEEEECCCCChHHHHHHHHHHHHH
Confidence            4467899987777776554 457799999999999999988755443

>KOG0339|consensus

Probab=95.34  E-value=0.012  Score=67.75  Aligned_cols=73  Identities=15%  Similarity=0.120  Sum_probs=59.1

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCc
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKT   86 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~   86 (795)
                      +.+.++... .|..|||+|    ..+..+...+.+++-.|-||+|||-||+.|.+..+.+..+          |.-+++|
T Consensus       233 qLm~airk~-Ey~kptpiq----~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~e----------L~~g~gP  297 (731)
T KOG0339|consen  233 QLMTAIRKS-EYEKPTPIQ----CQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPE----------LKPGEGP  297 (731)
T ss_pred             HHHHHHhhh-hcccCCccc----ccccccccccccchheeeccCcchhHHHHHHHHHhcchhh----------hcCCCCC
Confidence            344555554 788999999    6677777888999999999999999999999988876653          5656889


Q ss_pred             eeEEeccc
Q psy3462          87 SFVFCGRS   94 (795)
Q Consensus        87 ~~~yc~rt   94 (795)
                      .-+||+.|
T Consensus       298 i~vilvPT  305 (731)
T KOG0339|consen  298 IGVILVPT  305 (731)
T ss_pred             eEEEEecc
Confidence            99999755

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=95.31  E-value=0.016  Score=69.91  Aligned_cols=43  Identities=21%  Similarity=0.050  Sum_probs=31.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -+..||+.|.    ...-++..|.  |.|++||+||||++++|++..+.
T Consensus        53 lg~~p~~vQl----ig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL   95 (745)
T TIGR00963        53 LGMRPFDVQL----IGGIALHKGK--IAEMKTGEGKTLTATLPAYLNAL   95 (745)
T ss_pred             hCCCccchHH----hhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHH
Confidence            3668899993    2223455554  99999999999999999864443

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.21  E-value=0.03  Score=49.66  Aligned_cols=26  Identities=50%  Similarity=0.741  Sum_probs=21.2

Q ss_pred             CcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          40 KNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        40 ~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +++++.+|||+|||..++..+.....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~   26 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLD   26 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHh
Confidence            46899999999999888888666543

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>KOG0342|consensus

Probab=95.17  E-value=0.0091  Score=68.50  Aligned_cols=36  Identities=39%  Similarity=0.475  Sum_probs=31.2

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      |+.+..++.++.-|-||||||+|||+|++.|+...+
T Consensus       113 i~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~  148 (543)
T KOG0342|consen  113 IPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLK  148 (543)
T ss_pred             cCccCCCccceeeeccCCCceeeehhHHHHHHHhcc
Confidence            455667889999999999999999999999987653

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.04  E-value=0.042  Score=65.91  Aligned_cols=61  Identities=23%  Similarity=0.253  Sum_probs=45.8

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      .-|++.++.|.+.+..+.+.+ .                       ....++-||||+|||.+|+.++...+...++   
T Consensus       140 ~~~~~Lt~~Q~~ai~~i~~~~-~-----------------------~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLv  195 (679)
T PRK05580        140 FEPPTLNPEQAAAVEAIRAAA-G-----------------------FSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALV  195 (679)
T ss_pred             cCCCCCCHHHHHHHHHHHhcc-C-----------------------CCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEE
Confidence            456789999998888886543 1                       3568999999999999999887666655433   


Q ss_pred             -----HHHHHHHh
Q psy3462         322 -----LVQQKMFE  329 (795)
Q Consensus       322 -----~LQ~Ql~~  329 (795)
                           .|..|+.+
T Consensus       196 LvPt~~L~~Q~~~  208 (679)
T PRK05580        196 LVPEIALTPQMLA  208 (679)
T ss_pred             EeCcHHHHHHHHH
Confidence                 46666654

>PRK09401 reverse gyrase; Reviewed

Probab=95.01  E-value=0.039  Score=69.94  Aligned_cols=57  Identities=19%  Similarity=0.257  Sum_probs=38.8

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh-H---
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK-E---  321 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~-k---  321 (795)
                      +.++|+|.|...+..+.                           .++++++-||||||||. ++++++.++...+ +   
T Consensus        77 ~G~~pt~iQ~~~i~~il---------------------------~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~g~~alI  128 (1176)
T PRK09401         77 TGSKPWSLQRTWAKRLL---------------------------LGESFAIIAPTGVGKTT-FGLVMSLYLAKKGKKSYI  128 (1176)
T ss_pred             cCCCCcHHHHHHHHHHH---------------------------CCCcEEEEcCCCCCHHH-HHHHHHHHHHhcCCeEEE
Confidence            45789999987766542                           35789999999999996 5555555554322 2   


Q ss_pred             -----HHHHHHHhh
Q psy3462         322 -----LVQQKMFEQ  330 (795)
Q Consensus       322 -----~LQ~Ql~~k  330 (795)
                           .|-.|..++
T Consensus       129 L~PTreLa~Qi~~~  142 (1176)
T PRK09401        129 IFPTRLLVEQVVEK  142 (1176)
T ss_pred             EeccHHHHHHHHHH
Confidence                 566666543

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=94.93  E-value=0.029  Score=68.69  Aligned_cols=38  Identities=21%  Similarity=0.296  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +...+|.++|.++.++|+.||||+|||.+|.+|++...
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~   42 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP   42 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhh
Confidence            45678999999999999999999999999999988654

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>KOG0333|consensus

Probab=94.92  E-value=0.041  Score=63.87  Aligned_cols=30  Identities=33%  Similarity=0.473  Sum_probs=27.1

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      .++.|.-|.||+|||+||++|+|.|+....
T Consensus       282 ~rD~igvaETgsGktaaf~ipLl~~IsslP  311 (673)
T KOG0333|consen  282 NRDPIGVAETGSGKTAAFLIPLLIWISSLP  311 (673)
T ss_pred             cCCeeeEEeccCCccccchhhHHHHHHcCC
Confidence            577889999999999999999999998765

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=94.91  E-value=0.022  Score=69.67  Aligned_cols=40  Identities=25%  Similarity=0.361  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccC-cEEEeCCCCCChhHHHHHHHH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAK-NCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~-~~l~EaPTGTGKTlayL~~~l  313 (795)
                      .|+|+|+|.+.+..+.   +                        ++ ..++.||||||||.++.+..+
T Consensus        13 G~~PtpiQ~~~i~~il---~------------------------G~~~v~~~apTGSGKTaa~aafll   53 (844)
T TIGR02621        13 GYSPFPWQLSLAERFV---A------------------------GQPPESCSTPTGLGKTSIIAAWLL   53 (844)
T ss_pred             CCCCCHHHHHHHHHHH---c------------------------CCCcceEecCCCCcccHHHHHhhc
Confidence            5779999999998854   2                        33 578899999999997654444

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=94.73  E-value=0.026  Score=62.37  Aligned_cols=23  Identities=43%  Similarity=0.599  Sum_probs=20.2

Q ss_pred             CcEEEeCCCCCChhHHHHHHHHH
Q psy3462         292 KNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       292 ~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .++++.||||+|||+++++|++.
T Consensus        15 ~~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158        15 DIIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            35899999999999999998773

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>KOG0346|consensus

Probab=94.67  E-value=0.023  Score=64.70  Aligned_cols=38  Identities=34%  Similarity=0.346  Sum_probs=31.7

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      +||-+.+++.++.-|-||+|||.|||+|+|.-+-..++
T Consensus        49 aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~   86 (569)
T KOG0346|consen   49 AIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKK   86 (569)
T ss_pred             ccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhh
Confidence            56666788999999999999999999999877665543

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=94.52  E-value=0.069  Score=67.55  Aligned_cols=45  Identities=20%  Similarity=0.258  Sum_probs=35.3

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCS  311 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~  311 (795)
                      .+.+.+||.|.+.+..+.+++.++                      .+.+|+.+|||||||+..+..
T Consensus       409 ~~~~~lR~YQ~~AI~ai~~a~~~g----------------------~r~~Ll~maTGSGKT~tai~l  453 (1123)
T PRK11448        409 DYGLGLRYYQEDAIQAVEKAIVEG----------------------QREILLAMATGTGKTRTAIAL  453 (1123)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHhc----------------------cCCeEEEeCCCCCHHHHHHHH
Confidence            334679999999999998888642                      356899999999999875443

>PHA02558 uvsW UvsW helicase; Provisional

Probab=94.49  E-value=0.054  Score=62.51  Aligned_cols=36  Identities=22%  Similarity=0.063  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      .+.||+.|.+.+..+   + .+.++++.||||+|||+.+.
T Consensus       112 ~~~~r~~Q~~av~~~---l-~~~~~il~apTGsGKT~i~~  147 (501)
T PHA02558        112 KIEPHWYQYDAVYEG---L-KNNRRLLNLPTSAGKSLIQY  147 (501)
T ss_pred             cCCCCHHHHHHHHHH---H-hcCceEEEeCCCCCHHHHHH
Confidence            468999996654433   3 35678999999999998653

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.46  E-value=0.052  Score=57.50  Aligned_cols=36  Identities=22%  Similarity=0.371  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL   54 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTL   54 (795)
                      |.+.+..+++.+.+...+..+.++++++|+|||||.
T Consensus         1 ~~~t~~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~   36 (262)
T TIGR02640         1 FIETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTT   36 (262)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCeEEEEcCCCCCHHH
Confidence            567788889999999999999999999999999993

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=94.41  E-value=0.041  Score=59.69  Aligned_cols=25  Identities=40%  Similarity=0.446  Sum_probs=21.8

Q ss_pred             EEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         294 CLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       294 ~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +++.||||+|||++++.+++..+..
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~   26 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKS   26 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhh
Confidence            6899999999999999999866543

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

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

Probab=94.33  E-value=0.085  Score=52.16  Aligned_cols=59  Identities=17%  Similarity=0.212  Sum_probs=30.8

Q ss_pred             HHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          31 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        31 ~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      ++..++......+|.||.||||| ..+..++..+...-.         ......+.+++.|+.||..+.
T Consensus         9 Ai~~~~~~~~~~~i~GpPGTGKT-~~l~~~i~~~~~~~~---------~~~~~~~~~il~~~~sN~avd   67 (236)
T PF13086_consen    9 AIQSALSSNGITLIQGPPGTGKT-TTLASIIAQLLQRFK---------SRSADRGKKILVVSPSNAAVD   67 (236)
T ss_dssp             HHHHHCTSSE-EEEE-STTSSHH-HHHHHHHHHH----------------HCCCSS-EEEEESSHHHHH
T ss_pred             HHHHHHcCCCCEEEECCCCCChH-HHHHHHHHHhccchh---------hhhhhccccceeecCCchhHH
Confidence            33334444334999999999999 222333333311000         123446788888888887764

>KOG0326|consensus

Probab=94.30  E-value=0.0056  Score=67.34  Aligned_cols=53  Identities=21%  Similarity=0.189  Sum_probs=47.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQ   73 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~   73 (795)
                      ++-+|.|+|    ++.+.....|++++.-|-.|||||-||++|+|..++..+..+|+
T Consensus       104 G~ekPSPiQ----eesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~  156 (459)
T KOG0326|consen  104 GFEKPSPIQ----EESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQA  156 (459)
T ss_pred             ccCCCCCcc----ccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeE
Confidence            666899999    77777777889999999999999999999999999988888886

>PRK13766 Hef nuclease; Provisional

Probab=94.28  E-value=0.043  Score=66.07  Aligned_cols=43  Identities=28%  Similarity=0.263  Sum_probs=34.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.+.||+.|.++...+.   .+  ++++-+|||+|||+.+++++...+
T Consensus        12 ~~~~~r~yQ~~~~~~~l---~~--n~lv~~ptG~GKT~~a~~~i~~~l   54 (773)
T PRK13766         12 NTIEARLYQQLLAATAL---KK--NTLVVLPTGLGKTAIALLVIAERL   54 (773)
T ss_pred             CcCCccHHHHHHHHHHh---cC--CeEEEcCCCccHHHHHHHHHHHHH
Confidence            35678999987666543   32  899999999999999998877665

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=94.13  E-value=0.064  Score=64.23  Aligned_cols=46  Identities=20%  Similarity=0.116  Sum_probs=34.5

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .....|||.|..-.-.+.                           .|+  +.||.||+|||+++++|++..+...
T Consensus        99 ~lg~~p~~VQ~~~~~~ll---------------------------~G~--Iae~~TGeGKTla~~lp~~~~al~G  144 (656)
T PRK12898         99 VLGQRHFDVQLMGGLALL---------------------------SGR--LAEMQTGEGKTLTATLPAGTAALAG  144 (656)
T ss_pred             HhCCCCChHHHHHHHHHh---------------------------CCC--eeeeeCCCCcHHHHHHHHHHHhhcC
Confidence            356778888876544432                           344  8999999999999999998766544

>KOG0337|consensus

Probab=94.05  E-value=0.032  Score=63.33  Aligned_cols=56  Identities=16%  Similarity=0.193  Sum_probs=47.0

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      -|+++... .+-.|.|+|    .+.+..+.++.+++--|-||+|||.||++|++..+....
T Consensus        32 v~raI~kk-g~~~ptpiq----RKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s   87 (529)
T KOG0337|consen   32 VLRAIHKK-GFNTPTPIQ----RKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS   87 (529)
T ss_pred             HHHHHHHh-hcCCCCchh----cccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc
Confidence            34555555 566899999    777888888999999999999999999999999887665

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=94.05  E-value=0.041  Score=67.30  Aligned_cols=42  Identities=19%  Similarity=0.073  Sum_probs=32.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      -+..||+.|  ||-.+  +|+.|  -|.|+.||+||||++.+|++..+
T Consensus        78 lg~~~~dvQ--lig~l--~L~~G--~Iaem~TGeGKTLva~lpa~l~a  119 (830)
T PRK12904         78 LGMRHFDVQ--LIGGM--VLHEG--KIAEMKTGEGKTLVATLPAYLNA  119 (830)
T ss_pred             hCCCCCccH--HHhhH--HhcCC--chhhhhcCCCcHHHHHHHHHHHH
Confidence            356889998  44444  55665  49999999999999999986444

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=94.04  E-value=0.052  Score=48.14  Aligned_cols=24  Identities=54%  Similarity=0.769  Sum_probs=20.0

Q ss_pred             cEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         293 NCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       293 ~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ++++.+|||+|||..++..+....
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~   25 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELL   25 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHH
Confidence            589999999999999888765544

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR01054 rgy reverse gyrase

Probab=93.97  E-value=0.09  Score=66.82  Aligned_cols=44  Identities=20%  Similarity=0.254  Sum_probs=31.8

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      .++|+|.|...+..+.                           .++.+++.||||||||+ |++|++.++..
T Consensus        76 g~~p~~iQ~~~i~~il---------------------------~G~d~vi~ApTGsGKT~-f~l~~~~~l~~  119 (1171)
T TIGR01054        76 GSEPWSIQKMWAKRVL---------------------------RGDSFAIIAPTGVGKTT-FGLAMSLFLAK  119 (1171)
T ss_pred             CCCCcHHHHHHHHHHh---------------------------CCCeEEEECCCCCCHHH-HHHHHHHHHHh
Confidence            3578888876665532                           36789999999999997 65666666543

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=93.93  E-value=0.046  Score=67.16  Aligned_cols=43  Identities=19%  Similarity=0.061  Sum_probs=32.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -+..||+.|  +|-.+  +|+.|  -|.|++||+||||+|++|++..+.
T Consensus        79 lg~~~ydvQ--liGg~--~Lh~G--~Iaem~TGeGKTL~a~Lpa~~~al  121 (896)
T PRK13104         79 LGLRHFDVQ--LIGGM--VLHEG--NIAEMRTGEGKTLVATLPAYLNAI  121 (896)
T ss_pred             cCCCcchHH--Hhhhh--hhccC--ccccccCCCCchHHHHHHHHHHHh
Confidence            355788888  44433  34554  589999999999999999997764

>PHA02558 uvsW UvsW helicase; Provisional

Probab=93.85  E-value=0.12  Score=59.76  Aligned_cols=37  Identities=22%  Similarity=0.244  Sum_probs=27.9

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLC  310 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~  310 (795)
                      .++|||.|.+.+..+   +.                        +..+++.+|||+|||+.+..
T Consensus       112 ~~~~r~~Q~~av~~~---l~------------------------~~~~il~apTGsGKT~i~~~  148 (501)
T PHA02558        112 KIEPHWYQYDAVYEG---LK------------------------NNRRLLNLPTSAGKSLIQYL  148 (501)
T ss_pred             cCCCCHHHHHHHHHH---Hh------------------------cCceEEEeCCCCCHHHHHHH
Confidence            478999999866543   32                        24579999999999997643

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

Probab=93.64  E-value=0.096  Score=59.78  Aligned_cols=41  Identities=17%  Similarity=0.148  Sum_probs=33.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      +.+.+|+.|.+-++++...+.....+++-+|||+|||+..+
T Consensus        33 ~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~   73 (442)
T COG1061          33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAA   73 (442)
T ss_pred             cCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHH
Confidence            46679999988888888777767889999999999995443

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=93.53  E-value=0.11  Score=65.65  Aligned_cols=39  Identities=21%  Similarity=0.114  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC-CcEEEECCCCCchHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKA-KNCLLESPTGSGKTLALL   57 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~-~~~llEAPTGTGKTLAyL   57 (795)
                      +.+|+.|.+.+.++.+++.++ ..+++.+|||||||+..+
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai  451 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI  451 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH
Confidence            569999999999999999765 579999999999997643

>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 []

Probab=93.41  E-value=0.11  Score=54.17  Aligned_cols=39  Identities=21%  Similarity=0.359  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +.|..+++++.    +...+++.||.|||||+-.+..++....
T Consensus         7 ~~Q~~~~~al~----~~~~v~~~G~AGTGKT~LA~a~Al~~v~   45 (205)
T PF02562_consen    7 EEQKFALDALL----NNDLVIVNGPAGTGKTFLALAAALELVK   45 (205)
T ss_dssp             HHHHHHHHHHH----H-SEEEEE--TTSSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH----hCCeEEEECCCCCcHHHHHHHHHHHHHH
Confidence            78877776666    6678999999999999777766666544

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0352|consensus

Probab=93.35  E-value=0.084  Score=60.23  Aligned_cols=55  Identities=18%  Similarity=0.224  Sum_probs=36.6

Q ss_pred             hhHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462           4 KSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         4 ~~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      +-|++++.+-..-  -|-.+-|.+   ++.-++...+++.+..|||.||+|+|-+|+|-.
T Consensus         6 ~VreaLKK~FGh~--kFKs~LQE~---A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~   60 (641)
T KOG0352|consen    6 KVREALKKLFGHK--KFKSRLQEQ---AINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH   60 (641)
T ss_pred             HHHHHHHHHhCch--hhcChHHHH---HHHHHHhccCcEEEeccCCCchhhhhhchHHHh
Confidence            3455555443331  145577732   333345677899999999999999999998753

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=93.14  E-value=0.06  Score=65.36  Aligned_cols=25  Identities=28%  Similarity=0.259  Sum_probs=21.2

Q ss_pred             EEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         294 CLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       294 ~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      .++|++||+|||++|++|++..+..
T Consensus        86 ~Iaem~TGeGKTLta~Lpa~l~aL~  110 (762)
T TIGR03714        86 NIAEMKTGEGKTLTATMPLYLNALT  110 (762)
T ss_pred             ceeEecCCcchHHHHHHHHHHHhhc
Confidence            6999999999999999997655443

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=93.11  E-value=0.071  Score=65.36  Aligned_cols=32  Identities=31%  Similarity=0.487  Sum_probs=25.8

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      +++++.+++++++.||||||||.+|..++|..
T Consensus        13 i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~   44 (812)
T PRK11664         13 LLTALKTAPQVLLKAPTGAGKSTWLPLQLLQH   44 (812)
T ss_pred             HHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHc
Confidence            33444557899999999999999999988753

>KOG0343|consensus

Probab=93.09  E-value=0.056  Score=63.15  Aligned_cols=35  Identities=37%  Similarity=0.376  Sum_probs=28.3

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      |+.-..|+.+|--|-||||||||||+|+|..+-..
T Consensus       100 Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~  134 (758)
T KOG0343|consen  100 IPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRL  134 (758)
T ss_pred             cchhccCcccccccccCCCceeeehHHHHHHHHHc
Confidence            34444678899999999999999999998776543

>KOG0952|consensus

Probab=93.06  E-value=0.098  Score=64.77  Aligned_cols=57  Identities=25%  Similarity=0.291  Sum_probs=42.0

Q ss_pred             HHHHHH-HhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccc
Q psy3462          30 LQVIQG-CNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRS   94 (795)
Q Consensus        30 ~~i~~a-l~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rt   94 (795)
                      ..++.. .+.+.|+||.||||+|||.-+++.+|.-+....        ++-.-+.+..+++|=+.+
T Consensus       116 S~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~--------~~~~i~k~~fKiVYIaPm  173 (1230)
T KOG0952|consen  116 SEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHE--------EQGDIAKDDFKIVYIAPM  173 (1230)
T ss_pred             HHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhc--------cccccccCCceEEEEech
Confidence            455544 466889999999999999999999998887621        123445577788887644

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=93.03  E-value=0.078  Score=62.76  Aligned_cols=46  Identities=28%  Similarity=0.401  Sum_probs=35.5

Q ss_pred             eeccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         243 KVEFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       243 ~~~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      .-.|.|. .||.|.+.++.+                           .++++++.-.|||.||||.|-+|++-.
T Consensus        10 ~~~fGy~~FR~gQ~evI~~~---------------------------l~g~d~lvvmPTGgGKSlCyQiPAll~   56 (590)
T COG0514          10 KQVFGYASFRPGQQEIIDAL---------------------------LSGKDTLVVMPTGGGKSLCYQIPALLL   56 (590)
T ss_pred             HHHhCccccCCCHHHHHHHH---------------------------HcCCcEEEEccCCCCcchHhhhHHHhc
Confidence            3357774 688887665554                           246889999999999999999998765

>PRK13766 Hef nuclease; Provisional

Probab=92.62  E-value=0.23  Score=59.89  Aligned_cols=44  Identities=27%  Similarity=0.262  Sum_probs=34.3

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      .++++|+-|.++...+   ++                         +++++-+|||+|||+.+++++...+.
T Consensus        12 ~~~~~r~yQ~~~~~~~---l~-------------------------~n~lv~~ptG~GKT~~a~~~i~~~l~   55 (773)
T PRK13766         12 NTIEARLYQQLLAATA---LK-------------------------KNTLVVLPTGLGKTAIALLVIAERLH   55 (773)
T ss_pred             CcCCccHHHHHHHHHH---hc-------------------------CCeEEEcCCCccHHHHHHHHHHHHHH
Confidence            3468999999877653   32                         37899999999999999888766654

>KOG0327|consensus

Probab=92.54  E-value=0.12  Score=58.17  Aligned_cols=53  Identities=23%  Similarity=0.280  Sum_probs=43.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQ   73 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~   73 (795)
                      +|-.|..+|    +.++-.+-.|.++++.|.+|||||.||++++|...+......|+
T Consensus        45 GFekPSaIQ----qraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qa   97 (397)
T KOG0327|consen   45 GFEKPSAIQ----QRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQA   97 (397)
T ss_pred             ccCCchHHH----hccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHH
Confidence            445789999    55556666779999999999999999999999997666655555

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=91.94  E-value=0.13  Score=63.19  Aligned_cols=33  Identities=24%  Similarity=0.375  Sum_probs=27.1

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +++++.+++++++.||||||||.+|..+++...
T Consensus        10 i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~   42 (819)
T TIGR01970        10 LRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP   42 (819)
T ss_pred             HHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhh
Confidence            444555678999999999999999999987654

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=91.93  E-value=0.12  Score=63.77  Aligned_cols=43  Identities=19%  Similarity=0.050  Sum_probs=31.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -+..||+.|.  |-.+  +|+.  .-|.|++||+||||++.+|++..+.
T Consensus        79 lgm~~ydVQl--iGgl--~L~~--G~IaEm~TGEGKTL~a~lp~~l~al  121 (908)
T PRK13107         79 FEMRHFDVQL--LGGM--VLDS--NRIAEMRTGEGKTLTATLPAYLNAL  121 (908)
T ss_pred             hCCCcCchHH--hcch--HhcC--CccccccCCCCchHHHHHHHHHHHh
Confidence            3557888883  3322  2343  4689999999999999999987664

>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

Probab=91.93  E-value=0.16  Score=45.54  Aligned_cols=30  Identities=30%  Similarity=0.319  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHhc--CCcEEEECCCCCchH
Q psy3462          24 SCKILHLQVIQGCNK--AKNCLLESPTGSGKT   53 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~--~~~~llEAPTGTGKT   53 (795)
                      .+...+..+...+..  +.++++.||+|||||
T Consensus         2 ~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT   33 (151)
T cd00009           2 GQEEAIEALREALELPPPKNLLLYGPPGTGKT   33 (151)
T ss_pred             chHHHHHHHHHHHhCCCCCeEEEECCCCCCHH
Confidence            355667778888766  678999999999999

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=91.89  E-value=0.1  Score=62.82  Aligned_cols=44  Identities=20%  Similarity=0.129  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHH---------HHHHHHHHH
Q psy3462         250 AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLA---------LLCSVLAWQ  316 (795)
Q Consensus       250 ~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTla---------yL~~~l~~~  316 (795)
                      -++-|.+.=+++...+.                       +++++++.|+||||||.+         ||.|.+.++
T Consensus       161 l~~~~~~iQ~qil~~i~-----------------------~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l  213 (675)
T PHA02653        161 LASLQPDVQLKIFEAWI-----------------------SRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNL  213 (675)
T ss_pred             CCchhHHHHHHHHHHHH-----------------------hCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhh
Confidence            36677776666665554                       468999999999999997         666666655

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=91.60  E-value=0.21  Score=59.91  Aligned_cols=41  Identities=20%  Similarity=0.266  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHHHHhc------CCcEEEECCCCCchHHHHHHHH
Q psy3462          20 LKYSSCKILHLQVIQGCNK------AKNCLLESPTGSGKTLALLCSV   60 (795)
Q Consensus        20 ~p~~~Q~~mm~~i~~al~~------~~~~llEAPTGTGKTLAyL~pa   60 (795)
                      .||..|...++++.+.+.+      .+.+++..|||||||+..+.-+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la  284 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAA  284 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHH
Confidence            3788999999999999865      3579999999999997665544

Members of this family are assumed to differ from each other in DNA site specificity.

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=91.58  E-value=0.27  Score=59.04  Aligned_cols=64  Identities=16%  Similarity=0.209  Sum_probs=42.8

Q ss_pred             CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh---------
Q psy3462         250 AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK---------  320 (795)
Q Consensus       250 ~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~---------  320 (795)
                      +|+.|...++++...+.+..    .             -...+.+++.+|||||||+.-+..+...++..+         
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~----~-------------~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvd  301 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKT----W-------------GKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVD  301 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcc----c-------------CCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEEC
Confidence            79999999999988775310    0             001357999999999999877665543332221         


Q ss_pred             -HHHHHHHHhh
Q psy3462         321 -ELVQQKMFEQ  330 (795)
Q Consensus       321 -k~LQ~Ql~~k  330 (795)
                       ..|-+|+.+.
T Consensus       302 R~~L~~Q~~~~  312 (667)
T TIGR00348       302 RRELDYQLMKE  312 (667)
T ss_pred             cHHHHHHHHHH
Confidence             1577777654

Members of this family are assumed to differ from each other in DNA site specificity.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=91.12  E-value=0.24  Score=60.09  Aligned_cols=46  Identities=28%  Similarity=0.252  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          21 KYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +++-|...++.+...-..+..++++||||.|||.|.|.+++.-+..
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~  241 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDE  241 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhc
Confidence            4567755555555544444489999999999999999997766544

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

Probab=91.05  E-value=0.59  Score=47.60  Aligned_cols=57  Identities=12%  Similarity=0.118  Sum_probs=35.0

Q ss_pred             CHHHHHHHHHHHHHHhcC-CcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          22 YSSCKILHLQVIQGCNKA-KNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~-~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      .+.|.+++..+.   .++ ...++.+|.|||||-. |-.+......                 .+.+|+.|+.||.+..
T Consensus         3 ~~~Q~~a~~~~l---~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~-----------------~g~~v~~~apT~~Aa~   60 (196)
T PF13604_consen    3 NEEQREAVRAIL---TSGDRVSVLQGPAGTGKTTL-LKALAEALEA-----------------AGKRVIGLAPTNKAAK   60 (196)
T ss_dssp             -HHHHHHHHHHH---HCTCSEEEEEESTTSTHHHH-HHHHHHHHHH-----------------TT--EEEEESSHHHHH
T ss_pred             CHHHHHHHHHHH---hcCCeEEEEEECCCCCHHHH-HHHHHHHHHh-----------------CCCeEEEECCcHHHHH
Confidence            467877666653   343 4688999999999942 2222221111                 3478999999998765

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

Probab=91.05  E-value=0.32  Score=55.60  Aligned_cols=45  Identities=22%  Similarity=0.322  Sum_probs=36.7

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHH
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCS  311 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~  311 (795)
                      +.+.+++||.|.+.++++.+.+.+                       ++-+++-+|||+|||+..+-.
T Consensus        31 ~~~~~~lr~yQ~~al~a~~~~~~~-----------------------~~~gvivlpTGaGKT~va~~~   75 (442)
T COG1061          31 VAFEFELRPYQEEALDALVKNRRT-----------------------ERRGVIVLPTGAGKTVVAAEA   75 (442)
T ss_pred             cccCCCCcHHHHHHHHHHHhhccc-----------------------CCceEEEeCCCCCHHHHHHHH
Confidence            566688999999999999887763                       356899999999999866544

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=91.04  E-value=0.35  Score=60.37  Aligned_cols=72  Identities=15%  Similarity=0.143  Sum_probs=44.2

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhh-------------ccccCcEEEeCCCCCChhHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQG-------------CNKAKNCLLESPTGSGKTLALLCSV  312 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~a-------------l~~~~~~l~EaPTGTGKTlayL~~~  312 (795)
                      |-|+-=|.|.+.+.+|..+|+.-..  ..+....-+-.+++.             +...-+..++++||||||..||..+
T Consensus         3 ~~~e~l~hQ~~av~ai~~~F~~~~~--~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~n~~~~M~TGtGKT~~~~~~i   80 (986)
T PRK15483          3 ILLEELPHQEQALAAILAAFTGIDI--ASADPNHYANPLIKLRYENGIPGRSRTRIDDKANIDIKMETGTGKTYVYTRLM   80 (986)
T ss_pred             cccccChhHHHHHHHHHHHhcCCCc--cCCccccccCcccccchhhccccccccccCccceEEEEeCCCCCHHHHHHHHH
Confidence            4566689999999999999985210  000000000000000             1223578999999999999999887


Q ss_pred             HHHHHHh
Q psy3462         313 LAWQRKE  319 (795)
Q Consensus       313 l~~~~~~  319 (795)
                      +...+..
T Consensus        81 ~~l~~~~   87 (986)
T PRK15483         81 YELHQKY   87 (986)
T ss_pred             HHHHHHc
Confidence            6665553

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=90.92  E-value=0.13  Score=66.65  Aligned_cols=23  Identities=43%  Similarity=0.512  Sum_probs=20.3

Q ss_pred             EECCCCCchHHHHHHHHHHHHHH
Q psy3462          44 LESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        44 lEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      |.||||||||+||++|+|..+..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~   23 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFR   23 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHh
Confidence            46999999999999999988764

>PF13245 AAA_19: Part of AAA domain

Probab=90.59  E-value=0.37  Score=42.39  Aligned_cols=55  Identities=15%  Similarity=0.157  Sum_probs=31.7

Q ss_pred             HHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          31 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        31 ~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      +|..++.++..+++.||.|||||-..+--+..+..             .... ++.++++++-|+....
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~-------------~~~~-~~~~vlv~a~t~~aa~   56 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLA-------------ARAD-PGKRVLVLAPTRAAAD   56 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHH-------------HhcC-CCCeEEEECCCHHHHH
Confidence            45557774455777999999999443333222221             0111 2567777776665544

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=90.59  E-value=0.29  Score=59.53  Aligned_cols=57  Identities=19%  Similarity=0.210  Sum_probs=33.2

Q ss_pred             EEeCCCCCChhHHHHHHHHHHHHHhhH----HHHHHHHhhhhhhhhhcC-CCCceEEEeccc
Q psy3462         295 LLESPTGSGKTLALLCSVLAWQRKEKE----LVQQKMFEQRTQDLQKIP-FRKLKISRLKAK  351 (795)
Q Consensus       295 l~EaPTGTGKTlayL~~~l~~~~~~~k----~LQ~Ql~~kdip~l~~i~-~~~l~~~~~KGr  351 (795)
                      +.|++||+|||+++++|++..+.....    ..-+.|..+|...+..+. ...+++.++-|.
T Consensus        73 Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~  134 (745)
T TIGR00963        73 IAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSG  134 (745)
T ss_pred             eeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCC
Confidence            899999999999999998533333322    222334444444444332 233566555543

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=90.33  E-value=0.31  Score=59.80  Aligned_cols=25  Identities=28%  Similarity=0.292  Sum_probs=21.4

Q ss_pred             EEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         295 LLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       295 l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      +.|+.||+|||+++++|++..+...
T Consensus        95 Iaem~TGeGKTL~a~lp~~l~al~G  119 (790)
T PRK09200         95 IAEMQTGEGKTLTATMPLYLNALEG  119 (790)
T ss_pred             eeeecCCCcchHHHHHHHHHHHHcC
Confidence            9999999999999999987555444

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=90.26  E-value=0.34  Score=51.35  Aligned_cols=18  Identities=33%  Similarity=0.494  Sum_probs=15.5

Q ss_pred             ccCcEEEeCCCCCChhHH
Q psy3462         290 KAKNCLLESPTGSGKTLA  307 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTla  307 (795)
                      .+.+++++||+|||||..
T Consensus        20 ~g~~vLL~G~~GtGKT~l   37 (262)
T TIGR02640        20 SGYPVHLRGPAGTGKTTL   37 (262)
T ss_pred             cCCeEEEEcCCCCCHHHH
Confidence            367899999999999963

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=90.04  E-value=0.29  Score=60.53  Aligned_cols=26  Identities=27%  Similarity=0.197  Sum_probs=21.6

Q ss_pred             EEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         294 CLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       294 ~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      -+.||+||+|||+++++|++..+...
T Consensus        98 ~Iaem~TGeGKTL~a~Lpa~~~al~G  123 (896)
T PRK13104         98 NIAEMRTGEGKTLVATLPAYLNAISG  123 (896)
T ss_pred             ccccccCCCCchHHHHHHHHHHHhcC
Confidence            37899999999999999998665443

>COG1204 Superfamily II helicase [General function prediction only]

Probab=89.94  E-value=0.47  Score=58.13  Aligned_cols=58  Identities=22%  Similarity=0.359  Sum_probs=41.8

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHHh-hH--------HHHHHHHhhhhhhhhhcCCCCceEEEecccc
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRKE-KE--------LVQQKMFEQRTQDLQKIPFRKLKISRLKAKD  352 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~~-~k--------~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr~  352 (795)
                      ++|+|+.+|||+|||+-.++.++.-+.++ .+        +|.+|...+--    +.-...+++.+.-|--
T Consensus        47 ~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~----~~~~~GirV~~~TgD~  113 (766)
T COG1204          47 DENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFS----RLEELGIRVGISTGDY  113 (766)
T ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhh----hHHhcCCEEEEecCCc
Confidence            68999999999999999888888877765 22        78888876632    2223445666666653

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

Probab=89.87  E-value=0.4  Score=47.41  Aligned_cols=23  Identities=39%  Similarity=0.606  Sum_probs=14.9

Q ss_pred             cEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         293 NCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       293 ~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.++.||.|||||- .++.++..+
T Consensus        19 ~~~i~GpPGTGKT~-~l~~~i~~~   41 (236)
T PF13086_consen   19 ITLIQGPPGTGKTT-TLASIIAQL   41 (236)
T ss_dssp             -EEEE-STTSSHHH-HHHHHHHHH
T ss_pred             CEEEECCCCCChHH-HHHHHHHHh
Confidence            59999999999994 334444443

>PF13245 AAA_19: Part of AAA domain

Probab=89.84  E-value=0.41  Score=42.11  Aligned_cols=29  Identities=21%  Similarity=0.342  Sum_probs=19.6

Q ss_pred             ccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         288 CNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       288 l~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.+++.+++.||.|||||-..+--+..+.
T Consensus         7 l~~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    7 LAGSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             HhhCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            33356778899999999965544443433

>KOG0354|consensus

Probab=89.60  E-value=0.4  Score=58.10  Aligned_cols=46  Identities=22%  Similarity=0.151  Sum_probs=33.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      ..+.+|..|.++.+   .||  ++|.|+-+|||.|||.....-++.|.+..
T Consensus        59 ~~~~lR~YQ~eivq---~AL--gkNtii~lPTG~GKTfIAa~Vm~nh~rw~  104 (746)
T KOG0354|consen   59 TNLELRNYQEELVQ---PAL--GKNTIIALPTGSGKTFIAAVIMKNHFEWR  104 (746)
T ss_pred             CcccccHHHHHHhH---Hhh--cCCeEEEeecCCCccchHHHHHHHHHhcC
Confidence            35678899954433   445  89999999999999977666666665433

>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 []

Probab=89.55  E-value=0.58  Score=48.82  Aligned_cols=28  Identities=25%  Similarity=0.509  Sum_probs=20.2

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ..++++.||.|||||+--+..++..+.+
T Consensus        19 ~~~v~~~G~AGTGKT~LA~a~Al~~v~~   46 (205)
T PF02562_consen   19 NDLVIVNGPAGTGKTFLALAAALELVKE   46 (205)
T ss_dssp             -SEEEEE--TTSSTTHHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            4689999999999998777777666554

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0349|consensus

Probab=89.10  E-value=0.19  Score=57.51  Aligned_cols=80  Identities=18%  Similarity=0.148  Sum_probs=58.5

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEec
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCG   92 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~   92 (795)
                      .++++-..|...|    .+.+..+..+.+++.-|.||+|||=||.+|+|+..-++-+-.+.       -..++++....+
T Consensus        17 ~~e~dw~lptdvq----aeaiplilgggdvlmaaetgsgktgaf~lpilqiv~etlrd~~e-------gk~gk~~~~~ga   85 (725)
T KOG0349|consen   17 TDELDWTLPTDVQ----AEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWETLRDLEE-------GKAGKGGMADGA   85 (725)
T ss_pred             hhhhccccccccc----cccccEEecCCcEEEEeccCCCCccceehhhHHHHHHHHHhHhh-------cccCCCcccCCC
Confidence            4566777899999    77778888999999999999999999999999876655432221       112456666666


Q ss_pred             ccccccccccc
Q psy3462          93 RSDFFLLFRER  103 (795)
Q Consensus        93 rth~~l~~rer  103 (795)
                      .+.|++.+-.|
T Consensus        86 ~~~w~mn~~Dr   96 (725)
T KOG0349|consen   86 PREWKMNKQDR   96 (725)
T ss_pred             ccccccCcccc
Confidence            66676665444

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

Probab=88.87  E-value=0.39  Score=48.43  Aligned_cols=38  Identities=29%  Similarity=0.358  Sum_probs=19.7

Q ss_pred             HHHHHHHHHH--HHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          23 SSCKILHLQV--IQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        23 ~~Q~~mm~~i--~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      ..+.+.+..+  .+-+.++.++++.||||||||  +|.-++.
T Consensus        29 ~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKT--hLa~ai~   68 (178)
T PF01695_consen   29 GIDKAQIAQLAALEFIENGENLILYGPPGTGKT--HLAVAIA   68 (178)
T ss_dssp             -----HHHHHHHH-S-SC--EEEEEESTTSSHH--HHHHHHH
T ss_pred             hHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHH--HHHHHHH
Confidence            3444444433  223455788999999999999  4444443

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK10536 hypothetical protein; Provisional

Probab=88.75  E-value=0.84  Score=49.41  Aligned_cols=38  Identities=13%  Similarity=0.059  Sum_probs=26.1

Q ss_pred             CCC-HHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHH
Q psy3462          20 LKY-SSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL   61 (795)
Q Consensus        20 ~p~-~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL   61 (795)
                      .|+ ..|..++.    ++.+...+++.||+|||||+-.+.-++
T Consensus        58 ~p~n~~Q~~~l~----al~~~~lV~i~G~aGTGKT~La~a~a~   96 (262)
T PRK10536         58 LARNEAQAHYLK----AIESKQLIFATGEAGCGKTWISAAKAA   96 (262)
T ss_pred             cCCCHHHHHHHH----HHhcCCeEEEECCCCCCHHHHHHHHHH
Confidence            445 66756665    445567899999999999954444433

>PRK13531 regulatory ATPase RavA; Provisional

Probab=88.74  E-value=0.34  Score=56.48  Aligned_cols=47  Identities=11%  Similarity=0.077  Sum_probs=36.6

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL   54 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTL   54 (795)
                      ++.+..+.+++.-  -.-+|.+.++.+..++..+.++++++|+|||||+
T Consensus         8 ~~~i~~l~~~l~~--~i~gre~vI~lll~aalag~hVLL~GpPGTGKT~   54 (498)
T PRK13531          8 AERISRLSSALEK--GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSL   54 (498)
T ss_pred             HHHHHHHHHHHhh--hccCcHHHHHHHHHHHccCCCEEEECCCChhHHH
Confidence            3445555555543  2346778999999999999999999999999993

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

Probab=88.43  E-value=0.49  Score=47.74  Aligned_cols=25  Identities=36%  Similarity=0.589  Sum_probs=16.8

Q ss_pred             ccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         288 CNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       288 l~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      +.++.++++-||+|||||.  |+.+++
T Consensus        44 ~~~~~~l~l~G~~G~GKTh--La~ai~   68 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTH--LAVAIA   68 (178)
T ss_dssp             -SC--EEEEEESTTSSHHH--HHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHH--HHHHHH
Confidence            3457889999999999995  444443

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>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

Probab=88.34  E-value=0.47  Score=42.55  Aligned_cols=16  Identities=56%  Similarity=0.798  Sum_probs=14.4

Q ss_pred             cCcEEEeCCCCCChhH
Q psy3462         291 AKNCLLESPTGSGKTL  306 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTl  306 (795)
                      +.++++-||+|||||.
T Consensus        19 ~~~v~i~G~~G~GKT~   34 (151)
T cd00009          19 PKNLLLYGPPGTGKTT   34 (151)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            5789999999999994

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>KOG0341|consensus

Probab=88.32  E-value=0.13  Score=58.14  Aligned_cols=51  Identities=18%  Similarity=0.163  Sum_probs=39.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKEL   70 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~   70 (795)
                      .+.-.|.|+|.    .=+.++..|.+.|-.|-||+||||.|.+|++-++......
T Consensus       188 KGI~~PTpIQv----QGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~  238 (610)
T KOG0341|consen  188 KGIVHPTPIQV----QGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMM  238 (610)
T ss_pred             cCCCCCCceee----cCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhc
Confidence            35556777772    2345566788999999999999999999999988766543

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=88.01  E-value=0.47  Score=51.73  Aligned_cols=30  Identities=27%  Similarity=0.290  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          24 SCKILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      ++.+.+..+..++..+.++++++|+|||||
T Consensus        28 g~~~~~~~~l~a~~~~~~vll~G~PG~gKT   57 (329)
T COG0714          28 GDEEVIELALLALLAGGHVLLEGPPGVGKT   57 (329)
T ss_pred             ccHHHHHHHHHHHHcCCCEEEECCCCccHH
Confidence            377889999999999999999999999999

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=87.65  E-value=0.8  Score=57.29  Aligned_cols=28  Identities=25%  Similarity=0.262  Sum_probs=23.6

Q ss_pred             CcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          40 KNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        40 ~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .++.++.+||||||..||-.++......
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~   87 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKY   87 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHc
Confidence            3699999999999999998887776553

>KOG0351|consensus

Probab=87.55  E-value=0.2  Score=62.35  Aligned_cols=41  Identities=24%  Similarity=0.275  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          20 LKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        20 ~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      --|+.|+++    +.+...|++.+++.|||-||+|+|-+|++.+-
T Consensus       264 ~FR~~Q~ea----I~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~  304 (941)
T KOG0351|consen  264 GFRPNQLEA----INATLSGKDCFVLMPTGGGKSLCYQLPALLLG  304 (941)
T ss_pred             cCChhHHHH----HHHHHcCCceEEEeecCCceeeEeeccccccC
Confidence            346888544    44788899999999999999999999987664

>KOG0354|consensus

Probab=87.41  E-value=0.58  Score=56.82  Aligned_cols=46  Identities=22%  Similarity=0.246  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE  321 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k  321 (795)
                      +..|+-|.++.+.                          ||  +++.++.+|||.|||+....-++.|.+..++
T Consensus        61 ~~lR~YQ~eivq~--------------------------AL--gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~  106 (746)
T KOG0354|consen   61 LELRNYQEELVQP--------------------------AL--GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK  106 (746)
T ss_pred             ccccHHHHHHhHH--------------------------hh--cCCeEEEeecCCCccchHHHHHHHHHhcCCc
Confidence            6789999887654                          23  5899999999999999888888888876654

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=87.06  E-value=0.88  Score=50.25  Aligned_cols=33  Identities=30%  Similarity=0.469  Sum_probs=24.2

Q ss_pred             HHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          29 HLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        29 m~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      .+.+..++..+.++++-||||+||| .+|-.++.
T Consensus       138 ~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~  170 (319)
T PRK13894        138 REAIIAAVRAHRNILVIGGTGSGKT-TLVNAIIN  170 (319)
T ss_pred             HHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHH
Confidence            3445566678899999999999999 44444443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=86.71  E-value=0.7  Score=56.72  Aligned_cols=45  Identities=18%  Similarity=0.090  Sum_probs=34.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .-+..||+.|  +|..+  +|+.|.  |.|..||.||||...+|++..+..
T Consensus        76 ~~g~~~~dvQ--lig~l--~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~  120 (796)
T PRK12906         76 VLGLRPFDVQ--IIGGI--VLHEGN--IAEMKTGEGKTLTATLPVYLNALT  120 (796)
T ss_pred             HhCCCCchhH--HHHHH--HHhcCC--cccccCCCCCcHHHHHHHHHHHHc
Confidence            3467899999  44444  456654  999999999999999998776653

>TIGR00603 rad25 DNA repair helicase rad25

Probab=86.26  E-value=0.95  Score=55.24  Aligned_cols=39  Identities=13%  Similarity=0.129  Sum_probs=28.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCS   59 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~p   59 (795)
                      .+.+||.|.+-+.+.   +.++  ..++|..|||+|||+.-+..
T Consensus       253 ~~~LRpYQ~eAl~~~---~~~gr~r~GIIvLPtGaGKTlvai~a  293 (732)
T TIGR00603       253 TTQIRPYQEKSLSKM---FGNGRARSGIIVLPCGAGKSLVGVTA  293 (732)
T ss_pred             CCCcCHHHHHHHHHH---HhcCCCCCcEEEeCCCCChHHHHHHH
Confidence            467899998755544   3344  46999999999999776543

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0353|consensus

Probab=86.16  E-value=0.68  Score=52.38  Aligned_cols=38  Identities=26%  Similarity=0.328  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          21 KYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      -||-|    .+.+.+...++++++.-|||-||+|+|-+|+|-
T Consensus        95 frplq----~~ain~~ma~ed~~lil~tgggkslcyqlpal~  132 (695)
T KOG0353|consen   95 FRPLQ----LAAINATMAGEDAFLILPTGGGKSLCYQLPALC  132 (695)
T ss_pred             cChhH----HHHhhhhhccCceEEEEeCCCccchhhhhhHHh
Confidence            45778    566677788899999999999999999999874

>KOG0328|consensus

Probab=86.14  E-value=0.14  Score=56.04  Aligned_cols=60  Identities=17%  Similarity=0.147  Sum_probs=46.8

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQ   73 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~   73 (795)
                      .+.+.+- +|-.|..+|    +.++..+-.|.++|..|-.|||||.+|-|.+|.-.+-..+.+|+
T Consensus        39 LrgiY~y-GfekPS~IQ----qrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~   98 (400)
T KOG0328|consen   39 LRGIYAY-GFEKPSAIQ----QRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQA   98 (400)
T ss_pred             HHHHHHh-ccCCchHHH----hhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeE
Confidence            3344433 566799999    66667777889999999999999999999999888766665554

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=86.00  E-value=0.68  Score=40.79  Aligned_cols=18  Identities=39%  Similarity=0.534  Sum_probs=15.3

Q ss_pred             cCcEEEeCCCCCChhHHH
Q psy3462         291 AKNCLLESPTGSGKTLAL  308 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlay  308 (795)
                      +.++++.||+|||||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            467999999999999654

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK06835 DNA replication protein DnaC; Validated

Probab=85.95  E-value=1.2  Score=49.56  Aligned_cols=17  Identities=41%  Similarity=0.622  Sum_probs=14.7

Q ss_pred             cCCcEEEECCCCCchHH
Q psy3462          38 KAKNCLLESPTGSGKTL   54 (795)
Q Consensus        38 ~~~~~llEAPTGTGKTL   54 (795)
                      ...+++|.||||||||-
T Consensus       182 ~~~~Lll~G~~GtGKTh  198 (329)
T PRK06835        182 NNENLLFYGNTGTGKTF  198 (329)
T ss_pred             cCCcEEEECCCCCcHHH
Confidence            35789999999999993

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=85.83  E-value=0.92  Score=57.04  Aligned_cols=140  Identities=16%  Similarity=0.172  Sum_probs=81.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccccc
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDF   96 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~   96 (795)
                      .+|.+.+.|    +....+|+.+..++++||||+|||+.--.+ ++++               +  ++++++||=+..  
T Consensus       116 ~~F~LD~fQ----~~a~~~Ler~esVlV~ApTssGKTvVaeyA-i~~a---------------l--~~~qrviYTsPI--  171 (1041)
T COG4581         116 YPFELDPFQ----QEAIAILERGESVLVCAPTSSGKTVVAEYA-IALA---------------L--RDGQRVIYTSPI--  171 (1041)
T ss_pred             CCCCcCHHH----HHHHHHHhCCCcEEEEccCCCCcchHHHHH-HHHH---------------H--HcCCceEeccch--
Confidence            356888999    788889999999999999999999543222 1111               1  245667776533  


Q ss_pred             cccccccccccccccCCCCCCCCCcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhC----CC-----CeE-
Q psy3462          97 FLLFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMG----TE-----DVR-  166 (795)
Q Consensus        97 ~l~~rerr~SDt~~~~~k~~~s~~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mk----t~-----dVr-  166 (795)
                       .|.=-+..-|...+.-+-  ...-...|+.++||-.-.+--+.     .   ..+|.++-+.-.    ++     .|+ 
T Consensus       172 -KALsNQKyrdl~~~fgdv--~~~vGL~TGDv~IN~~A~clvMT-----T---EILRnMlyrg~~~~~~i~~ViFDEvHy  240 (1041)
T COG4581         172 -KALSNQKYRDLLAKFGDV--ADMVGLMTGDVSINPDAPCLVMT-----T---EILRNMLYRGSESLRDIEWVVFDEVHY  240 (1041)
T ss_pred             -hhhhhhHHHHHHHHhhhh--hhhccceecceeeCCCCceEEee-----H---HHHHHHhccCcccccccceEEEEeeee
Confidence             222222222443322211  22234579999999654332211     1   556666655411    11     222 


Q ss_pred             eCccchHHHHhcCCCCCCCceEEEe
Q psy3462         167 IDTRLNKHIWSKGINNHTLGTAYFD  191 (795)
Q Consensus       167 ID~~LNk~IWsrGirnpP~rirV~~  191 (795)
                      |...-==.||+-=|-..|..|++-.
T Consensus       241 i~D~eRG~VWEE~Ii~lP~~v~~v~  265 (1041)
T COG4581         241 IGDRERGVVWEEVIILLPDHVRFVF  265 (1041)
T ss_pred             ccccccchhHHHHHHhcCCCCcEEE
Confidence            2222233579999999999887765

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

Probab=85.71  E-value=1.1  Score=50.54  Aligned_cols=33  Identities=24%  Similarity=0.249  Sum_probs=25.9

Q ss_pred             CHHHH-HHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          22 YSSCK-ILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        22 ~~~Q~-~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      |..|. +++..+..++.++  .++++.+|||||||.
T Consensus        22 Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~   57 (366)
T COG1474          22 REEEINQLASFLAPALRGERPSNIIIYGPTGTGKTA   57 (366)
T ss_pred             cHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhH
Confidence            46776 7777777777665  469999999999993

>KOG0340|consensus

Probab=85.71  E-value=0.41  Score=53.81  Aligned_cols=35  Identities=29%  Similarity=0.424  Sum_probs=28.8

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ||+|.+|+.|+-.|-||||||.||-+|.|.-+..+
T Consensus        38 IpkILeGrdcig~AkTGsGKT~AFaLPil~rLsed   72 (442)
T KOG0340|consen   38 IPKILEGRDCIGCAKTGSGKTAAFALPILNRLSED   72 (442)
T ss_pred             hHHHhcccccccccccCCCcchhhhHHHHHhhccC
Confidence            34445688999999999999999999998777654

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

Probab=85.64  E-value=0.69  Score=56.61  Aligned_cols=37  Identities=32%  Similarity=0.284  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCc-EEEECCCCCchHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKN-CLLESPTGSGKTLA   55 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~-~llEAPTGTGKTLA   55 (795)
                      -.||..|..-+..+.++++++.+ +++-..||||||-.
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrT  201 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRT  201 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCccee
Confidence            45889999999999999998754 99999999999943

>TIGR00376 DNA helicase, putative

Probab=85.42  E-value=1.2  Score=53.60  Aligned_cols=64  Identities=19%  Similarity=0.187  Sum_probs=39.7

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccccc
Q psy3462          22 YSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLLFR  101 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~~r  101 (795)
                      -+.|.+   ++..++.+....+|.||+|||||-. +..++..+               ..  .+.+|+.|+.|+..+.-=
T Consensus       159 n~~Q~~---Av~~~l~~~~~~lI~GpPGTGKT~t-~~~ii~~~---------------~~--~g~~VLv~a~sn~Avd~l  217 (637)
T TIGR00376       159 NESQKE---AVSFALSSKDLFLIHGPPGTGKTRT-LVELIRQL---------------VK--RGLRVLVTAPSNIAVDNL  217 (637)
T ss_pred             CHHHHH---HHHHHhcCCCeEEEEcCCCCCHHHH-HHHHHHHH---------------HH--cCCCEEEEcCcHHHHHHH
Confidence            367754   4455666667899999999999922 22222111               11  234899999999887544


Q ss_pred             ccccc
Q psy3462         102 ERRIS  106 (795)
Q Consensus       102 err~S  106 (795)
                      -.++.
T Consensus       218 ~e~l~  222 (637)
T TIGR00376       218 LERLA  222 (637)
T ss_pred             HHHHH
Confidence            33343

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>KOG4284|consensus

Probab=85.37  E-value=0.15  Score=60.69  Aligned_cols=62  Identities=13%  Similarity=0.170  Sum_probs=50.0

Q ss_pred             hhHHHHHHHHhCCC---CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhH
Q psy3462           4 KSSDIFKTYLNEPN---YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE   69 (795)
Q Consensus         4 ~~~~~~~~~~~~~~---~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~   69 (795)
                      .+...|+.++.++.   +-.|.++|    .+++.+...+-++|+.|-.||||||.|-+.++.-+.....
T Consensus        28 e~l~l~r~vl~glrrn~f~~ptkiQ----aaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~   92 (980)
T KOG4284|consen   28 EQLALWREVLLGLRRNAFALPTKIQ----AAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSS   92 (980)
T ss_pred             HHHHHHHHHHHHHHhhcccCCCchh----hhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccC
Confidence            34567788887776   44799999    7888888888899999999999999999888877654433

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=85.29  E-value=1.3  Score=49.13  Aligned_cols=25  Identities=28%  Similarity=0.340  Sum_probs=20.7

Q ss_pred             HHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          29 HLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        29 m~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      ++.+..++..+.++|+-+|||+|||
T Consensus       134 ~~~L~~~v~~~~nilI~G~tGSGKT  158 (323)
T PRK13833        134 ASVIRSAIDSRLNIVISGGTGSGKT  158 (323)
T ss_pred             HHHHHHHHHcCCeEEEECCCCCCHH
Confidence            3445667777889999999999999

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=85.24  E-value=1.2  Score=49.33  Aligned_cols=27  Identities=22%  Similarity=0.259  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      .+.+-+..++..+.++++-+|||+|||
T Consensus       148 ~~~~~L~~~v~~~~nili~G~tgSGKT  174 (332)
T PRK13900        148 KIKEFLEHAVISKKNIIISGGTSTGKT  174 (332)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHH
Confidence            556667777888999999999999999

>PHA02244 ATPase-like protein

Probab=85.13  E-value=1.3  Score=50.35  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      |........+.+.+..+.+++|.+|||||||
T Consensus       103 p~~~~~~~ri~r~l~~~~PVLL~GppGtGKT  133 (383)
T PHA02244        103 PTFHYETADIAKIVNANIPVFLKGGAGSGKN  133 (383)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEECCCCCCHH
Confidence            4444455577888899999999999999999

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=85.12  E-value=0.71  Score=56.93  Aligned_cols=56  Identities=20%  Similarity=0.193  Sum_probs=35.1

Q ss_pred             EEEeCCCCCChhHHHHHHHH-HHHHHhhH----HHHHHHHhhhhhhhhhcC-CCCceEEEecc
Q psy3462         294 CLLESPTGSGKTLALLCSVL-AWQRKEKE----LVQQKMFEQRTQDLQKIP-FRKLKISRLKA  350 (795)
Q Consensus       294 ~l~EaPTGTGKTlayL~~~l-~~~~~~~k----~LQ~Ql~~kdip~l~~i~-~~~l~~~~~KG  350 (795)
                      -+.|+.||+|||+++.+|++ .++. ...    ..-+.|..+|...+..+. ...+++.++-|
T Consensus        97 ~Iaem~TGeGKTLva~lpa~l~aL~-G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~i~~  158 (830)
T PRK12904         97 KIAEMKTGEGKTLVATLPAYLNALT-GKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGVILS  158 (830)
T ss_pred             chhhhhcCCCcHHHHHHHHHHHHHc-CCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEEEcC
Confidence            48899999999999999995 4443 222    233455555555555543 23455555544

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=85.11  E-value=1.6  Score=46.65  Aligned_cols=34  Identities=24%  Similarity=0.348  Sum_probs=25.8

Q ss_pred             HHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          31 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        31 ~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      ...+.+.+++++++-||+|||||  +|..|+.....
T Consensus        97 ~~~~~~~~~~nl~l~G~~G~GKT--hLa~Ai~~~l~  130 (254)
T COG1484          97 SLVEFFERGENLVLLGPPGVGKT--HLAIAIGNELL  130 (254)
T ss_pred             HHHHHhccCCcEEEECCCCCcHH--HHHHHHHHHHH
Confidence            44456677889999999999999  66666665444

>KOG0952|consensus

Probab=85.08  E-value=1.2  Score=55.77  Aligned_cols=47  Identities=26%  Similarity=0.395  Sum_probs=36.1

Q ss_pred             cccCcEEEeCCCCCChhHHHHHHHHHHHHHh------------------hHHHHHHHHhhhhhhh
Q psy3462         289 NKAKNCLLESPTGSGKTLALLCSVLAWQRKE------------------KELVQQKMFEQRTQDL  335 (795)
Q Consensus       289 ~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~------------------~k~LQ~Ql~~kdip~l  335 (795)
                      ..+.|+||.||||+|||.-+++.+|.-++.+                  .++|-.++.++--+.|
T Consensus       124 ~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl  188 (1230)
T KOG0952|consen  124 KSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKL  188 (1230)
T ss_pred             cCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhhc
Confidence            4578999999999999999998888877752                  1267777777655544

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=85.05  E-value=1.2  Score=46.24  Aligned_cols=36  Identities=22%  Similarity=0.299  Sum_probs=27.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCC-cEEEECCCCCchH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAK-NCLLESPTGSGKT   53 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~-~~llEAPTGTGKT   53 (795)
                      +|++.+.+.+.+..+...+..+. .+++.||+|+|||
T Consensus        21 ~~~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKT   57 (269)
T TIGR03015        21 FFYPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKT   57 (269)
T ss_pred             HhCCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHH
Confidence            44566777777777777776655 6899999999999

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR00595 priA primosomal protein N'

Probab=84.78  E-value=0.7  Score=53.91  Aligned_cols=35  Identities=31%  Similarity=0.295  Sum_probs=23.9

Q ss_pred             EEeCCCCCChhHHHHHHHHHHHHHhhH--------HHHHHHHh
Q psy3462         295 LLESPTGSGKTLALLCSVLAWQRKEKE--------LVQQKMFE  329 (795)
Q Consensus       295 l~EaPTGTGKTlayL~~~l~~~~~~~k--------~LQ~Ql~~  329 (795)
                      |+.||||+|||..|+-.+...+...++        .|..|+.+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~   43 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQ   43 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHH
Confidence            578999999999998765444444333        46666653

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=84.62  E-value=0.5  Score=61.42  Aligned_cols=22  Identities=45%  Similarity=0.495  Sum_probs=19.2

Q ss_pred             EeCCCCCChhHHHHHHHHHHHH
Q psy3462         296 LESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       296 ~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.||||||||++|++|+|.-+.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll   22 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLF   22 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHH
Confidence            4689999999999999987764

>PRK08939 primosomal protein DnaI; Reviewed

Probab=84.62  E-value=1.7  Score=47.72  Aligned_cols=39  Identities=21%  Similarity=0.156  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHh------cCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          24 SCKILHLQVIQGCN------KAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        24 ~Q~~mm~~i~~al~------~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+.+++..+.+-+.      .+++++|.||+|||||  ||+.++...
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKT--hLa~Aia~~  179 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKS--YLLAAIANE  179 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHH--HHHHHHHHH
Confidence            45455555555554      2457999999999999  666665543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=84.25  E-value=0.86  Score=40.16  Aligned_cols=15  Identities=47%  Similarity=0.722  Sum_probs=13.6

Q ss_pred             CCcEEEECCCCCchH
Q psy3462          39 AKNCLLESPTGSGKT   53 (795)
Q Consensus        39 ~~~~llEAPTGTGKT   53 (795)
                      +.+++|.||+|||||
T Consensus         2 ~~~~~l~G~~G~GKT   16 (148)
T smart00382        2 GEVILIVGPPGSGKT   16 (148)
T ss_pred             CCEEEEECCCCCcHH
Confidence            467999999999999

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PLN03025 replication factor C subunit; Provisional

Probab=84.04  E-value=1.2  Score=48.32  Aligned_cols=30  Identities=23%  Similarity=0.281  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEECCCCCchH
Q psy3462          24 SCKILHLQVIQGCNKA--KNCLLESPTGSGKT   53 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~~--~~~llEAPTGTGKT   53 (795)
                      +|.+.++.+...+.++  .+++|.||.|||||
T Consensus        17 g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKT   48 (319)
T PLN03025         17 GNEDAVSRLQVIARDGNMPNLILSGPPGTGKT   48 (319)
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHH
Confidence            4555566666656554  47999999999999

>PHA02244 ATPase-like protein

Probab=83.95  E-value=2.1  Score=48.78  Aligned_cols=41  Identities=15%  Similarity=0.229  Sum_probs=27.5

Q ss_pred             eeccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhH
Q psy3462         243 KVEFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       243 ~~~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTl  306 (795)
                      .+.+||. .-|.+......+.+.+..                       +.+++|.||||||||.
T Consensus        93 ~~d~~~ig~sp~~~~~~~ri~r~l~~-----------------------~~PVLL~GppGtGKTt  134 (383)
T PHA02244         93 GIDTTKIASNPTFHYETADIAKIVNA-----------------------NIPVFLKGGAGSGKNH  134 (383)
T ss_pred             hCCCcccCCCHHHHHHHHHHHHHHhc-----------------------CCCEEEECCCCCCHHH
Confidence            4567763 445444444555555543                       5789999999999994

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=83.59  E-value=0.99  Score=47.48  Aligned_cols=37  Identities=32%  Similarity=0.381  Sum_probs=24.4

Q ss_pred             HHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          28 LHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        28 mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +.+.+..++..+.++++-||||+||| .+|...+.+..
T Consensus       116 ~~~~l~~~v~~~~~ili~G~tGSGKT-T~l~all~~i~  152 (270)
T PF00437_consen  116 IAEFLRSAVRGRGNILISGPTGSGKT-TLLNALLEEIP  152 (270)
T ss_dssp             HHHHHHHCHHTTEEEEEEESTTSSHH-HHHHHHHHHCH
T ss_pred             HHHHHhhccccceEEEEECCCccccc-hHHHHHhhhcc
Confidence            33444455566789999999999999 33344444433

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=83.42  E-value=0.98  Score=48.33  Aligned_cols=30  Identities=23%  Similarity=0.402  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHhcCC--cEEEECCCCCchH
Q psy3462          24 SCKILHLQVIQGCNKAK--NCLLESPTGSGKT   53 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~~~--~~llEAPTGTGKT   53 (795)
                      +|.+..+.+.+++.++.  ++++.||+|||||
T Consensus        19 g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT   50 (337)
T PRK12402         19 GQDEVVERLSRAVDSPNLPHLLVQGPPGSGKT   50 (337)
T ss_pred             CCHHHHHHHHHHHhCCCCceEEEECCCCCCHH
Confidence            46667777888888877  8999999999999

>COG4889 Predicted helicase [General function prediction only]

Probab=83.21  E-value=1.1  Score=55.21  Aligned_cols=60  Identities=20%  Similarity=0.170  Sum_probs=40.1

Q ss_pred             ccccCCCCCcceeeCCeeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChh
Q psy3462         226 KDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKT  305 (795)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKT  305 (795)
                      .||.+--  ..-...++.+.-|++|||.|...++...+.|...                       .-+-+-+..|||||
T Consensus       140 IDW~~f~--p~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n-----------------------~RGkLIMAcGTGKT  194 (1518)
T COG4889         140 IDWDIFD--PTELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDN-----------------------DRGKLIMACGTGKT  194 (1518)
T ss_pred             CChhhcC--ccccccccccCCCCCCChhHHHHHHHHHhhcccc-----------------------cCCcEEEecCCCcc
Confidence            3888621  1112235566678999999999999988887641                       22334467899999


Q ss_pred             HHHHH
Q psy3462         306 LALLC  310 (795)
Q Consensus       306 layL~  310 (795)
                      +.-|=
T Consensus       195 fTsLk  199 (1518)
T COG4889         195 FTSLK  199 (1518)
T ss_pred             chHHH
Confidence            87553

>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

Probab=83.17  E-value=1.4  Score=45.92  Aligned_cols=24  Identities=33%  Similarity=0.425  Sum_probs=17.3

Q ss_pred             cCCcEEEECCCCCchHHHHHHHHH
Q psy3462          38 KAKNCLLESPTGSGKTLALLCSVL   61 (795)
Q Consensus        38 ~~~~~llEAPTGTGKTLAyL~paL   61 (795)
                      ...+++|.|+.|||||.+.+-=++
T Consensus        12 ~~~~~lV~a~AGSGKT~~l~~ri~   35 (315)
T PF00580_consen   12 TEGPLLVNAGAGSGKTTTLLERIA   35 (315)
T ss_dssp             -SSEEEEEE-TTSSHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCchHHHHHHHH
Confidence            467899999999999976554433

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PRK08181 transposase; Validated

Probab=83.08  E-value=2.6  Score=45.58  Aligned_cols=20  Identities=40%  Similarity=0.509  Sum_probs=17.4

Q ss_pred             HHHhcCCcEEEECCCCCchH
Q psy3462          34 QGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        34 ~al~~~~~~llEAPTGTGKT   53 (795)
                      +-+..+.+++|.||+|||||
T Consensus       101 ~~~~~~~nlll~Gp~GtGKT  120 (269)
T PRK08181        101 SWLAKGANLLLFGPPGGGKS  120 (269)
T ss_pred             HHHhcCceEEEEecCCCcHH
Confidence            34567889999999999999

>KOG0920|consensus

Probab=82.84  E-value=2.1  Score=53.44  Aligned_cols=97  Identities=19%  Similarity=0.321  Sum_probs=59.3

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCC
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQK   85 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~   85 (795)
                      .+.|+.....-.-..-+    .|-+.|.+++.+...++|-|.||+|||-  -+|  +++.+.           .... +.
T Consensus       159 s~~~~~~~~~R~~LPa~----~~r~~Il~~i~~~qVvvIsGeTGcGKTT--Qvp--QfiLd~-----------~~~~-~~  218 (924)
T KOG0920|consen  159 SESYKEMLRFRESLPAY----KMRDTILDAIEENQVVVISGETGCGKTT--QVP--QFILDE-----------AIES-GA  218 (924)
T ss_pred             hhHHHHHHHHHHhCccH----HHHHHHHHHHHhCceEEEeCCCCCCchh--hhh--HHHHHH-----------HHhc-CC
Confidence            45555555543222222    3337899999999999999999999992  122  222211           1112 24


Q ss_pred             ceeEEeccccccccccccccccccccC----CCCCCCCCcccceeEEEEecCc
Q psy3462          86 TSFVFCGRSDFFLLFRERRISDTMVKK----PATKKKPLNEVVTRDYTIHMHK  134 (795)
Q Consensus        86 ~~~~yc~rth~~l~~rerr~SDt~~~~----~k~~~s~~~e~vtreyTInL~K  134 (795)
                      ..-|+||        -+||||-.-+-+    ++ +.+ +.  .+--|-|.|++
T Consensus       219 ~~~IicT--------QPRRIsAIsvAeRVa~ER-~~~-~g--~~VGYqvrl~~  259 (924)
T KOG0920|consen  219 ACNIICT--------QPRRISAISVAERVAKER-GES-LG--EEVGYQVRLES  259 (924)
T ss_pred             CCeEEec--------CCchHHHHHHHHHHHHHh-ccc-cC--CeeeEEEeeec
Confidence            5559999        799999865532    22 211 11  46689999887

>PRK09183 transposase/IS protein; Provisional

Probab=82.80  E-value=1.4  Score=47.08  Aligned_cols=18  Identities=39%  Similarity=0.676  Sum_probs=16.7

Q ss_pred             HhcCCcEEEECCCCCchH
Q psy3462          36 CNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        36 l~~~~~~llEAPTGTGKT   53 (795)
                      +..+.+++|.||+|||||
T Consensus        99 i~~~~~v~l~Gp~GtGKT  116 (259)
T PRK09183         99 IERNENIVLLGPSGVGKT  116 (259)
T ss_pred             hhcCCeEEEEeCCCCCHH
Confidence            677889999999999999

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=82.61  E-value=1.5  Score=48.85  Aligned_cols=35  Identities=14%  Similarity=0.246  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHHHHHH-HHhcC-CcEEEECCCCCchH
Q psy3462          19 FLKYSSCKILHLQVIQ-GCNKA-KNCLLESPTGSGKT   53 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~-al~~~-~~~llEAPTGTGKT   53 (795)
                      |.-.-+|.+.++.+.- ++..+ .++++++|.|||||
T Consensus         7 f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT   43 (334)
T PRK13407          7 FSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKS   43 (334)
T ss_pred             HHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHH
Confidence            3334678888886664 44355 68999999999999

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=82.40  E-value=1.4  Score=53.58  Aligned_cols=46  Identities=33%  Similarity=0.353  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccC-cEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAK-NCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~-~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ..++.|...++.+.+.-.                        .+ ..+++||||.|||.+-+.+++.-+..
T Consensus       195 ~~~~~~~~~~~~~~~~~~------------------------~~~~~vl~aPTG~GKT~asl~~a~~~~~~  241 (733)
T COG1203         195 EGYELQEKALELILRLEK------------------------RSLLVVLEAPTGYGKTEASLILALALLDE  241 (733)
T ss_pred             hhhHHHHHHHHHHHhccc------------------------ccccEEEEeCCCCChHHHHHHHHHHHhhc
Confidence            457888877777654332                        23 89999999999999998887665544

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=82.34  E-value=1.4  Score=44.24  Aligned_cols=26  Identities=35%  Similarity=0.371  Sum_probs=21.2

Q ss_pred             HHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          28 LHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        28 mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +.+.+..++..+..++|-+|||+|||
T Consensus        14 ~~~~l~~~v~~g~~i~I~G~tGSGKT   39 (186)
T cd01130          14 QAAYLWLAVEARKNILISGGTGSGKT   39 (186)
T ss_pred             HHHHHHHHHhCCCEEEEECCCCCCHH
Confidence            34455566777899999999999999

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=82.30  E-value=1.3  Score=48.41  Aligned_cols=26  Identities=35%  Similarity=0.300  Sum_probs=21.0

Q ss_pred             HHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          28 LHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        28 mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +.+.+..++..+.++++-+|||+|||
T Consensus       121 ~~~~L~~~v~~~~~ilI~G~tGSGKT  146 (299)
T TIGR02782       121 QRDVLREAVLARKNILVVGGTGSGKT  146 (299)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCCCHH
Confidence            34455566677889999999999999

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=82.21  E-value=2.1  Score=54.04  Aligned_cols=47  Identities=26%  Similarity=0.410  Sum_probs=35.9

Q ss_pred             eCCeeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHH
Q psy3462         239 IGGVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSV  312 (795)
Q Consensus       239 ~~~~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~  312 (795)
                      ..+....|||++.|.|.+.+..|    +                       .+.-++++||||+|||+.--.++
T Consensus       109 ~~~~~~~~~F~LD~fQ~~a~~~L----e-----------------------r~esVlV~ApTssGKTvVaeyAi  155 (1041)
T COG4581         109 LAPPAREYPFELDPFQQEAIAIL----E-----------------------RGESVLVCAPTSSGKTVVAEYAI  155 (1041)
T ss_pred             cCcHHHhCCCCcCHHHHHHHHHH----h-----------------------CCCcEEEEccCCCCcchHHHHHH
Confidence            34455579999999998776654    2                       35679999999999998765553

>PRK08181 transposase; Validated

Probab=82.01  E-value=2.9  Score=45.27  Aligned_cols=17  Identities=47%  Similarity=0.671  Sum_probs=15.0

Q ss_pred             ccCcEEEeCCCCCChhH
Q psy3462         290 KAKNCLLESPTGSGKTL  306 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTl  306 (795)
                      ++.++++-||+|||||.
T Consensus       105 ~~~nlll~Gp~GtGKTH  121 (269)
T PRK08181        105 KGANLLLFGPPGGGKSH  121 (269)
T ss_pred             cCceEEEEecCCCcHHH
Confidence            46789999999999994

>KOG0347|consensus

Probab=82.00  E-value=0.42  Score=56.25  Aligned_cols=34  Identities=29%  Similarity=0.305  Sum_probs=26.4

Q ss_pred             HHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         281 HLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       281 ~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      ++.+-+|+.....++--|.||+||||||-+|+++
T Consensus       209 sl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~  242 (731)
T KOG0347|consen  209 SLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVE  242 (731)
T ss_pred             hhcccHhhccchhcccccccCCCceeeecchhhh
Confidence            3333344444577899999999999999999998

>TIGR00603 rad25 DNA repair helicase rad25

Probab=81.98  E-value=1.8  Score=52.85  Aligned_cols=41  Identities=20%  Similarity=0.344  Sum_probs=30.0

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCS  311 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~  311 (795)
                      .++.||-|.+.+....   .+.                     ..+.+++.+|||+|||+.-+..
T Consensus       253 ~~~LRpYQ~eAl~~~~---~~g---------------------r~r~GIIvLPtGaGKTlvai~a  293 (732)
T TIGR00603       253 TTQIRPYQEKSLSKMF---GNG---------------------RARSGIIVLPCGAGKSLVGVTA  293 (732)
T ss_pred             CCCcCHHHHHHHHHHH---hcC---------------------CCCCcEEEeCCCCChHHHHHHH
Confidence            4789999998776553   221                     1246899999999999987654

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=81.70  E-value=3.4  Score=47.90  Aligned_cols=31  Identities=19%  Similarity=0.273  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +.+...+.....-++++.|+++.||+|||||
T Consensus       193 r~k~~~L~rl~~fve~~~Nli~lGp~GTGKT  223 (449)
T TIGR02688       193 RQKLLLLARLLPLVEPNYNLIELGPKGTGKS  223 (449)
T ss_pred             HHHHHHHHhhHHHHhcCCcEEEECCCCCCHH
Confidence            4444555566677899999999999999999

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=81.58  E-value=1.1  Score=49.06  Aligned_cols=18  Identities=50%  Similarity=0.719  Sum_probs=16.0

Q ss_pred             cccCcEEEeCCCCCChhH
Q psy3462         289 NKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       289 ~~~~~~l~EaPTGTGKTl  306 (795)
                      ..++++++|+|+|||||+
T Consensus        41 ~~~~~vll~G~PG~gKT~   58 (329)
T COG0714          41 LAGGHVLLEGPPGVGKTL   58 (329)
T ss_pred             HcCCCEEEECCCCccHHH
Confidence            357899999999999995

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=81.57  E-value=0.97  Score=56.09  Aligned_cols=25  Identities=28%  Similarity=0.219  Sum_probs=21.2

Q ss_pred             EEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         294 CLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       294 ~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      -+.|++||+||||++++|++..+..
T Consensus        98 ~IaEm~TGEGKTL~a~lp~~l~al~  122 (908)
T PRK13107         98 RIAEMRTGEGKTLTATLPAYLNALT  122 (908)
T ss_pred             ccccccCCCCchHHHHHHHHHHHhc
Confidence            4789999999999999998765543

>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

Probab=81.44  E-value=1.4  Score=46.11  Aligned_cols=32  Identities=22%  Similarity=0.280  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTL   54 (795)
                      .+|.+.-.++.=|...+.++++.+|.|||||+
T Consensus         6 ~GQe~aKrAL~iAAaG~h~lLl~GppGtGKTm   37 (206)
T PF01078_consen    6 VGQEEAKRALEIAAAGGHHLLLIGPPGTGKTM   37 (206)
T ss_dssp             SSTHHHHHHHHHHHHCC--EEEES-CCCTHHH
T ss_pred             cCcHHHHHHHHHHHcCCCCeEEECCCCCCHHH
Confidence            46777777777777788899999999999994

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK10536 hypothetical protein; Provisional

Probab=81.37  E-value=1.7  Score=47.14  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=17.8

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHH
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l  313 (795)
                      ..++++.||+|||||+-.+..++
T Consensus        74 ~~lV~i~G~aGTGKT~La~a~a~   96 (262)
T PRK10536         74 KQLIFATGEAGCGKTWISAAKAA   96 (262)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999975555444

>PRK06526 transposase; Provisional

Probab=81.37  E-value=1.3  Score=47.26  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=15.7

Q ss_pred             cccCcEEEeCCCCCChhH
Q psy3462         289 NKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       289 ~~~~~~l~EaPTGTGKTl  306 (795)
                      ..+.++++-||+|||||.
T Consensus        96 ~~~~nlll~Gp~GtGKTh  113 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTH  113 (254)
T ss_pred             hcCceEEEEeCCCCchHH
Confidence            356789999999999995

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=81.25  E-value=2.1  Score=47.15  Aligned_cols=39  Identities=23%  Similarity=0.217  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+++.++.+++.++++++.+|||+||| .+|.+++...-.
T Consensus       131 ~~~ayL~~~ie~~~siii~G~t~sGKT-t~lnall~~Ip~  169 (312)
T COG0630         131 EQAAYLWLAIEARKSIIICGGTASGKT-TLLNALLDFIPP  169 (312)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHH-HHHHHHHHhCCc
Confidence            345668999999999999999999999 455555555443

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=81.22  E-value=2.2  Score=55.03  Aligned_cols=35  Identities=17%  Similarity=0.261  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      +.-++|.+++.++..+|+.|+||||||.  .+|.+.+
T Consensus        77 ~~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~ll  111 (1294)
T PRK11131         77 QKKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICL  111 (1294)
T ss_pred             HHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHH
Confidence            4447889999998999999999999998  5784443

>PRK06526 transposase; Provisional

Probab=81.06  E-value=1.7  Score=46.37  Aligned_cols=21  Identities=29%  Similarity=0.509  Sum_probs=17.5

Q ss_pred             HHHHhcCCcEEEECCCCCchH
Q psy3462          33 IQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        33 ~~al~~~~~~llEAPTGTGKT   53 (795)
                      .+-+.++.++++.||+|||||
T Consensus        92 ~~fi~~~~nlll~Gp~GtGKT  112 (254)
T PRK06526         92 LDFVTGKENVVFLGPPGTGKT  112 (254)
T ss_pred             CchhhcCceEEEEeCCCCchH
Confidence            344566789999999999999

>KOG0336|consensus

Probab=81.04  E-value=0.59  Score=53.42  Aligned_cols=35  Identities=23%  Similarity=0.152  Sum_probs=28.9

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +-|-+..+..++--|.|||||||+||.|.+..+..
T Consensus       250 aWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~a  284 (629)
T KOG0336|consen  250 AWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDA  284 (629)
T ss_pred             ccceeecCcceEEEEecCCCcCHHHhccceeeeec
Confidence            44446788899999999999999999998776544

>KOG0349|consensus

Probab=80.98  E-value=0.94  Score=52.15  Aligned_cols=37  Identities=27%  Similarity=0.254  Sum_probs=31.0

Q ss_pred             HHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         282 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       282 ~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ++.||-|..++.++..|.||+|||=||.+|+|...-.
T Consensus        30 aeaiplilgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen   30 AEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             cccccEEecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            3556777889999999999999999999999766543

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=80.97  E-value=1.2  Score=42.87  Aligned_cols=17  Identities=47%  Similarity=0.661  Sum_probs=10.4

Q ss_pred             ccCcEEEeCCCCCChhH
Q psy3462         290 KAKNCLLESPTGSGKTL  306 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTl  306 (795)
                      .+.++++.||.|+|||-
T Consensus        23 ~~~~~ll~G~~G~GKT~   39 (185)
T PF13191_consen   23 SPRNLLLTGESGSGKTS   39 (185)
T ss_dssp             ----EEE-B-TTSSHHH
T ss_pred             CCcEEEEECCCCCCHHH
Confidence            35789999999999995

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=80.65  E-value=1.9  Score=43.18  Aligned_cols=28  Identities=29%  Similarity=0.363  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          26 KILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        26 ~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +++++.+.++.....+++|++++||||+
T Consensus         9 ~~~~~~~~~~a~~~~pVlI~GE~GtGK~   36 (168)
T PF00158_consen    9 KRLREQAKRAASSDLPVLITGETGTGKE   36 (168)
T ss_dssp             HHHHHHHHHHTTSTS-EEEECSTTSSHH
T ss_pred             HHHHHHHHHHhCCCCCEEEEcCCCCcHH
Confidence            3666777777777889999999999999

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=80.34  E-value=1.6  Score=48.85  Aligned_cols=26  Identities=38%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             HHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          28 LHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        28 mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +.+-+..++..+.++++-+|||+|||
T Consensus       151 ~~~~l~~~v~~~~nilI~G~tGSGKT  176 (344)
T PRK13851        151 LEAFLHACVVGRLTMLLCGPTGSGKT  176 (344)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCccHH
Confidence            44556667778899999999999999

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=80.18  E-value=2.3  Score=49.17  Aligned_cols=37  Identities=30%  Similarity=0.270  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHhc----------------CCcEEEECCCCCchH-HHHHHH
Q psy3462          23 SSCKILHLQVIQGCNK----------------AKNCLLESPTGSGKT-LALLCS   59 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~----------------~~~~llEAPTGTGKT-LAyL~p   59 (795)
                      -+|.+....+..++.+                ..++++.+|||+||| +|-.++
T Consensus        18 iGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LA   71 (443)
T PRK05201         18 IGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLA   71 (443)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHH
Confidence            4677777777766643                368999999999999 444333

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=80.13  E-value=6.4  Score=49.70  Aligned_cols=55  Identities=24%  Similarity=0.323  Sum_probs=40.0

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .|.++-....+|.|...|+-    =.+-+-.|+.--+.||||+|||-=-++-++..+.+
T Consensus        70 ~~~~fF~k~~G~~~ws~QR~----WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~k  124 (1187)
T COG1110          70 EFEEFFKKATGFRPWSAQRV----WAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKK  124 (1187)
T ss_pred             HHHHHHHHhhCCCchHHHHH----HHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhc
Confidence            34455555667899999944    44556677888889999999997666667777653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	795
2zkr_x	125	Structure Of A Mammalian Ribosomal 60s Subunit With		1e-21
2go5_6	123	Structure Of Signal Recognition Particle Receptor (		3e-18
3izr_g	123	Localization Of The Large Subunit Ribosomal Protein		2e-16
1s1i_W	112	Structure Of The Ribosomal 80s-Eef2-Sordarin Comple		4e-16
2ww9_M	113	Cryo-Em Structure Of The Active Yeast Ssh1 Complex		4e-16
4a17_W	111	T.Thermophila 60s Ribosomal Subunit In Complex With		7e-15
3jyw_W	79	Structure Of The 60s Proteins For Eukaryotic Riboso		8e-14
3zf7_h	188	High-resolution Cryo-electron Microscopy Structure		4e-09
3j21_a	95	Promiscuous Behavior Of Proteins In Archaeal Riboso		1e-04

>pdb|2ZKR|XX Chain x, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 125

Iteration: 1
 Score =  101 bits (252), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 45/66 (68%), Positives = 56/66 (84%)
Query: 117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIW 176
           +  +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F  K+MGT DVRIDTRLNK +W
Sbjct: 14  RSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVW 73
Query: 177 SKGINN 182
           +KGI N
Sbjct: 74  AKGIRN 79

>pdb|2GO5|6 Chain 6, Structure Of Signal Recognition Particle Receptor (Sr) In Complex With Signal Recognition Particle (Srp) And Ribosome Nascent Chain Complex Length = 123

Iteration: 1
 Score = 90.9 bits (224), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 42/70 (60%), Positives = 53/70 (75%), Gaps = 3/70 (4%)
Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
           + P  +K   +EVVTR+YT+++HKRLH   FKK+AP AIK +R F +K MGT DVRID +
Sbjct: 6   RAPGPRK---DEVVTREYTVNLHKRLHGCTFKKKAPNAIKEIRKFAQKAMGTNDVRIDVK 62
Query: 171 LNKHIWSKGI 180
           LNKHIWS GI
Sbjct: 63  LNKHIWSSGI 72

>pdb|3IZR|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 123

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 40/69 (57%), Positives = 52/69 (75%), Gaps = 2/69 (2%)
Query: 111 KKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTR 170
           K+ A  +K  +EVVTR+YTI++HKRLH   FKK+AP AIK +R F +K MGT D+RID +
Sbjct: 5   KRGAGTRK--DEVVTREYTINLHKRLHGCTFKKKAPNAIKEIRKFAQKAMGTTDIRIDVK 62
Query: 171 LNKHIWSKG 179
           LNK IW+ G
Sbjct: 63  LNKAIWTNG 71

>pdb|1S1I|W Chain W, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h Length = 112

Iteration: 1
 Score = 83.6 bits (205), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKG 179
           L +VVTR+YTI++HKRLH V FKKRAPRA+K ++ F K  MGT+DVR+   LN+ IW +G
Sbjct: 3   LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRG 62
Query: 180 I 180
           +
Sbjct: 63  V 63

>pdb|2WW9|M Chain M, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound To The Yeast 80s Ribosome Length = 113

Iteration: 1
 Score = 83.6 bits (205), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKG 179
           L +VVTR+YTI++HKRLH V FKKRAPRA+K ++ F K  MGT+DVR+   LN+ IW +G
Sbjct: 4   LKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRG 63
Query: 180 I 180
           +
Sbjct: 64  V 64

>pdb|4A17|W Chain W, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 5s Rrna, 5.8s Rrna And Proteins Of Molecule 2. Length = 111

Iteration: 1
 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 35/56 (62%), Positives = 44/56 (78%)
Query: 127 DYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINN 182
           D T+++HK+ HK+ FKK+APRAI+ + A  KK MGT+DVRIDT LNK IWS GI N
Sbjct: 10  DTTVNLHKQCHKISFKKKAPRAIREIVAIAKKTMGTDDVRIDTELNKFIWSNGIRN 65

>pdb|3JYW|W Chain W, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 79

Iteration: 1
 Score = 75.9 bits (185), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 33/56 (58%), Positives = 44/56 (78%)
Query: 125 TRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
           TR+YTI++HKRLH V FKKRAPRA+K ++ F K  MGT+DVR+   LN+ IW +G+
Sbjct: 1   TREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGV 56

>pdb|3ZF7|HH Chain h, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 188

Iteration: 1
 Score = 60.5 bits (145), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/66 (51%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 115 TKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKH 174
           T +KP N V+  + +IH+ K L K  F KRAP AIK +R+FV K M T+D RID  LN  
Sbjct: 77  TGRKPDNIVM--EASIHLSKLLKKRTFHKRAPIAIKRIRSFVGKLMKTKDNRIDASLNTF 134
Query: 175 IWSKGI 180
           IW KG+
Sbjct: 135 IWHKGV 140

>pdb|3J21|AA Chain a, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Proteins) Length = 95

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/38 (50%), Positives = 27/38 (71%)
Query: 143 KRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
           KRAPRA+K VR FV +    ++V ID ++N+ IW +GI
Sbjct: 26  KRAPRAVKFVREFVARHAKAQEVIIDPKVNEKIWERGI 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	795
3iz5_G	219	60S ribosomal protein L6 (L6E); eukaryotic ribosom	2e-30
3u5e_D	297	60S ribosomal protein L5; translation, ribosome, r	4e-29
2zkr_x	125	60S ribosomal protein L31; protein-RNA complex, 60	7e-29
4a17_W	111	RPL31, 60S ribosomal protein L31; eukaryotic ribos	5e-28
1vq8_X	92	50S ribosomal protein L31E; ribosome 50S, protein-	1e-27
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	4e-04
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	1e-15
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	5e-04
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	4e-13
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-09

>3u5e_D 60S ribosomal protein L5; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_D 3izc_Q 3izs_Q 3o58_E 3o5h_E 3jyw_E 1s1i_E Length = 297

 Score =  111 bits (278), Expect = 4e-29
 Identities = 8/63 (12%), Positives = 16/63 (25%)

Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKG 179
             +  +  Y+        +    K      K +    K +  T   R+  R         
Sbjct: 4   QKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQ 63

Query: 180 INN 182
           I +
Sbjct: 64  IIS 66

>2zkr_x 60S ribosomal protein L31; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 125

 Score =  110 bits (277), Expect = 7e-29
 Identities = 50/75 (66%), Positives = 60/75 (80%), Gaps = 3/75 (4%)

Query: 111 KKPATKKK---PLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRI 167
           KK   KKK    +NEVVTR+YTI++HKR+H VGFKKRAPRA+K +R F  K+MGT DVRI
Sbjct: 5   KKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRI 64

Query: 168 DTRLNKHIWSKGINN 182
           DTRLNK +W+KGI N
Sbjct: 65  DTRLNKAVWAKGIRN 79

>4a17_W RPL31, 60S ribosomal protein L31; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_W 4a1c_W 4a1e_W Length = 111

 Score =  107 bits (270), Expect = 5e-28
 Identities = 36/62 (58%), Positives = 46/62 (74%)

Query: 121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGI 180
            E  + D T+++HK+ HK+ FKK+APRAI+ + A  KK MGT+DVRIDT LNK IWS GI
Sbjct: 4   QEEKSIDTTVNLHKQCHKISFKKKAPRAIREIVAIAKKTMGTDDVRIDTELNKFIWSNGI 63

Query: 181 NN 182
            N
Sbjct: 64  RN 65

>1vq8_X 50S ribosomal protein L31E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: d.29.1.1 PDB: 1vq4_X* 1vq5_X* 1vq6_X* 1vq7_X* 1s72_X* 1vq9_X* 1vqk_X* 1vql_X* 1vqm_X* 1vqn_X* 1vqo_X* 1vqp_X* 1yhq_X* 1yi2_X* 1yij_X* 1yit_X* 1yj9_X* 1yjn_X* 1yjw_X* 2otj_X* ... Length = 92

 Score =  105 bits (265), Expect = 1e-27
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTED--VRIDTRLNKHIWS 177
            ++   R  TI +          KRA +A+ ++R  + K    ++  VR+D  +N+  W+
Sbjct: 3   ASDFEERVVTIPLRD-ARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWA 61

Query: 178 KGINN 182
           +G  N
Sbjct: 62  RGRAN 66

>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

 Score = 85.5 bits (211), Expect = 2e-17
 Identities = 16/59 (27%), Positives = 28/59 (47%)

Query: 612 GLLKGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQ 670
                   ++I A   + QA+GR IR   D   + L+D+RF S   ++ L     N+++
Sbjct: 492 NRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRFESLYWKKNLKCLNANKMK 550

>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

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQK-MFEQRTQDLQKIPFRK 342
           VI+G        L +PTGSGKTL  L   L  + K   +V+    F    +DL KI  ++
Sbjct: 15  VIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNEFYPIYRDLTKIREKR 74

Query: 343 -LKISRLKAKD 352
            +  S L  K 
Sbjct: 75  NITFSFLVGKP 85

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

 Score = 79.6 bits (196), Expect = 1e-15
 Identities = 11/50 (22%), Positives = 18/50 (36%)

Query: 615 KGGDWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKW 664
                        + Q +GR  R   D+  I L D R+    +  G+S+ 
Sbjct: 485 DEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRYREYFADLGISEK 534

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

 Score = 42.7 bits (100), Expect = 5e-04
 Identities = 19/107 (17%), Positives = 30/107 (28%), Gaps = 25/107 (23%)

Query: 246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKT 305
             ++    Q   + +                        I      K  LL +  G GKT
Sbjct: 4   LKLQLRQWQAEKLGEA-----------------------INALKHGKTLLLNAKPGLGKT 40

Query: 306 LALLCSVLAWQRKEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKD 352
           + +    L  Q K+K L+  +   Q     +      LK   L  K 
Sbjct: 41  VFVEV--LGMQLKKKVLIFTRTHSQLDSIYKNAKLLGLKTGFLIGKS 85

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

 Score = 71.7 bits (176), Expect = 4e-13
 Identities = 12/74 (16%), Positives = 23/74 (31%), Gaps = 10/74 (13%)

Query: 618 DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNT 677
                     + Q +GR IR   D GA +++D+R         +    +         + 
Sbjct: 551 YSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRAGQFRKF--IPDMKKT--------SD 600

Query: 678 FMENLRNFVRRRME 691
              ++ NF      
Sbjct: 601 PASDIYNFFISAQA 614

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

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELV-----QQKMFEQRTQDLQKI 338
           +     K+    LESPTGSGKT+  L S L +  + K  V          EQ  ++L+ +
Sbjct: 15  LRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSL 74

Query: 339 PFR-KLKISRLKAKD 352
               K++   ++ + 
Sbjct: 75  SSTMKIRAIPMQGRV 89

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

 Score = 70.7 bits (172), Expect = 1e-12
 Identities = 85/598 (14%), Positives = 173/598 (28%), Gaps = 188/598 (31%)

Query: 2   TKKSSDIFKTYL-------NEPNYFLKYSSCKILHLQVIQGC----NKAKNCLLESPTGS 50
            ++ S + + Y+       N+   F KY+  ++     ++        AKN L++   GS
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS 161

Query: 51  GKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVF------CGRSDFF------L 98
           GK      + +A        VQ KM  +          +F      C   +        L
Sbjct: 162 GK------TWVALDVCLSYKVQCKMDFK----------IFWLNLKNCNSPETVLEMLQKL 205

Query: 99  LFRERRISDTMVKKPATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKK 158
           L++      +     +  K  ++ +          +RL K    K     + V+      
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAEL------RRLLK---SKPYENCLLVLL----- 251

Query: 159 QMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAKCHKEMRYRNRVVKLTGFDQLIGE 218
                +V+     N   W+            F+    C        +++ LT   +    
Sbjct: 252 -----NVQ-----NAKAWN-----------AFN--LSC--------KIL-LTTRFK---- 275

Query: 219 SAVLPSVKDKLKPSAATSYTIGGVKVEFPVKAYPSQISMMNQVSNLFEQPNH---FLKYS 275
                 V D L  +  T  +                   ++  S            LKY 
Sbjct: 276 -----QVTDFLSAATTTHIS-------------------LDHHSMTLTPDEVKSLLLKYL 311

Query: 276 SCKILHL--QVIQGCNKAKNCLLESPTGSGKTLALLCSVLA---------WQR------- 317
            C+   L  +V+            +P           S++A         W         
Sbjct: 312 DCRPQDLPREVLTT----------NP--------RRLSIIAESIRDGLATWDNWKHVNCD 353

Query: 318 KEKELVQQKMFEQRTQDLQKIPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDEL 377
           K   +++  +      + +K+ F +L +       F  +  +   LL  +   +  + ++
Sbjct: 354 KLTTIIESSLNVLEPAEYRKM-FDRLSV-------FPPSAHIPTILL-SLIWFDVIKSDV 404

Query: 378 RQSTKKTRVDKLKVLNGRSKNLVSSI-DFILGLLYKGI------QTCITTINQQEDELRQ 430
                K    K  ++  + K    SI    L L  K        ++ +   N  +     
Sbjct: 405 MVVVNKLH--KYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462

Query: 431 STKKTKVDK---------LKVL-NGRSKNLVSSIDFILGLLYKGVNCEDYHVCMESSVAF 480
                 +D+         LK + +     L   +      L + +  +        S+  
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSIL- 521

Query: 481 DQLIQLDLMLD---EHLNPYVLKVKDTPCIED-LEQFSTRALVSPCFQLIQLDLMLDE 534
           + L QL        ++   Y   V     I D L +     + S    L+++ LM ++
Sbjct: 522 NTLQQLKFYKPYICDNDPKYERLVNA---ILDFLPKIEENLICSKYTDLLRIALMAED 576

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

 Score = 59.5 bits (143), Expect = 3e-09
 Identities = 84/584 (14%), Positives = 158/584 (27%), Gaps = 180/584 (30%)

Query: 352 DFSTNNGMEQQLLTC--ITTINQQ-----------EDELRQSTKKTRVDKLKVLNGRSKN 398
           DF T    E Q      I ++ +            +D  +    K  +D   ++   SK+
Sbjct: 8   DFETG---EHQY-QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID--HIIM--SKD 59

Query: 399 LVSSIDFILGLL-------------------YKGIQTCITTINQQE-------------- 425
            VS    +   L                   YK + + I T  +Q               
Sbjct: 60  AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 426 ------------------DELRQSTKKTKVDKLKVLNG--------------RSKNLVSS 453
                              +LRQ+  + +  K  +++G               S  +   
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179

Query: 454 IDFILGLLYKGV-NCEDYHVCMESSVAFDQLIQLDLMLDEHLNPYVLKVKDTPC-IEDLE 511
           +DF   + +  + NC      +E       L +L   +D +         +    I  ++
Sbjct: 180 MDF--KIFWLNLKNCNSPETVLE------MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 512 QFSTRALVSPCFQ--LIQLDLMLDEHLNPYVLKVKDTPC-IEDLVLKRNIFYDTLMLCDV 568
               R L S  ++  L    L+L    N       +  C I  L+  R       +   +
Sbjct: 232 AELRRLLKSKPYENCL----LVLLNVQNAKAWNAFNLSCKI--LLTTR----FKQVTDFL 281

Query: 569 QTKETKHRDSVKQVMG---KGNLELCKGVFWTRF----PNTCQYSVVYPTGL------LK 615
               T H       M         L       R           +   P  L      ++
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN---PRRLSIIAESIR 338

Query: 616 GG----DWYQIQAYRALNQALGRCI--------RHRYDWGAILLVDQRFYSKNSQQGLSK 663
            G    D ++      L   +   +        R  +D  ++        +      LS 
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS----AHIPTILLSL 394

Query: 664 -W---VRNQVQN--TSSHNTFM--ENLRNFVRRRMEIQLEEERVKREEANLNEE------ 709
            W   +++ V       H   +  +  +        I LE +     E  L+        
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454

Query: 710 -EEVMDDTDRASSSQES----------TGGTQSQNSTVMPQ-----RWAYLSLLKKLSPL 753
             +  D  D      +                 +  T+        R+    L +K+   
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF----LEQKIRHD 510

Query: 754 APTWGPPLKIQS-VPQVIFHKP--CDNKSIF--KLISIKYMLIR 792
           +  W     I + + Q+ F+KP  CDN   +   + +I   L +
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPK 554

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	795
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.97
3iz5_g	123	60S ribosomal protein L31 (L31E); eukaryotic ribos	99.96
3u5e_d	113	L34, YL28, 60S ribosomal protein L31-A; translatio	99.96
2zkr_x	125	60S ribosomal protein L31; protein-RNA complex, 60	99.96
3j21_a	95	50S ribosomal protein L31E; archaea, archaeal, KIN	99.96
4a17_W	111	RPL31, 60S ribosomal protein L31; eukaryotic ribos	99.95
1vq8_X	92	50S ribosomal protein L31E; ribosome 50S, protein-	99.95
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.91
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.88
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.24
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.02
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.95
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.39
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.36
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.31
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.28
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.26
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.25
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	98.24
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	98.22
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.21
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	98.2
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.19
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.15
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	98.15
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.15
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.1
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	98.08
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.07
3bor_A	237	Human initiation factor 4A-II; translation initiat	98.03
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.0
3b6e_A	216	Interferon-induced helicase C domain-containing P;	97.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	97.97
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	97.96
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	97.91
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	97.88
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	97.87
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	97.85
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	97.82
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	97.81
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	97.81
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	97.8
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	97.78
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.77
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	97.76
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	97.76
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	97.72
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	97.71
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	97.7
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	97.7
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	97.7
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	97.69
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	97.68
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	97.64
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	97.61
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	97.59
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	97.57
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	97.56
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	97.56
3b6e_A	216	Interferon-induced helicase C domain-containing P;	97.55
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	97.53
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	97.53
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	97.52
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	97.5
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	97.49
3bor_A	237	Human initiation factor 4A-II; translation initiat	97.47
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	97.45
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	97.45
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	97.44
4gl2_A	699	Interferon-induced helicase C domain-containing P;	97.44
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	97.41
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	97.38
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	97.37
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	97.31
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	97.29
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	97.28
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	97.27
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	97.26
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	97.26
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	97.25
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	97.25
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.23
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	97.22
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	97.22
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.2
4gl2_A	699	Interferon-induced helicase C domain-containing P;	97.19
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	97.17
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	97.13
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	97.11
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	97.1
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	97.09
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	97.08
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	97.08
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	97.07
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	97.06
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.02
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	97.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	96.98
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	96.97
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	96.96
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	96.96
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.94
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	96.9
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.9
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	96.88
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	96.83
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.83
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	96.82
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	96.82
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	96.82
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.81
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	96.8
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.78
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	96.73
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	96.73
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	96.68
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	96.66
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	96.62
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	96.55
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	96.55
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.54
3h1t_A	590	Type I site-specific restriction-modification syst	96.48
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	96.4
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	96.4
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	96.4
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.37
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	96.32
1yks_A	440	Genome polyprotein [contains: flavivirin protease	96.3
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	96.25
3h1t_A	590	Type I site-specific restriction-modification syst	96.24
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	96.12
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	96.08
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	96.08
1yks_A	440	Genome polyprotein [contains: flavivirin protease	96.03
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	96.03
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	95.83
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	95.79
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	95.79
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.75
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	95.75
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	95.7
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	95.7
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	95.54
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.41
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	95.07
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	94.91
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	94.68
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	94.47
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	94.43
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	93.72
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	93.57
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	93.53
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	93.08
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	92.66
3jux_A	822	Protein translocase subunit SECA; protein transloc	92.52
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	91.93
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	91.61
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.22
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	91.16
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	90.77
2r44_A	331	Uncharacterized protein; putative ATPase, structur	90.67
3co5_A	143	Putative two-component system transcriptional RES	90.64
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	90.32
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	90.21
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	89.32
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.92
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	88.4
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	88.38
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	88.28
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	87.93
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	87.52
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	87.42
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	87.35
2qgz_A	308	Helicase loader, putative primosome component; str	87.34
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	87.13
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	86.96
2chg_A	226	Replication factor C small subunit; DNA-binding pr	86.55
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	86.32
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	86.21
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	86.13
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	86.06
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	85.88
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	85.6
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	85.42
3bos_A	242	Putative DNA replication factor; P-loop containing	85.39
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	85.29
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	85.0
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	84.45
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	83.5
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	82.73
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	82.11
3co5_A	143	Putative two-component system transcriptional RES	81.93
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	81.8
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	81.5
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	81.48
2chg_A	226	Replication factor C small subunit; DNA-binding pr	81.23
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	80.89
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	80.87
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	80.71
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	80.08

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

Probab=99.97  E-value=7.6e-32  Score=308.55  Aligned_cols=101  Identities=19%  Similarity=0.138  Sum_probs=82.0

Q ss_pred             eEeecCc---------cccceEEEEecCCCCCCCccccccc-----ccCCcccc-hHHHHHHHHHhccCccccccCceeE
Q psy3462         580 KQVMGKG---------NLELCKGVFWTRFPNTCQYSVVYPT-----GLLKGGDW-YQIQAYRALNQALGRCIRHRYDWGA  644 (795)
Q Consensus       580 fAV~GGK---------nl~rcViVVGIPYPn~~d~~Lk~~~-----~~~~G~ew-Y~~~AmRaVNQAIGRvIRHknDyGa  644 (795)
                      |||+||+         +.++||||+|||||++ |+.++...     ...+|+.| |..+||++|+||+||+|||++|||+
T Consensus       499 ~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~-~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~  577 (620)
T 4a15_A          499 FAVSGGRLSEGINFPGNELEMIILAGLPFPRP-DAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGA  577 (620)
T ss_dssp             EEETTSCC--------CCCCEEEESSCCCCCC-CHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEE
T ss_pred             EEEecCceeccccCCCCceEEEEEEcCCCCCC-CHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEE
Confidence            8999996         6899999999999999 68776321     12233444 8899999999999999999999999


Q ss_pred             EEEeecccCChhhhhhHhHHHHhhccccCChhHHHHHHHHHHHHHHH
Q psy3462         645 ILLVDQRFYSKNSQQGLSKWVRNQVQNTSSHNTFMENLRNFVRRRME  691 (795)
Q Consensus       645 IiLlD~Rf~~~~~~~~LP~WIr~~l~~~~sfe~~~~~l~~Ffk~~k~  691 (795)
                      |+|+|+||  +++++.||. ++....       ..+.+.+||...+.
T Consensus       578 v~llD~R~--~~~~~~LP~-~~~~~~-------~~~~~~~f~~~~~~  614 (620)
T 4a15_A          578 CVILDKRA--GQFRKFIPD-MKKTSD-------PASDIYNFFISAQA  614 (620)
T ss_dssp             EEEECGGG--GGGGGGSTT-CEEESC-------HHHHHHHHHHHHHT
T ss_pred             EEEEccch--HHHHHhCCc-hhhhcC-------cHHHHHHHHhChhh
Confidence            99999999  889999999 655433       34678899987743

>3u5e_d L34, YL28, 60S ribosomal protein L31-A; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_M 2ww9_M 3izc_g 3izs_g 2wwb_M 3o5h_a 3o58_a 3u5i_d 4b6a_d 1s1i_W 3jyw_W

Probab=99.96  E-value=2.4e-30  Score=238.55  Aligned_cols=78  Identities=47%  Similarity=0.776  Sum_probs=73.5

Q ss_pred             CCCCcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         117 KKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       117 ~s~~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      +|+++|++||||||||||++||++|+||||+|+++||+||+|||||+||+||++||++||++||+|||++|||+.+..
T Consensus         1 ~sa~~evvtreyTInlhK~ihgv~fkKrAprAlkeIrkFa~K~Mgt~dV~ID~~LNk~vWakGirnvP~rIrVrlsRk   78 (113)
T 3u5e_d            1 MAGLKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLRLRISRK   78 (113)
T ss_dssp             ---CCCCEEEEEEEEHHHHHTTCCTTTHHHHHHHHHHHHHHHHHCCSCEEECHHHHHHHHTTCTTCCCSEEEEEEEEE
T ss_pred             CCcccCceeeEEEEeCcceeccCCCcccCHHHHHHHHHHHHHHcCCCceEECcHHHHHHHhccccCCCceEEEEEEEe
Confidence            478999999999999999999999999999999999999999999999999999999999999999999999998765

>2zkr_x 60S ribosomal protein L31; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=99.96  E-value=4.4e-30  Score=240.43  Aligned_cols=81  Identities=57%  Similarity=0.874  Sum_probs=68.6

Q ss_pred             CCCCCCCcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEecc
Q psy3462         114 ATKKKPLNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSA  193 (795)
Q Consensus       114 k~~~s~~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~  193 (795)
                      ++++|++++++||||||||||++|+++|+||||+||++||+||+|||||+||+||++||++||++||+|||++|||+.+.
T Consensus        11 ~~~~s~~~evvtreyTInL~K~ihgv~fkKRAprAik~IrkFa~K~Mgt~dVrID~~LNk~IWskGirnvP~rIRVrlsR   90 (125)
T 2zkr_x           11 KKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIRNVPYRIRVRLSR   90 (125)
T ss_dssp             -----------CEEEEEECHHHHSSBSSSBHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHTTCSSCCCSEEEEEEEE
T ss_pred             cCCCcccccceeeEEEeccccccccCCCCccCHHHHHHHHHHHHHhcCCCcEEECHHHHHHHHhccCCCCCceEEEEEEE
Confidence            34899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             c
Q psy3462         194 A  194 (795)
Q Consensus       194 ~  194 (795)
                      .
T Consensus        91 k   91 (125)
T 2zkr_x           91 K   91 (125)
T ss_dssp             E
T ss_pred             e
Confidence            5

>3j21_a 50S ribosomal protein L31E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=99.96  E-value=1.4e-29  Score=227.23  Aligned_cols=76  Identities=29%  Similarity=0.420  Sum_probs=72.7

Q ss_pred             CcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEecccc
Q psy3462         120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAAK  195 (795)
Q Consensus       120 ~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~~  195 (795)
                      ++|++||||||||||++||++|+||||+|+++||+||+|||||+||+|||+||++||++||+|||++|+|+.+...
T Consensus         3 ~~e~vtreyTInlhK~~hgv~fkKrAprAlkeIrkFa~K~mgt~dV~ID~~LNk~vWakGirnvP~rIrVrlsRk~   78 (95)
T 3j21_a            3 IKAGEEVIFTVPIKKIKKIVPRWKRAPRAVKFVREFVARHAKAQEVIIDPKVNEKIWERGIEKPPSKLRVKVKVEE   78 (95)
T ss_dssp             -CCSSCEEEEEECTTHHHHBCSGGGHHHHHHHHHHHHHHHHTCSSCEECHHHHHHHHTTCSSCCCSEEEEEEEEEC
T ss_pred             CCCCceEEEEEEChheecCCCccccCHHHHHHHHHHHHHhcCCCcEEEChHHHHHHHhccccCCCCeEEEEEEEec
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999987653

>4a17_W RPL31, 60S ribosomal protein L31; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_W 4a1c_W 4a1e_W

Probab=99.95  E-value=3.5e-29  Score=230.19  Aligned_cols=74  Identities=49%  Similarity=0.700  Sum_probs=71.7

Q ss_pred             cccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCCeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         121 NEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTEDVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       121 ~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      .|++||||||||||++||++|+||||+|+++||+||+|||||+||+||++||++||++||+|||++|||+.+..
T Consensus         4 ~~vvtreyTInlhK~ihgv~fkKrAprAlkeIrkFa~K~Mgt~dV~ID~~LNk~vWakGirnvP~rIrVrlsRk   77 (111)
T 4a17_W            4 QEEKSIDTTVNLHKQCHKISFKKKAPRAIREIVAIAKKTMGTDDVRIDTELNKFIWSNGIRNIPRRVRVRLCKR   77 (111)
T ss_dssp             CCCCEEEEEEEHHHHTTTCCGGGHHHHHHHHHHHHHHHHHCCSCEEECHHHHHHHHTTCSSSCCSEEEEEEEEE
T ss_pred             CcceEEEEEEECeeeeecCCccccCHHHHHHHHHHHHHHcCCCceEECcHHHHHHHhccccCCCcEEEEEEEEe
Confidence            47899999999999999999999999999999999999999999999999999999999999999999998765

>1vq8_X 50S ribosomal protein L31E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: d.29.1.1 PDB: 1vq4_X* 1vq5_X* 1vq6_X* 1vq7_X* 1s72_X* 1vq9_X* 1vqk_X* 1vql_X* 1vqm_X* 1vqn_X* 1vqo_X* 1vqp_X* 1yhq_X* 1yi2_X* 1yij_X* 1yit_X* 1yj9_X* 1yjn_X* 1yjw_X* 2otj_X* ...

Probab=99.95  E-value=1.1e-28  Score=220.66  Aligned_cols=74  Identities=22%  Similarity=0.338  Sum_probs=67.5

Q ss_pred             CcccceeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCC--CeEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         120 LNEVVTRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTE--DVRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       120 ~~e~vtreyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~--dVrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      +++++|||||||||| +||++|+||||+|+++||+||+|||||+  ||+|||+||++||++||+|||++|||+.+..
T Consensus         3 ~~~~vtreyTInl~k-i~~~~~kkRAprAik~Irkfa~k~m~t~~~dVriD~~LNk~iW~rGir~vP~rIRVr~sR~   78 (92)
T 1vq8_X            3 ASDFEERVVTIPLRD-ARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWARGRANTPSKIRVRAARF   78 (92)
T ss_dssp             -----CEEEEEECGG-GGGSCGGGHHHHHHHHHHHHHHHHTTCCGGGEEECHHHHHHHTTTCSSCCCSEEEEEEEEE
T ss_pred             cccceeEEEEEEhHH-hcCCCccccCHHHHHHHHHHHHHHhCCCcccEEECcHHHHHHHhcccCCCCceEEEEEEEE
Confidence            468899999999999 9999999999999999999999999999  9999999999999999999999999998764

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

Probab=99.91  E-value=5e-24  Score=239.52  Aligned_cols=108  Identities=17%  Similarity=0.155  Sum_probs=85.0

Q ss_pred             cCcEEEcCCCcchhhHHhhhcc---cce-eEeecCc-----c-------ccceEEEEecCCCCCCCcccccc----cccC
Q psy3462         555 KRNIFYDTLMLCDVQTKETKHR---DSV-KQVMGKG-----N-------LELCKGVFWTRFPNTCQYSVVYP----TGLL  614 (795)
Q Consensus       555 ~K~IFiE~kd~~e~~~~L~~Y~---~ai-fAV~GGK-----n-------l~rcViVVGIPYPn~~d~~Lk~~----~~~~  614 (795)
                      .++||+|+++++ ..++++.|+   .+| |||+||+     +       ..+||||+|||||++ |+.++..    +...
T Consensus       414 ~~~v~~q~~~~~-~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~viI~~lPfp~~-dp~~~ar~~~~~~~~  491 (551)
T 3crv_A          414 SLPKYVESEDSS-VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVIVGIPYPPP-DDYLKILAQRVSLKM  491 (551)
T ss_dssp             CSSEEECCSSCC-HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEEEEESCCCCCC-SHHHHHHHHHTTCCS
T ss_pred             CCcEEEcCCCCC-HHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEEEEEcCCCCCC-CHHHHHHHHHHHHhh
Confidence            589999999753 456677773   344 9999996     2       358999999999999 9988732    2121


Q ss_pred             Ccccc---hHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhHhHHHHhhcccc
Q psy3462         615 KGGDW---YQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGLSKWVRNQVQNT  672 (795)
Q Consensus       615 ~G~ew---Y~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~LP~WIr~~l~~~  672 (795)
                      .+++|   |..+||++|+||+||+|||++|||+|+|+|+||..        +|+...+.+.
T Consensus       492 g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~~~--------~~~~~~~~~~  544 (551)
T 3crv_A          492 NRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRFES--------LYWKKNLKCL  544 (551)
T ss_dssp             STTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESGGGGS--------HHHHHHTTCT
T ss_pred             CCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeehhccc--------chhhhhceeC
Confidence            22356   88999999999999999999999999999999976        5777766543

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.88  E-value=1.8e-23  Score=234.84  Aligned_cols=106  Identities=16%  Similarity=0.092  Sum_probs=80.4

Q ss_pred             cCcEEEcCCCcchhhHHhhhcc--cce-eEeecCc--------c---ccceEEEEecCCCCCCCccccccc-----ccCC
Q psy3462         555 KRNIFYDTLMLCDVQTKETKHR--DSV-KQVMGKG--------N---LELCKGVFWTRFPNTCQYSVVYPT-----GLLK  615 (795)
Q Consensus       555 ~K~IFiE~kd~~e~~~~L~~Y~--~ai-fAV~GGK--------n---l~rcViVVGIPYPn~~d~~Lk~~~-----~~~~  615 (795)
                      .+++|+|+++ .+.+.++++|+  .+| |||+||+        +   +.+||||+|+|||++.|+.++...     ...+
T Consensus       406 ~~~~~~q~~~-~~~~~~l~~f~~~~~il~~V~~~~~~EGiD~~~~~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~  484 (540)
T 2vl7_A          406 GIPVIEENKK-TRHEEVLELMKTGKYLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGK  484 (540)
T ss_dssp             TSCEEESTTT-CCHHHHHHHHHTSCCEEEEEC---------------CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTC
T ss_pred             cCceEecCCC-CcHHHHHHHHhcCCeEEEEEecCceecceecCCCcccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCC
Confidence            3789999886 56777888884  344 8999986        2   589999999999999999887321     1122


Q ss_pred             cc-cchHHHHHHHHHhccCccccccCceeEEEEeecccCChhhhhhH
Q psy3462         616 GG-DWYQIQAYRALNQALGRCIRHRYDWGAILLVDQRFYSKNSQQGL  661 (795)
Q Consensus       616 G~-ewY~~~AmRaVNQAIGRvIRHknDyGaIiLlD~Rf~~~~~~~~L  661 (795)
                      +. ++....+|++++||+||+|||++|||+|+|+|+||...+|...|
T Consensus       485 ~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~R~~~~~yg~~l  531 (540)
T 2vl7_A          485 DEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRYREYFADLGI  531 (540)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESGGGGGGTTTTTC
T ss_pred             ChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEccccCcchhhccc
Confidence            22 23344559999999999999999999999999999998877666

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

Probab=99.24  E-value=5.1e-12  Score=145.09  Aligned_cols=64  Identities=25%  Similarity=0.215  Sum_probs=55.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccccccc
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFL   98 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l   98 (795)
                      |.|||+|.+||++|++++.+++++++|||||||||+|||+|++.++..                 .+++++||+|||.+.
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~-----------------~~~kvli~t~T~~l~   64 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE-----------------RKLKVLYLVRTNSQE   64 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH-----------------HTCEEEEEESSHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh-----------------cCCeEEEECCCHHHH
Confidence            789999999999999999999999999999999999999999999753                 136899999999865


Q ss_pred             c
Q psy3462          99 L   99 (795)
Q Consensus        99 ~   99 (795)
                      .
T Consensus        65 ~   65 (620)
T 4a15_A           65 E   65 (620)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=99.02  E-value=2.9e-10  Score=127.98  Aligned_cols=61  Identities=30%  Similarity=0.263  Sum_probs=55.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccc
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFF   97 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~   97 (795)
                      +|.|||.|.+||++|++++.++++++++||||||||+|||+|++.                     ..++++|+++||.+
T Consensus         1 ~~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---------------------~~~~v~i~~pt~~l   59 (551)
T 3crv_A            1 MVKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---------------------VKPKVLFVVRTHNE   59 (551)
T ss_dssp             CCSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---------------------HCSEEEEEESSGGG
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---------------------CCCeEEEEcCCHHH
Confidence            368999999999999999999999999999999999999999987                     14789999999985


Q ss_pred             cc
Q psy3462          98 LL   99 (795)
Q Consensus        98 l~   99 (795)
                      ..
T Consensus        60 ~~   61 (551)
T 3crv_A           60 FY   61 (551)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.95  E-value=5.3e-10  Score=125.87  Aligned_cols=62  Identities=18%  Similarity=0.073  Sum_probs=51.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccc
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSD   95 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth   95 (795)
                      +++|.|||+|.+||.+|++++.++++++++||||||||+|||+|++.+                     .++++|+++||
T Consensus         3 ~~~~~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~---------------------~~~~~~~~~t~   61 (540)
T 2vl7_A            3 VLKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL---------------------KKKVLIFTRTH   61 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH---------------------TCEEEEEESCH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC---------------------CCcEEEEcCCH
Confidence            456799999999999999999999999999999999999999998642                     47999999999


Q ss_pred             ccc
Q psy3462          96 FFL   98 (795)
Q Consensus        96 ~~l   98 (795)
                      .+.
T Consensus        62 ~l~   64 (540)
T 2vl7_A           62 SQL   64 (540)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            854

>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}

Probab=98.39  E-value=4.5e-07  Score=89.14  Aligned_cols=47  Identities=17%  Similarity=0.107  Sum_probs=38.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .++..|++.|.    +++..+.+++++++.||||+|||++|++|++..+..
T Consensus        38 ~g~~~~~~~Q~----~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~   84 (228)
T 3iuy_A           38 VGILKPTPIQS----QAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDS   84 (228)
T ss_dssp             HTCCSCCHHHH----HHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCHHHH----HHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            36779999995    445566678999999999999999999999987653

>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

Probab=98.36  E-value=7e-07  Score=89.08  Aligned_cols=51  Identities=18%  Similarity=0.103  Sum_probs=40.7

Q ss_pred             HHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          12 YLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        12 ~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+...++..|++.|.+.+    .++.+++++++.||||+|||++|++|++..+..
T Consensus        43 ~l~~~g~~~~~~~Q~~~i----~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           43 VIARQNFTEPTAIQAQGW----PVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             HHHTTTCCSCCHHHHHHH----HHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHCCCCCCCHHHHHHH----HHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            344456778999995544    555578899999999999999999999987653

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

Probab=98.31  E-value=1.4e-06  Score=86.00  Aligned_cols=50  Identities=40%  Similarity=0.397  Sum_probs=40.9

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +...++..|++.|.    +++.++.+++++++.||||+|||++|++|++..+..
T Consensus        40 l~~~~~~~~~~~Q~----~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~   89 (236)
T 2pl3_A           40 LQEAQYRLVTEIQK----QTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYR   89 (236)
T ss_dssp             HHHTTCCBCCHHHH----HHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCCCHHHH----HHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHh
Confidence            34457789999995    445556678999999999999999999999987754

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

Probab=98.28  E-value=1.3e-06  Score=84.01  Aligned_cols=50  Identities=16%  Similarity=0.052  Sum_probs=39.9

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.+...++..|++.|.+.+    +++.+++++++.||||+|||++|++|++...
T Consensus        16 ~~l~~~g~~~~~~~Q~~~i----~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~   65 (206)
T 1vec_A           16 MGIFEMGWEKPSPIQEESI----PIALSGRDILARAKNGTGKSGAYLIPLLERL   65 (206)
T ss_dssp             HHHHTTTCCSCCHHHHHHH----HHHHTTCCEEEECCSSSTTHHHHHHHHHHHC
T ss_pred             HHHHHCCCCCCCHHHHHHH----HHHccCCCEEEECCCCCchHHHHHHHHHHHh
Confidence            3444557779999995554    4555678999999999999999999988764

>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

Probab=98.26  E-value=1.3e-06  Score=87.24  Aligned_cols=51  Identities=20%  Similarity=0.131  Sum_probs=40.8

Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          14 NEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        14 ~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      ...++..|++.|.+.+    +++.+++++++.||||+|||++|++|++..+...+
T Consensus        39 ~~~g~~~~~~~Q~~~i----~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~   89 (253)
T 1wrb_A           39 LLASYQRPTPIQKNAI----PAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQD   89 (253)
T ss_dssp             TTTTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTC
T ss_pred             HHCCCCCCCHHHHHHH----HHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhc
Confidence            3446778999995554    45556789999999999999999999998876543

>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}

Probab=98.25  E-value=1.3e-06  Score=86.70  Aligned_cols=46  Identities=26%  Similarity=0.296  Sum_probs=38.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..++..|++.|.+.    +.++.+++++++.||||+|||++|++|++..+
T Consensus        46 ~~g~~~~~~~Q~~~----i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l   91 (245)
T 3dkp_A           46 DAGFQMPTPIQMQA----IPVMLHGRELLASAPTGSGKTLAFSIPILMQL   91 (245)
T ss_dssp             HTTCCSCCHHHHHH----HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             HCCCCCCCHHHHHH----HHHHhCCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            34677899999544    45566678999999999999999999998765

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

Probab=98.24  E-value=2e-06  Score=90.60  Aligned_cols=52  Identities=23%  Similarity=0.234  Sum_probs=42.6

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhh
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK   68 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~   68 (795)
                      +...++..|+|.|.+    ++.++.+++++++.||||+|||++|++|++..+...+
T Consensus        30 l~~~~~~~~~~~Q~~----~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~   81 (417)
T 2i4i_A           30 IELTRYTRPTPVQKH----AIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDG   81 (417)
T ss_dssp             HHHHTCCSCCHHHHH----HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHC
T ss_pred             HHHCCCCCCCHHHHH----HHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhcc
Confidence            334577799999954    4556677899999999999999999999998876554

>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

Probab=98.22  E-value=1.8e-06  Score=84.21  Aligned_cols=51  Identities=12%  Similarity=0.076  Sum_probs=39.8

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+.+. ..++..|++.|.+.+    ..+.++.++++.||||+|||++|++|++.++
T Consensus        26 ~~~l~-~~g~~~~~~~Q~~~i----~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           26 LRGVF-GYGFEEPSAIQQRAI----MPIIEGHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             HHHHH-HHTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HHHHH-HCCCCCCcHHHHHHH----HHHhcCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            33443 346778999995544    4555678999999999999999999998775

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

Probab=98.21  E-value=1.3e-06  Score=85.55  Aligned_cols=49  Identities=18%  Similarity=0.236  Sum_probs=39.7

Q ss_pred             HHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          12 YLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        12 ~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+...++..|++.|.+.+.    ++.+++++++.||||+|||++|++|++..+
T Consensus        18 ~l~~~g~~~~~~~Q~~~i~----~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l   66 (219)
T 1q0u_A           18 AIKTLRFYKPTEIQERIIP----GALRGESMVGQSQTGTGKTHAYLLPIMEKI   66 (219)
T ss_dssp             HHHHTTCCSCCHHHHHHHH----HHHHTCCEEEECCSSHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCCCHHHHHHHH----HHhCCCCEEEECCCCChHHHHHHHHHHHHH
Confidence            3344578899999965554    445678999999999999999999988775

>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

Probab=98.20  E-value=2.1e-06  Score=82.43  Aligned_cols=50  Identities=18%  Similarity=0.092  Sum_probs=40.1

Q ss_pred             HHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          12 YLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        12 ~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+...++..|++.|.+.+    +.+.+++++++.||||+|||++|++|++..+.
T Consensus        15 ~l~~~~~~~~~~~Q~~~i----~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~   64 (207)
T 2gxq_A           15 ALHGRGLTTPTPIQAAAL----PLALEGKDLIGQARTGTGKTLAFALPIAERLA   64 (207)
T ss_dssp             HHHHTTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             HHHHcCCCCCCHHHHHHH----HHHcCCCCEEEECCCCChHHHHHHHHHHHHHh
Confidence            334457779999995554    45556789999999999999999999887754

>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}

Probab=98.19  E-value=2.4e-06  Score=86.38  Aligned_cols=54  Identities=17%  Similarity=0.036  Sum_probs=42.5

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +.+.+...++..|++.|.+.    +..+.+++++++.||||+|||++|++|++..+..
T Consensus        54 l~~~l~~~g~~~~~~~Q~~~----i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~  107 (249)
T 3ber_A           54 LCEACDQLGWTKPTKIQIEA----IPLALQGRDIIGLAETGSGKTGAFALPILNALLE  107 (249)
T ss_dssp             HHHHHHHTTCCSCCHHHHHH----HHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCHHHHHH----HHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhc
Confidence            33445556778999999554    4555677999999999999999999999877643

>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*

Probab=98.15  E-value=2.8e-06  Score=84.12  Aligned_cols=49  Identities=12%  Similarity=0.007  Sum_probs=38.9

Q ss_pred             HHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          12 YLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        12 ~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+...++..|++.|.+.+    .++.+++++++.||||+|||++|++|++..+
T Consensus        38 ~l~~~g~~~~~~~Q~~~i----~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l   86 (230)
T 2oxc_A           38 GLRAAGFERPSPVQLKAI----PLGRCGLDLIVQAKSGTGKTCVFSTIALDSL   86 (230)
T ss_dssp             HHHHTTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCCCHHHHHHH----HHHhCCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            334456667999995554    4566688999999999999999999988764

>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}

Probab=98.15  E-value=3.2e-06  Score=91.96  Aligned_cols=50  Identities=24%  Similarity=0.266  Sum_probs=41.5

Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          14 NEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        14 ~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      ...++..|+|.|    ..++..+.+++++++.||||+|||+||++|++..+...
T Consensus        72 ~~~g~~~pt~iQ----~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~  121 (434)
T 2db3_A           72 NKSGYKIPTPIQ----KCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLED  121 (434)
T ss_dssp             HHTTCCSCCHHH----HHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             HHcCCCCCCHHH----HHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhc
Confidence            345777899999    45555667889999999999999999999999887654

>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}

Probab=98.15  E-value=4.3e-06  Score=85.11  Aligned_cols=48  Identities=23%  Similarity=0.136  Sum_probs=39.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .++..|++.|.+++..    +..++++++.||||+|||++|++|++..+...
T Consensus        72 ~g~~~~~~~Q~~~i~~----~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~  119 (262)
T 3ly5_A           72 MGFTNMTEIQHKSIRP----LLEGRDLLAAAKTGSGKTLAFLIPAVELIVKL  119 (262)
T ss_dssp             TTCCBCCHHHHHHHHH----HHHTCCCEECCCTTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHH----HhCCCcEEEEccCCCCchHHHHHHHHHHHHhc
Confidence            4677799999655554    44568899999999999999999999877643

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

Probab=98.10  E-value=2.8e-06  Score=90.62  Aligned_cols=54  Identities=17%  Similarity=0.097  Sum_probs=41.7

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.+.++.....+|.|+|.|    .++++++.+++++++.||||+|||++|++|++..+
T Consensus         8 ~~~~~~l~~~~~~~~~~~Q----~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~   61 (414)
T 3oiy_A            8 EDFRSFFKKKFGKDLTGYQ----RLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA   61 (414)
T ss_dssp             HHHHHHHHHHHSSCCCHHH----HHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCHHH----HHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh
Confidence            3444555555577999999    45555566778999999999999999999987654

>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

Probab=98.08  E-value=5e-06  Score=81.05  Aligned_cols=53  Identities=11%  Similarity=0.130  Sum_probs=39.8

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ...+.+.+ .++..|++.|.+.+    .++.++.++++.||||+|||++|++|++..+
T Consensus        24 ~l~~~l~~-~g~~~~~~~Q~~~i----~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~   76 (220)
T 1t6n_A           24 ELLRAIVD-CGFEHPSEVQHECI----PQAILGMDVLCQAKSGMGKTAVFVLATLQQL   76 (220)
T ss_dssp             HHHHHHHH-TTCCCCCHHHHHHH----HHHHTTCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHH-CCCCCCCHHHHHHH----HHHhCCCCEEEECCCCCchhhhhhHHHHHhh
Confidence            33444443 45667999995555    4455578899999999999999999988764

>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}

Probab=98.07  E-value=4.5e-06  Score=87.08  Aligned_cols=46  Identities=17%  Similarity=0.156  Sum_probs=38.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..++..|+++|    ..++.++..+  .++++.||||||||+||++|++..+
T Consensus       109 ~~g~~~pt~iQ----~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B          109 AMGFNRPSKIQ----ENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             HTTCCSCCHHH----HHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HcCCCCCCHHH----HHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            35788999999    5555666665  8999999999999999999998754

>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*

Probab=98.03  E-value=3.5e-06  Score=83.90  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=37.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..++..|++.|.+.+    ..+.++.++++.||||+|||++|++|++..+
T Consensus        47 ~~g~~~~~~~Q~~ai----~~i~~~~~~li~apTGsGKT~~~~l~~l~~l   92 (237)
T 3bor_A           47 AYGFEKPSAIQQRAI----IPCIKGYDVIAQAQSGTGKTATFAISILQQL   92 (237)
T ss_dssp             HHTCCSCCHHHHHHH----HHHHTTCCEEECCCSSHHHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHH----HHHhCCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            346667999995544    4455678999999999999999999998764

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

Probab=98.00  E-value=1.1e-05  Score=90.74  Aligned_cols=55  Identities=13%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      +.+...++..|+|.|.+.+..+..  ..++++++.||||+|||+||++|++..+...
T Consensus        34 ~~l~~~g~~~~~~~Q~~~i~~il~--~~~~dvlv~apTGsGKTl~~~lpil~~l~~~   88 (579)
T 3sqw_A           34 KAITRMEFPGLTPVQQKTIKPILS--SEDHDVIARAKTGTGKTFAFLIPIFQHLINT   88 (579)
T ss_dssp             HHHHTTTCSSCCHHHHHHHHHHHC--SSSEEEEEECCTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHHc--cCCCeEEEEcCCCcHHHHHHHHHHHHHHHhc
Confidence            334455777899999665554431  1567899999999999999999999887654

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

Probab=97.97  E-value=9.3e-06  Score=77.83  Aligned_cols=56  Identities=18%  Similarity=0.108  Sum_probs=43.9

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +.+.......+.+.|++.|.+.+..+.    ++.++++.+|||+|||+++++|++..+..
T Consensus        20 ~~~~~~~~~~~~~~l~~~Q~~~i~~~~----~~~~~li~~~tGsGKT~~~~~~~~~~~~~   75 (216)
T 3b6e_A           20 ENVAARASPEPELQLRPYQMEVAQPAL----EGKNIIICLPTGSGKTRVAVYIAKDHLDK   75 (216)
T ss_dssp             HHHHHHTCCSCCCCCCHHHHHHHHHHH----TTCCEEEECSCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCccCCCCchHHHHHHHHHHh----cCCCEEEEcCCCCCHHHHHHHHHHHHHhh
Confidence            344555566678899999976665544    56899999999999999999998877643

>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*

Probab=97.97  E-value=1.4e-05  Score=82.72  Aligned_cols=53  Identities=17%  Similarity=0.162  Sum_probs=40.3

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ...+.+.+ .++..|+|.|.+.+..    +.++  .++++.||||+|||++|++|++..+
T Consensus        15 ~l~~~l~~-~~~~~~~~~Q~~~i~~----~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~   69 (395)
T 3pey_A           15 ELLKGIYA-MKFQKPSKIQERALPL----LLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV   69 (395)
T ss_dssp             HHHHHHHH-TTCCSCCHHHHHHHHH----HHCSSCCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHH-CCCCCCCHHHHHHHHH----HHcCCCCeEEEECCCCCcHHHHHHHHHHHHh
Confidence            34444544 4778999999655544    4444  8999999999999999999988654

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

Probab=97.96  E-value=9.6e-06  Score=82.40  Aligned_cols=46  Identities=24%  Similarity=0.180  Sum_probs=37.4

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      +...++..|+|.|.+.+    +.+.+++++++.||||+|||++|++|++.
T Consensus         9 l~~~g~~~l~~~Q~~~i----~~i~~~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A            9 IREMGFKNFTEVQSKTI----PLMLQGKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             HHHTTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHcCCCCCCHHHHHHH----HHHhcCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            34457778999995544    55557889999999999999999999764

>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

Probab=97.91  E-value=1.3e-05  Score=89.06  Aligned_cols=52  Identities=13%  Similarity=0.191  Sum_probs=40.3

Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          14 NEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        14 ~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      ...++..|+|.|.+.+..+..  ..++++|+.||||+|||++|++|++..+...
T Consensus        88 ~~~g~~~~~~~Q~~~i~~~l~--~~~~~~lv~apTGsGKTl~~~lpil~~l~~~  139 (563)
T 3i5x_A           88 TRMEFPGLTPVQQKTIKPILS--SEDHDVIARAKTGTGKTFAFLIPIFQHLINT  139 (563)
T ss_dssp             HTTCCSSCCHHHHHHHHHHHS--SSSEEEEEECCTTSCHHHHHHHHHHHHHHHT
T ss_pred             HHCCCCCCCHHHHHHHHHHhc--CCCCeEEEECCCCCCccHHHHHHHHHHHHhc
Confidence            444777899999665554431  1467899999999999999999999887643

>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

Probab=97.88  E-value=1.7e-05  Score=83.11  Aligned_cols=54  Identities=15%  Similarity=0.174  Sum_probs=39.3

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+.+. ..++..|+|.|.+.+..+...  .+.++++.||||+|||++|++|++..+
T Consensus        36 l~~~l~-~~g~~~~~~~Q~~~i~~~~~~--~~~~~lv~apTGsGKT~~~~~~~~~~~   89 (412)
T 3fht_A           36 LLQGVY-AMGFNRPSKIQENALPLMLAE--PPQNLIAQSQSGTGKTAAFVLAMLSQV   89 (412)
T ss_dssp             HHHHHH-HTTCCSCCHHHHHHHHHHHSS--SCCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHH-HcCCCCCCHHHHHHHHHHhcC--CCCeEEEECCCCchHHHHHHHHHHHHh
Confidence            334444 357789999995555444321  248999999999999999999988653

>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

Probab=97.87  E-value=2e-05  Score=82.83  Aligned_cols=53  Identities=13%  Similarity=0.140  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ...+.+.. .++..|+|.|.+.+..    +.+++++++.||||+|||++|++|++..+
T Consensus        31 ~l~~~l~~-~g~~~~~~~Q~~~i~~----i~~~~~~li~a~TGsGKT~~~~~~~~~~~   83 (400)
T 1s2m_A           31 ELLMGIFE-AGFEKPSPIQEEAIPV----AITGRDILARAKNGTGKTAAFVIPTLEKV   83 (400)
T ss_dssp             HHHHHHHH-TTCCSCCHHHHHHHHH----HHHTCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHH-CCCCCCCHHHHHHHHH----HhcCCCEEEECCCCcHHHHHHHHHHHHHH
Confidence            33444444 3666799999665554    44678899999999999999999988764

>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

Probab=97.85  E-value=1.6e-05  Score=82.82  Aligned_cols=46  Identities=13%  Similarity=0.067  Sum_probs=37.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..++..|+|.|.+.+    +.+..+.++++.||||+|||++|++|++..+
T Consensus        25 ~~g~~~~~~~Q~~~i----~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l   70 (391)
T 1xti_A           25 DCGFEHPSEVQHECI----PQAILGMDVLCQAKSGMGKTAVFVLATLQQL   70 (391)
T ss_dssp             HHSCCSCCHHHHHHH----HHHTTTCCEEEECSSCSSHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHH----HHHhcCCcEEEECCCCCcHHHHHHHHHHHhh
Confidence            346667999995544    5555678999999999999999999988664

>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

Probab=97.82  E-value=1.8e-05  Score=83.51  Aligned_cols=45  Identities=20%  Similarity=0.179  Sum_probs=36.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .++..|+|.|.+.+    +.+.+++++++.||||+|||++|++|++..+
T Consensus        55 ~g~~~~~~~Q~~ai----~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l   99 (410)
T 2j0s_A           55 YGFEKPSAIQQRAI----KQIIKGRDVIAQSQSGTGKTATFSISVLQCL   99 (410)
T ss_dssp             HTCCSCCHHHHHHH----HHHHTTCCEEEECCTTSSHHHHHHHHHHHTC
T ss_pred             cCCCCCCHHHHHHH----HHHhCCCCEEEECCCCCCchHHHHHHHHHHH
Confidence            36667999995554    4455678999999999999999999988754

>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*

Probab=97.81  E-value=1.9e-05  Score=90.30  Aligned_cols=52  Identities=21%  Similarity=0.109  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      ...+.+.+..++..|+|.|.+.    ++++.+++++++.+|||+|||++|++|++.
T Consensus        31 ~l~~~L~~~fg~~~~rp~Q~~~----i~~il~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           31 KVKDILQNVFKLEKFRPLQLET----INVTMAGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             HHHHHHHHTSCCCSCCTTHHHH----HHHHHTTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCCCHHHHHH----HHHHHcCCCEEEEECCCChHHHHHHHHHHH
Confidence            3444445545677899999554    455556889999999999999999999874

>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}

Probab=97.81  E-value=2.2e-05  Score=82.52  Aligned_cols=52  Identities=15%  Similarity=0.202  Sum_probs=40.1

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+.+. ..++..|++.|.+.+    .++.+++++++.||||+|||++|++|++..+
T Consensus        51 ~~~~l~-~~~~~~~~~~Q~~~i----~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~  102 (414)
T 3eiq_A           51 LLRGIY-AYGFEKPSAIQQRAI----LPCIKGYDVIAQAQSGTGKTATFAISILQQI  102 (414)
T ss_dssp             HHHHHH-HTTCCSCCHHHHHHH----HHHHTTCCEEECCCSCSSSHHHHHHHHHHHC
T ss_pred             HHHHHH-HcCCCCCCHHHHHHh----HHHhCCCCEEEECCCCCcccHHHHHHHHHHH
Confidence            333443 357778999995554    5555688999999999999999999988654

>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*

Probab=97.80  E-value=1.4e-05  Score=83.22  Aligned_cols=53  Identities=11%  Similarity=0.136  Sum_probs=40.6

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ...+.+.. .++..|+|.|.+.+.    .+.++.++++.||||+|||++|++|++..+
T Consensus        31 ~l~~~l~~-~g~~~~~~~Q~~~i~----~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l   83 (394)
T 1fuu_A           31 NLLRGVFG-YGFEEPSAIQQRAIM----PIIEGHDVLAQAQSGTGKTGTFSIAALQRI   83 (394)
T ss_dssp             HHHHHHHH-HTCCSCCHHHHHHHH----HHHHTCCEEECCCSSHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHH-cCCCCCCHHHHHHHH----HHhCCCCEEEECCCCChHHHHHHHHHHHHh
Confidence            34444444 467799999955544    455578999999999999999999998764

>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

Probab=97.78  E-value=2.2e-05  Score=80.48  Aligned_cols=49  Identities=16%  Similarity=0.173  Sum_probs=38.0

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +...++..|+|.|.+.+..+.   .++.++++.||||+|||++|++|++..+
T Consensus        21 l~~~g~~~~~~~Q~~~i~~~~---~~~~~~l~~~~TGsGKT~~~~~~~~~~~   69 (367)
T 1hv8_A           21 IRNKGFEKPTDIQMKVIPLFL---NDEYNIVAQARTGSGKTASFAIPLIELV   69 (367)
T ss_dssp             HHHHTCCSCCHHHHHHHHHHH---HTCSEEEEECCSSSSHHHHHHHHHHHHS
T ss_pred             HHHcCCCCCCHHHHHHHHHHh---CCCCCEEEECCCCChHHHHHHHHHHHHh
Confidence            344577789999966554442   3447999999999999999999988654

>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}

Probab=97.77  E-value=2.8e-05  Score=84.73  Aligned_cols=52  Identities=15%  Similarity=0.172  Sum_probs=39.7

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ...+.+.. .++..|+|+|.+.    +..+..+  .++++.||||+|||++|++|++..
T Consensus       102 ~l~~~l~~-~g~~~p~~~Q~~a----i~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~  155 (479)
T 3fmp_B          102 QLLQGVYA-MGFNRPSKIQENA----LPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ  155 (479)
T ss_dssp             HHHHHHHH-TTCCSCCHHHHHH----HHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTT
T ss_pred             HHHHHHHH-cCCCCCCHHHHHH----HHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHH
Confidence            34444444 5788999999544    4555444  899999999999999999998754

>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

Probab=97.76  E-value=2.8e-05  Score=77.44  Aligned_cols=46  Identities=20%  Similarity=0.122  Sum_probs=37.9

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.|+ |+|.|.+.+..+.+                           ++++++.||||+|||++|++|++..+..
T Consensus        47 ~g~~~~~~~Q~~~i~~~~~---------------------------g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           47 QNFTEPTAIQAQGWPVALS---------------------------GLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             TTCCSCCHHHHHHHHHHHH---------------------------TCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHhC---------------------------CCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            5665 89999998877542                           4689999999999999999999877643

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

Probab=97.76  E-value=2.6e-05  Score=83.14  Aligned_cols=76  Identities=26%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      .|+|+|+|.|.+.+..+.                           +++++++.||||+|||++|+.+++..+....+   
T Consensus        17 ~~~~~~~~~Q~~~i~~i~---------------------------~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~li   69 (414)
T 3oiy_A           17 KFGKDLTGYQRLWAKRIV---------------------------QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSAL   69 (414)
T ss_dssp             HHSSCCCHHHHHHHHHHT---------------------------TTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEE
T ss_pred             hcCCCCCHHHHHHHHHHh---------------------------cCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEE
Confidence            478999999998887753                           24689999999999999999998876644332   


Q ss_pred             -----HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 -----LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 -----~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                           .|-.|..+.    +.+.....+++..+-|.
T Consensus        70 l~Pt~~L~~q~~~~----~~~~~~~~~~v~~~~g~  100 (414)
T 3oiy_A           70 VFPTVTLVKQTLER----LQKLADEKVKIFGFYSS  100 (414)
T ss_dssp             EESSHHHHHHHHHH----HHHHCCSSCCEEECCTT
T ss_pred             EECCHHHHHHHHHH----HHHHccCCceEEEEECC
Confidence                 566665543    22222234555555554

>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}

Probab=97.72  E-value=3e-05  Score=76.08  Aligned_cols=46  Identities=22%  Similarity=0.274  Sum_probs=36.9

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| +|+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+..
T Consensus        38 ~g~~~~~~~Q~~~i~~~~---------------------------~~~~~l~~apTGsGKT~~~~l~~~~~l~~   84 (228)
T 3iuy_A           38 VGILKPTPIQSQAWPIIL---------------------------QGIDLIVVAQTGTGKTLSYLMPGFIHLDS   84 (228)
T ss_dssp             HTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            455 68999998886653                           25689999999999999999998877643

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

Probab=97.71  E-value=3.5e-05  Score=73.99  Aligned_cols=44  Identities=23%  Similarity=0.253  Sum_probs=36.3

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.| +|+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+
T Consensus        21 ~g~~~~~~~Q~~~i~~~~---------------------------~~~~~lv~apTGsGKT~~~~~~~~~~~   65 (206)
T 1vec_A           21 MGWEKPSPIQEESIPIAL---------------------------SGRDILARAKNGTGKSGAYLIPLLERL   65 (206)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCSSSTTHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHc---------------------------cCCCEEEECCCCCchHHHHHHHHHHHh
Confidence            566 58999999887753                           246799999999999999999987654

>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*

Probab=97.70  E-value=2.6e-05  Score=87.59  Aligned_cols=52  Identities=21%  Similarity=0.322  Sum_probs=40.0

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      ...+.+.+..++..|+|.|.    ++++++.+++++++.||||+|||++|++|++.
T Consensus        12 ~~~~~l~~~~g~~~~r~~Q~----~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~   63 (523)
T 1oyw_A           12 GAKQVLQETFGYQQFRPGQE----EIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL   63 (523)
T ss_dssp             HHHHHHHHTTCCSSCCTTHH----HHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCHHHH----HHHHHHHcCCCEEEECCCCcHHHHHHHHHHHH
Confidence            34444555456678999995    45555567889999999999999999999873

>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

Probab=97.70  E-value=5.7e-05  Score=75.41  Aligned_cols=46  Identities=22%  Similarity=0.284  Sum_probs=37.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| +|+|.|.+.+..+.+                           ++++++.||||+|||++|++|++..+..
T Consensus        41 ~g~~~~~~~Q~~~i~~i~~---------------------------~~~~l~~a~TGsGKT~~~~~~~l~~l~~   87 (253)
T 1wrb_A           41 ASYQRPTPIQKNAIPAILE---------------------------HRDIMACAQTGSGKTAAFLIPIINHLVC   87 (253)
T ss_dssp             TTCCSCCHHHHHHHHHHHT---------------------------TCCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHhC---------------------------CCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            345 589999998887532                           4679999999999999999999887654

>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}

Probab=97.70  E-value=3.7e-05  Score=76.23  Aligned_cols=45  Identities=29%  Similarity=0.409  Sum_probs=36.6

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ..|. |+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+.
T Consensus        47 ~g~~~~~~~Q~~~i~~~~---------------------------~~~~~l~~a~TGsGKT~~~~l~~l~~l~   92 (245)
T 3dkp_A           47 AGFQMPTPIQMQAIPVML---------------------------HGRELLASAPTGSGKTLAFSIPILMQLK   92 (245)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4564 8999999887753                           2467999999999999999999887653

>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*

Probab=97.69  E-value=3.4e-05  Score=84.22  Aligned_cols=46  Identities=26%  Similarity=0.138  Sum_probs=34.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ++.+.|+|.|.+.+.    .+.++.++++.||||+|||++|++|++..+.
T Consensus         3 ~~~~~~~~~Q~~~i~----~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~   48 (556)
T 4a2p_A            3 METKKARSYQIELAQ----PAINGKNALICAPTGSGKTFVSILICEHHFQ   48 (556)
T ss_dssp             -----CCHHHHHHHH----HHHTTCCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHH----HHHcCCCEEEEcCCCChHHHHHHHHHHHHHH
Confidence            467899999965544    4456789999999999999999999887654

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

Probab=97.68  E-value=4.3e-05  Score=83.07  Aligned_cols=45  Identities=29%  Similarity=0.273  Sum_probs=37.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .+.|+|.|.+.+.    .+.++.++++.||||+|||++|++|++..+..
T Consensus         2 ~~~~~~~Q~~~i~----~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~   46 (555)
T 3tbk_A            2 PLKPRNYQLELAL----PAKKGKNTIICAPTGCGKTFVSLLICEHHLKK   46 (555)
T ss_dssp             CCCCCHHHHHHHH----HHHTTCCEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCcHHHHHHHH----HHhCCCCEEEEeCCCChHHHHHHHHHHHHHHh
Confidence            4789999965555    44567899999999999999999999877643

>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}

Probab=97.64  E-value=6.7e-05  Score=75.72  Aligned_cols=47  Identities=23%  Similarity=0.192  Sum_probs=38.2

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      .+.| +|+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+..
T Consensus        60 ~~g~~~~~~~Q~~~i~~i~---------------------------~~~~~lv~a~TGsGKT~~~~~~il~~l~~  107 (249)
T 3ber_A           60 QLGWTKPTKIQIEAIPLAL---------------------------QGRDIIGLAETGSGKTGAFALPILNALLE  107 (249)
T ss_dssp             HTTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCCCCHHHHHHHHHHh---------------------------CCCCEEEEcCCCCCchhHhHHHHHHHHhc
Confidence            3566 68999998887753                           24679999999999999999999876654

>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

Probab=97.61  E-value=4.3e-05  Score=74.44  Aligned_cols=45  Identities=16%  Similarity=0.228  Sum_probs=36.8

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      .++| +++|.|.+.+..+.                           +++++++.||||+|||++|++|++.++
T Consensus        31 ~~g~~~~~~~Q~~~i~~~~---------------------------~~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           31 GYGFEEPSAIQQRAIMPII---------------------------EGHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             HHTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HCCCCCCcHHHHHHHHHHh---------------------------cCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            3566 58999998887753                           246799999999999999999988765

>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

Probab=97.59  E-value=6.5e-05  Score=73.16  Aligned_cols=44  Identities=18%  Similarity=0.169  Sum_probs=36.4

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.|+ |+|.|.+.+..+.+                           ++++++.||||+|||++|++|++..+
T Consensus        32 ~g~~~~~~~Q~~~i~~~~~---------------------------~~~~li~~~TGsGKT~~~~~~~~~~~   76 (220)
T 1t6n_A           32 CGFEHPSEVQHECIPQAIL---------------------------GMDVLCQAKSGMGKTAVFVLATLQQL   76 (220)
T ss_dssp             TTCCCCCHHHHHHHHHHHT---------------------------TCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHhC---------------------------CCCEEEECCCCCchhhhhhHHHHHhh
Confidence            5675 99999998877642                           45799999999999999999987654

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

Probab=97.57  E-value=7e-05  Score=85.18  Aligned_cols=49  Identities=29%  Similarity=0.226  Sum_probs=37.9

Q ss_pred             HhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          13 LNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        13 ~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +...+++.||+.|.+.+.    .+..+.++|+.+|||+|||++|++|++..+.
T Consensus         6 l~~~g~~~lr~~Q~~~i~----~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~   54 (696)
T 2ykg_A            6 TNLYSPFKPRNYQLELAL----PAMKGKNTIICAPTGCGKTFVSLLICEHHLK   54 (696)
T ss_dssp             -CTTC--CCCHHHHHHHH----HHHTTCCEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             ccccCCCCccHHHHHHHH----HHHcCCCEEEEcCCCchHHHHHHHHHHHHHH
Confidence            445678899999955554    4556789999999999999999999987654

>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}

Probab=97.56  E-value=7.7e-05  Score=75.85  Aligned_cols=46  Identities=26%  Similarity=0.297  Sum_probs=37.9

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.|+ |+|.|.+++..+.+                           ++++++.||||+|||++|++|++..+..
T Consensus        72 ~g~~~~~~~Q~~~i~~~~~---------------------------~~~~lv~a~TGsGKT~~~~l~~l~~l~~  118 (262)
T 3ly5_A           72 MGFTNMTEIQHKSIRPLLE---------------------------GRDLLAAAKTGSGKTLAFLIPAVELIVK  118 (262)
T ss_dssp             TTCCBCCHHHHHHHHHHHH---------------------------TCCCEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHhC---------------------------CCcEEEEccCCCCchHHHHHHHHHHHHh
Confidence            5665 89999998877642                           4678999999999999999999877654

>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*

Probab=97.56  E-value=7.6e-05  Score=73.77  Aligned_cols=45  Identities=16%  Similarity=0.179  Sum_probs=36.5

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      .+.|+ |+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+
T Consensus        41 ~~g~~~~~~~Q~~~i~~~~---------------------------~~~~~l~~a~TGsGKT~~~~l~~l~~l   86 (230)
T 2oxc_A           41 AAGFERPSPVQLKAIPLGR---------------------------CGLDLIVQAKSGTGKTCVFSTIALDSL   86 (230)
T ss_dssp             HTTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            35665 8999998887653                           246799999999999999999987654

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

Probab=97.55  E-value=0.00016  Score=69.21  Aligned_cols=47  Identities=26%  Similarity=0.293  Sum_probs=38.7

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ..+++||.|.+.+..+.+                           ++++++.+|||+|||++++.+++..+...
T Consensus        30 ~~~~l~~~Q~~~i~~~~~---------------------------~~~~li~~~tGsGKT~~~~~~~~~~~~~~   76 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALE---------------------------GKNIIICLPTGSGKTRVAVYIAKDHLDKK   76 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHT---------------------------TCCEEEECSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHhc---------------------------CCCEEEEcCCCCCHHHHHHHHHHHHHhhc
Confidence            447899999999887641                           36799999999999999999988776543

>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

Probab=97.53  E-value=8e-05  Score=71.34  Aligned_cols=45  Identities=22%  Similarity=0.260  Sum_probs=36.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| +|+|.|.+.+..+.                           +++++++.||||||||++|++|++..+.
T Consensus        19 ~~~~~~~~~Q~~~i~~~~---------------------------~~~~~li~~~TGsGKT~~~~~~~~~~l~   64 (207)
T 2gxq_A           19 RGLTTPTPIQAAALPLAL---------------------------EGKDLIGQARTGTGKTLAFALPIAERLA   64 (207)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             cCCCCCCHHHHHHHHHHc---------------------------CCCCEEEECCCCChHHHHHHHHHHHHHh
Confidence            455 68999999887753                           2467999999999999999999877653

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

Probab=97.53  E-value=8.5e-05  Score=73.24  Aligned_cols=46  Identities=30%  Similarity=0.268  Sum_probs=37.0

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| .|+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+..
T Consensus        43 ~~~~~~~~~Q~~~i~~~~---------------------------~~~~~li~a~TGsGKT~~~~~~~l~~l~~   89 (236)
T 2pl3_A           43 AQYRLVTEIQKQTIGLAL---------------------------QGKDVLGAAKTGSGKTLAFLVPVLEALYR   89 (236)
T ss_dssp             TTCCBCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCCEEEEeCCCCcHHHHHHHHHHHHHHh
Confidence            455 58999988877653                           25689999999999999999999877643

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

Probab=97.52  E-value=6.3e-05  Score=73.52  Aligned_cols=44  Identities=23%  Similarity=0.239  Sum_probs=36.3

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.| +|+|.|.+.+..+.+                           ++++++.||||+|||++|++|++..+
T Consensus        22 ~g~~~~~~~Q~~~i~~~~~---------------------------~~~~lv~a~TGsGKT~~~~~~~l~~l   66 (219)
T 1q0u_A           22 LRFYKPTEIQERIIPGALR---------------------------GESMVGQSQTGTGKTHAYLLPIMEKI   66 (219)
T ss_dssp             TTCCSCCHHHHHHHHHHHH---------------------------TCCEEEECCSSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHhC---------------------------CCCEEEECCCCChHHHHHHHHHHHHH
Confidence            444 689999999877642                           46799999999999999999987665

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

Probab=97.50  E-value=0.00017  Score=78.32  Aligned_cols=46  Identities=30%  Similarity=0.384  Sum_probs=39.5

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ||+|||.|.+.+..+.                           .++++++.+|||+|||++|++|++..+...
T Consensus         2 ~~~~~~~Q~~~i~~~~---------------------------~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~   47 (555)
T 3tbk_A            2 PLKPRNYQLELALPAK---------------------------KGKNTIICAPTGCGKTFVSLLICEHHLKKF   47 (555)
T ss_dssp             CCCCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCcHHHHHHHHHHh---------------------------CCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            6899999999988763                           246799999999999999999998887753

>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

Probab=97.49  E-value=0.00012  Score=86.54  Aligned_cols=58  Identities=19%  Similarity=0.239  Sum_probs=49.7

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ...+++.+..++ .|++.|.+.+.++.+.+..+  .++++.||||+|||++|++|++..+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~  415 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE  415 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            566777777666 99999999999999988776  48999999999999999999987753

>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*

Probab=97.47  E-value=6.5e-05  Score=74.75  Aligned_cols=45  Identities=18%  Similarity=0.247  Sum_probs=36.7

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      .+.|. |+|.|.+.+..+.                           +++++++.||||||||++|++|++..+
T Consensus        47 ~~g~~~~~~~Q~~ai~~i~---------------------------~~~~~li~apTGsGKT~~~~l~~l~~l   92 (237)
T 3bor_A           47 AYGFEKPSAIQQRAIIPCI---------------------------KGYDVIAQAQSGTGKTATFAISILQQL   92 (237)
T ss_dssp             HHTCCSCCHHHHHHHHHHH---------------------------TTCCEEECCCSSHHHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            35675 9999998887753                           246799999999999999999987654

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

Probab=97.45  E-value=0.00016  Score=81.26  Aligned_cols=50  Identities=18%  Similarity=0.332  Sum_probs=40.9

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .++|+ |+|.|.+.+..+..   .                      .++++++.||||||||++|++|++..+...
T Consensus        38 ~~g~~~~~~~Q~~~i~~il~---~----------------------~~~dvlv~apTGsGKTl~~~lpil~~l~~~   88 (579)
T 3sqw_A           38 RMEFPGLTPVQQKTIKPILS---S----------------------EDHDVIARAKTGTGKTFAFLIPIFQHLINT   88 (579)
T ss_dssp             TTTCSSCCHHHHHHHHHHHC---S----------------------SSEEEEEECCTTSCHHHHHHHHHHHHHHHT
T ss_pred             HCCCCCCCHHHHHHHHHHHc---c----------------------CCCeEEEEcCCCcHHHHHHHHHHHHHHHhc
Confidence            46775 99999998877641   1                      257899999999999999999999887654

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

Probab=97.45  E-value=0.00011  Score=77.30  Aligned_cols=47  Identities=23%  Similarity=0.314  Sum_probs=38.3

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ..| +|+|.|.+.+..+.                           .++++++.||||+|||++|++|++..+...
T Consensus        33 ~~~~~~~~~Q~~~i~~i~---------------------------~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~   80 (417)
T 2i4i_A           33 TRYTRPTPVQKHAIPIIK---------------------------EKRDLMACAQTGSGKTAAFLLPILSQIYSD   80 (417)
T ss_dssp             HTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHc---------------------------cCCCEEEEcCCCCHHHHHHHHHHHHHHHhc
Confidence            455 68999999887643                           257899999999999999999998877543

>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

Probab=97.44  E-value=0.00018  Score=79.97  Aligned_cols=51  Identities=20%  Similarity=0.342  Sum_probs=41.0

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      .++|. ++|.|.+.+..+.   ..                      .++++++.||||||||++|++|++..+...+
T Consensus        89 ~~g~~~~~~~Q~~~i~~~l---~~----------------------~~~~~lv~apTGsGKTl~~~lpil~~l~~~~  140 (563)
T 3i5x_A           89 RMEFPGLTPVQQKTIKPIL---SS----------------------EDHDVIARAKTGTGKTFAFLIPIFQHLINTK  140 (563)
T ss_dssp             TTCCSSCCHHHHHHHHHHH---SS----------------------SSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCCCHHHHHHHHHHh---cC----------------------CCCeEEEECCCCCCccHHHHHHHHHHHHhcc
Confidence            35664 8999999887764   11                      2578999999999999999999998887653

>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}

Probab=97.44  E-value=0.00012  Score=83.25  Aligned_cols=47  Identities=19%  Similarity=0.126  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      ..+.|+|.|.+.+..    +.++.++|+.+|||+|||++|++|++..+...
T Consensus         4 ~~~~l~~~Q~~~i~~----il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~   50 (699)
T 4gl2_A            4 AMLQLRPYQMEVAQP----ALEGKNIIICLPTGCGKTRVAVYIAKDHLDKK   50 (699)
T ss_dssp             ---CCCHHHHHHHHH----HHSSCCEEECCCTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHH----HHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhc
Confidence            467899999555544    44578999999999999999999999887654

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

Probab=97.41  E-value=0.00025  Score=81.69  Aligned_cols=54  Identities=20%  Similarity=0.161  Sum_probs=42.7

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHH-HhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQG-CNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~a-l~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.+.....++..|+|.|.+.+    ++ +.+++++++.||||+|||++|.+|++..+.
T Consensus        18 ~~~~~l~~~g~~~l~~~Q~~~i----~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~   72 (715)
T 2va8_A           18 NVIEIIKKRGIKKLNPPQTEAV----KKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLL   72 (715)
T ss_dssp             HHHHHHHTTSCCBCCHHHHHHH----HTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHH----HHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            4455566666669999995444    44 567899999999999999999999987654

>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*

Probab=97.38  E-value=0.00019  Score=83.04  Aligned_cols=54  Identities=26%  Similarity=0.241  Sum_probs=41.9

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHH-HhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQG-CNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~a-l~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.+.+...++..|+|.|.+    ++++ +.+++++++.||||+|||++|++|++....
T Consensus        11 ~~~~~l~~~g~~~l~~~Q~~----~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~   65 (720)
T 2zj8_A           11 RIKSTLKERGIESFYPPQAE----ALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL   65 (720)
T ss_dssp             HHHHHHHHTTCCBCCHHHHH----HHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCCCHHHHH----HHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHH
Confidence            34445555566689999954    4444 667899999999999999999999987654

>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

Probab=97.37  E-value=0.00013  Score=84.17  Aligned_cols=54  Identities=22%  Similarity=0.183  Sum_probs=41.0

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.+.+...++..|+|.|.    ++++++.+++++++.||||+|||+++++|++..+.
T Consensus        13 ~~~~~l~~~g~~~l~~~Q~----~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~   66 (702)
T 2p6r_A           13 YAVGILKEEGIEELFPPQA----EAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI   66 (702)
T ss_dssp             HHHHHHHCC---CCCCCCH----HHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHH----HHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHH
Confidence            4455666666668999994    45555667899999999999999999999987654

>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

Probab=97.31  E-value=0.00042  Score=82.07  Aligned_cols=83  Identities=18%  Similarity=0.243  Sum_probs=59.8

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      .+||+++|.|.+.+..|.+.+..+                     ...++++.||||+|||++|+.|++..+....+   
T Consensus       364 ~lpf~lt~~Q~~ai~~I~~~l~~~---------------------~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlv  422 (780)
T 1gm5_A          364 SLPFKLTNAQKRAHQEIRNDMISE---------------------KPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAF  422 (780)
T ss_dssp             HSSSCCCHHHHHHHHHHHHHHHSS---------------------SCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEE
T ss_pred             hCCCCCCHHHHHHHHHHHhhcccc---------------------CCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEE
Confidence            689999999999999998877542                     13579999999999999999999988765533   


Q ss_pred             -----HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 -----LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 -----~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                           .|-+|..+.-...+   .+..+++..+-|.
T Consensus       423 laPtr~La~Q~~~~l~~~~---~~~gi~v~~l~G~  454 (780)
T 1gm5_A          423 MVPTSILAIQHYRRTVESF---SKFNIHVALLIGA  454 (780)
T ss_dssp             ECSCHHHHHHHHHHHHHHH---TCSSCCEEECCSS
T ss_pred             EeCcHHHHHHHHHHHHHHh---hhcCceEEEEeCC
Confidence                 56666554322211   2234566666555

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

Probab=97.29  E-value=0.00028  Score=86.40  Aligned_cols=52  Identities=17%  Similarity=0.107  Sum_probs=40.8

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      |.++.....+|.|+|.|    ..++..+.+++++++.||||+|||++||.|++..+
T Consensus        67 ~~~~~~~~~gf~pt~iQ----~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~  118 (1104)
T 4ddu_A           67 FRSFFKKKFGKDLTGYQ----RLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA  118 (1104)
T ss_dssp             HHHHHHHHSSSCCCHHH----HHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCHHH----HHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH
Confidence            33444444467899999    55566666789999999999999999999988766

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

Probab=97.28  E-value=0.00024  Score=72.13  Aligned_cols=43  Identities=28%  Similarity=0.329  Sum_probs=35.2

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .+.| ++||.|.+.+..+.                           +++++++.||||+|||++|+.|++.
T Consensus        11 ~~g~~~l~~~Q~~~i~~i~---------------------------~~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           11 EMGFKNFTEVQSKTIPLML---------------------------QGKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             HTTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HcCCCCCCHHHHHHHHHHh---------------------------cCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            3566 48999999887754                           2467999999999999999999765

>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

Probab=97.27  E-value=0.00019  Score=74.67  Aligned_cols=45  Identities=18%  Similarity=0.175  Sum_probs=37.0

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.|+ |||.|.+.+..+.                           .++++++.||||+|||++|++|++..+.
T Consensus        26 ~g~~~~~~~Q~~~i~~~~---------------------------~~~~~lv~a~TGsGKT~~~~~~~~~~l~   71 (391)
T 1xti_A           26 CGFEHPSEVQHECIPQAI---------------------------LGMDVLCQAKSGMGKTAVFVLATLQQLE   71 (391)
T ss_dssp             HSCCSCCHHHHHHHHHHT---------------------------TTCCEEEECSSCSSHHHHHHHHHHHHCC
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------cCCcEEEECCCCCcHHHHHHHHHHHhhc
Confidence            5665 9999998887653                           2467999999999999999999887754

>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

Probab=97.26  E-value=0.00022  Score=75.20  Aligned_cols=46  Identities=24%  Similarity=0.359  Sum_probs=38.0

Q ss_pred             ccCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         245 EFPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       245 ~fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      .+.|+ |+|.|.+.+..+.                           +++++++.||||+|||++|++|++..+.
T Consensus        54 ~~g~~~~~~~Q~~ai~~i~---------------------------~~~~~lv~a~TGsGKT~~~~~~~~~~l~  100 (410)
T 2j0s_A           54 AYGFEKPSAIQQRAIKQII---------------------------KGRDVIAQSQSGTGKTATFSISVLQCLD  100 (410)
T ss_dssp             HHTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHTCC
T ss_pred             HcCCCCCCHHHHHHHHHHh---------------------------CCCCEEEECCCCCCchHHHHHHHHHHHh
Confidence            36775 9999999888754                           2467999999999999999999887654

>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}

Probab=97.26  E-value=0.00025  Score=77.01  Aligned_cols=46  Identities=28%  Similarity=0.305  Sum_probs=38.0

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.|+ |+|.|.+.+..+.                           .++++++.||||||||++|++|++..+..
T Consensus        74 ~g~~~pt~iQ~~ai~~i~---------------------------~g~d~i~~a~TGsGKT~a~~lpil~~l~~  120 (434)
T 2db3_A           74 SGYKIPTPIQKCSIPVIS---------------------------SGRDLMACAQTGSGKTAAFLLPILSKLLE  120 (434)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHh---------------------------cCCCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            5664 9999998877652                           25789999999999999999999887754

>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}

Probab=97.25  E-value=0.00025  Score=83.15  Aligned_cols=45  Identities=27%  Similarity=0.158  Sum_probs=35.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      +++.|+|.|.+.+.    .+.++.++|+.+|||+|||++|++|++..+.
T Consensus       245 g~~~l~~~Q~~~i~----~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~  289 (797)
T 4a2q_A          245 ETKKARSYQIELAQ----PAINGKNALICAPTGSGKTFVSILICEHHFQ  289 (797)
T ss_dssp             ---CCCHHHHHHHH----HHHTTCCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHH----HHHhCCCEEEEeCCCChHHHHHHHHHHHHHH
Confidence            36789999965544    4556789999999999999999999887754

>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

Probab=97.25  E-value=0.0003  Score=73.78  Aligned_cols=45  Identities=20%  Similarity=0.260  Sum_probs=37.2

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.|+ |+|.|.+.+..+.+                           ++++++.||||+|||++|++|++..+.
T Consensus        39 ~g~~~~~~~Q~~~i~~i~~---------------------------~~~~li~a~TGsGKT~~~~~~~~~~~~   84 (400)
T 1s2m_A           39 AGFEKPSPIQEEAIPVAIT---------------------------GRDILARAKNGTGKTAAFVIPTLEKVK   84 (400)
T ss_dssp             TTCCSCCHHHHHHHHHHHH---------------------------TCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCCCCCCHHHHHHHHHHhc---------------------------CCCEEEECCCCcHHHHHHHHHHHHHHh
Confidence            4564 99999999887642                           457999999999999999999987764

>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}

Probab=97.23  E-value=0.00018  Score=75.02  Aligned_cols=46  Identities=20%  Similarity=0.279  Sum_probs=35.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +.| .|+|.|...+..+.   ..                      .++++++.||||||||++|++|++..+
T Consensus       110 ~g~~~pt~iQ~~ai~~il---~~----------------------~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B          110 MGFNRPSKIQENALPLML---AE----------------------PPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             TTCCSCCHHHHHHHHHHT---SS----------------------SCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             cCCCCCCHHHHHHHHHHH---cC----------------------CCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            455 58999998876642   21                      137899999999999999999988654

>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*

Probab=97.22  E-value=0.00025  Score=77.37  Aligned_cols=46  Identities=30%  Similarity=0.322  Sum_probs=36.1

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      .+++|+|.|.+.+..+.                           .++++++.+|||+|||++|++|++..+..
T Consensus         4 ~~~~~~~~Q~~~i~~~~---------------------------~~~~~l~~~~tGsGKT~~~~~~~~~~~~~   49 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAI---------------------------NGKNALICAPTGSGKTFVSILICEHHFQN   49 (556)
T ss_dssp             ----CCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCChHHHHHHHHHHHHHHh
Confidence            46899999999887763                           14679999999999999999999887765

>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}

Probab=97.22  E-value=0.00039  Score=85.14  Aligned_cols=47  Identities=15%  Similarity=0.123  Sum_probs=39.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          15 EPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        15 ~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ...+|.|++.|    ..++.++.++.++|+.||||+|||++|++|++..+.
T Consensus       179 ~~~~f~ltp~Q----~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~  225 (1108)
T 3l9o_A          179 RTYPFTLDPFQ----DTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK  225 (1108)
T ss_dssp             SCCSSCCCHHH----HHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH
T ss_pred             HhCCCCCCHHH----HHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh
Confidence            34577899999    555666788899999999999999999999887764

>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}

Probab=97.20  E-value=0.00024  Score=70.84  Aligned_cols=44  Identities=14%  Similarity=0.111  Sum_probs=35.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+..++.|    ++++.++.+++++++.||||+|||.++.++++....
T Consensus        59 ~~p~~~~q----~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~  102 (235)
T 3llm_A           59 LLPVKKFE----SEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFI  102 (235)
T ss_dssp             TSGGGGGH----HHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             cCChHHHH----HHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchh
Confidence            44567889    666677788999999999999999999988776544

>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}

Probab=97.19  E-value=0.00043  Score=78.78  Aligned_cols=75  Identities=20%  Similarity=0.278  Sum_probs=50.0

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh------
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK------  320 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~------  320 (795)
                      +|++||.|.+.+..+.+                           ++++++.+|||+|||++|+.|++..+....      
T Consensus         5 ~~~l~~~Q~~~i~~il~---------------------------g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~   57 (699)
T 4gl2_A            5 MLQLRPYQMEVAQPALE---------------------------GKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPG   57 (699)
T ss_dssp             --CCCHHHHHHHHHHHS---------------------------SCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCccHHHHHHHHHHHh---------------------------CCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCC
Confidence            58899999998887642                           467999999999999999999988776542      


Q ss_pred             H--------HHHHHH-HhhhhhhhhhcCCCCceEEEecccc
Q psy3462         321 E--------LVQQKM-FEQRTQDLQKIPFRKLKISRLKAKD  352 (795)
Q Consensus       321 k--------~LQ~Ql-~~kdip~l~~i~~~~l~~~~~KGr~  352 (795)
                      +        .|..|. .+.    +.+..+..+++..+-|..
T Consensus        58 ~vlvl~P~~~L~~Q~~~~~----l~~~~~~~~~v~~~~g~~   94 (699)
T 4gl2_A           58 KVIVLVNKVLLVEQLFRKE----FQPFLKKWYRVIGLSGDT   94 (699)
T ss_dssp             CBCCEESCSHHHHHHHHHT----HHHHHTTTSCEEEEC---
T ss_pred             eEEEEECCHHHHHHHHHHH----HHHHcCcCceEEEEeCCc
Confidence            2        466666 432    233333346666666553

>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*

Probab=97.17  E-value=0.00023  Score=74.06  Aligned_cols=46  Identities=15%  Similarity=0.225  Sum_probs=37.9

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ++| +|+|.|.+.+..+.+                           ++++++.||||+|||++|++|++.++..
T Consensus        39 ~g~~~~~~~Q~~~i~~i~~---------------------------~~~~lv~~~TGsGKT~~~~~~~~~~l~~   85 (394)
T 1fuu_A           39 YGFEEPSAIQQRAIMPIIE---------------------------GHDVLAQAQSGTGKTGTFSIAALQRIDT   85 (394)
T ss_dssp             HTCCSCCHHHHHHHHHHHH---------------------------TCCEEECCCSSHHHHHHHHHHHHHHCCT
T ss_pred             cCCCCCCHHHHHHHHHHhC---------------------------CCCEEEECCCCChHHHHHHHHHHHHhhc
Confidence            566 699999988877642                           4679999999999999999999877643

>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*

Probab=97.13  E-value=0.00026  Score=80.98  Aligned_cols=43  Identities=33%  Similarity=0.475  Sum_probs=35.8

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .|+| .+||.|.+.+..+.                           +++++++.||||+|||++|++|++.
T Consensus        39 ~fg~~~~rp~Q~~~i~~il---------------------------~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           39 VFKLEKFRPLQLETINVTM---------------------------AGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             TSCCCSCCTTHHHHHHHHH---------------------------TTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             HhCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEECCCChHHHHHHHHHHH
Confidence            4787 58999998887753                           2567999999999999999999864

>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}

Probab=97.11  E-value=0.00042  Score=72.70  Aligned_cols=45  Identities=20%  Similarity=0.261  Sum_probs=37.0

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| .|+|.|.+.+..+.                           +++++++.||||+|||++|+++++..+.
T Consensus        58 ~~~~~~~~~Q~~~i~~~~---------------------------~~~~~lv~a~TGsGKT~~~~~~~~~~~~  103 (414)
T 3eiq_A           58 YGFEKPSAIQQRAILPCI---------------------------KGYDVIAQAQSGTGKTATFAISILQQIE  103 (414)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEECCCSCSSSHHHHHHHHHHHCC
T ss_pred             cCCCCCCHHHHHHhHHHh---------------------------CCCCEEEECCCCCcccHHHHHHHHHHHh
Confidence            566 58999998887654                           2467999999999999999999887654

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

Probab=97.09  E-value=0.00065  Score=82.50  Aligned_cols=45  Identities=16%  Similarity=0.144  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+|.|++.|.+.    +.++.++.++++.||||+|||++|++|++..+.
T Consensus        83 ~~f~L~~~Q~ea----i~~l~~g~~vLV~apTGSGKTlva~lai~~~l~  127 (1010)
T 2xgj_A           83 YPFTLDPFQDTA----ISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK  127 (1010)
T ss_dssp             CSSCCCHHHHHH----HHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHH----HHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc
Confidence            457899999554    455667889999999999999999999887653

>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

Probab=97.08  E-value=0.00044  Score=72.35  Aligned_cols=47  Identities=19%  Similarity=0.242  Sum_probs=37.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| .|+|.|.+.+..+.+.                         .++++++.||||+|||++|++|++..+.
T Consensus        43 ~g~~~~~~~Q~~~i~~~~~~-------------------------~~~~~lv~apTGsGKT~~~~~~~~~~~~   90 (412)
T 3fht_A           43 MGFNRPSKIQENALPLMLAE-------------------------PPQNLIAQSQSGTGKTAAFVLAMLSQVE   90 (412)
T ss_dssp             TTCCSCCHHHHHHHHHHHSS-------------------------SCCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             cCCCCCCHHHHHHHHHHhcC-------------------------CCCeEEEECCCCchHHHHHHHHHHHHhh
Confidence            455 5899999988776431                         1478999999999999999999887654

>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*

Probab=97.08  E-value=0.00044  Score=71.59  Aligned_cols=47  Identities=21%  Similarity=0.273  Sum_probs=37.2

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| +|+|.|.+.+..+.+   .                      .++++++.||||+|||++|+.+++..+.
T Consensus        23 ~~~~~~~~~Q~~~i~~~~~---~----------------------~~~~~lv~a~TGsGKT~~~~~~~~~~~~   70 (395)
T 3pey_A           23 MKFQKPSKIQERALPLLLH---N----------------------PPRNMIAQSQSGTGKTAAFSLTMLTRVN   70 (395)
T ss_dssp             TTCCSCCHHHHHHHHHHHC---S----------------------SCCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCCCCCCHHHHHHHHHHHc---C----------------------CCCeEEEECCCCCcHHHHHHHHHHHHhc
Confidence            344 699999998877642   1                      1378999999999999999999887653

>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

Probab=97.07  E-value=0.00044  Score=82.44  Aligned_cols=39  Identities=23%  Similarity=0.207  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      |.|+|+|    ...+.++..|+  |.+|+||+||||||++|++..
T Consensus        82 ~~pt~VQ----~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~  120 (844)
T 1tf5_A           82 MFPFKVQ----LMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLN  120 (844)
T ss_dssp             CCCCHHH----HHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcHHH----HHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHH
Confidence            3999999    55556677776  999999999999999998854

>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

Probab=97.06  E-value=0.00056  Score=70.08  Aligned_cols=47  Identities=21%  Similarity=0.244  Sum_probs=37.4

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +.| +|+|.|.+.+..+.+                          .++++++.||||+|||++|+.+++.++..
T Consensus        24 ~g~~~~~~~Q~~~i~~~~~--------------------------~~~~~l~~~~TGsGKT~~~~~~~~~~~~~   71 (367)
T 1hv8_A           24 KGFEKPTDIQMKVIPLFLN--------------------------DEYNIVAQARTGSGKTASFAIPLIELVNE   71 (367)
T ss_dssp             HTCCSCCHHHHHHHHHHHH--------------------------TCSEEEEECCSSSSHHHHHHHHHHHHSCS
T ss_pred             cCCCCCCHHHHHHHHHHhC--------------------------CCCCEEEECCCCChHHHHHHHHHHHHhcc
Confidence            455 699999998877532                          13689999999999999999998877643

>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

Probab=97.02  E-value=0.00094  Score=68.06  Aligned_cols=42  Identities=14%  Similarity=0.075  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.|++.|.+.+..+.+    +.++++.+|||+|||++++.++....
T Consensus       112 ~~l~~~Q~~ai~~~l~----~~~~ll~~~tGsGKT~~~~~~~~~~~  153 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLARYYL  153 (282)
T ss_dssp             CCCCHHHHHHHHHHHH----HSEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             cCccHHHHHHHHHHHh----cCCeEEEcCCCCCcHHHHHHHHHHHH
Confidence            5899999776665544    36688999999999999988876643

>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

Probab=97.00  E-value=0.001  Score=81.75  Aligned_cols=57  Identities=12%  Similarity=0.082  Sum_probs=47.1

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCC--cEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAK--NCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+++++.+. .+|.|+|.|.+.+..+.+.+.++.  ++++.||||+|||++++.+++..+
T Consensus       591 ~~~~~~~~~-f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~  649 (1151)
T 2eyq_A          591 EQYQLFCDS-FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAV  649 (1151)
T ss_dssp             HHHHHHHHT-CCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-CCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHH
Confidence            345555555 456789999999999999888776  899999999999999999987653

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

Probab=96.98  E-value=0.00026  Score=78.06  Aligned_cols=38  Identities=21%  Similarity=0.156  Sum_probs=29.4

Q ss_pred             HHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          28 LHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        28 mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      |-+...+++.+++++|+.||||+|||++|++|++..+.
T Consensus        10 ~~~~~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~   47 (459)
T 2z83_A           10 MGRGSPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAI   47 (459)
T ss_dssp             -----CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHH
Confidence            33444667788899999999999999999999997653

>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

Probab=96.97  E-value=0.00066  Score=71.20  Aligned_cols=43  Identities=23%  Similarity=0.292  Sum_probs=34.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.|||.|.+.+..+    .++ ++++.+|||+|||++++++++..+.
T Consensus         7 ~~~l~~~Q~~~i~~~----~~~-~~ll~~~tG~GKT~~~~~~~~~~~~   49 (494)
T 1wp9_A            7 LIQPRIYQEVIYAKC----KET-NCLIVLPTGLGKTLIAMMIAEYRLT   49 (494)
T ss_dssp             HHCCCHHHHHHHHHG----GGS-CEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHH----hhC-CEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            467999996666544    344 9999999999999999999887654

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

Probab=96.96  E-value=0.00099  Score=81.62  Aligned_cols=76  Identities=26%  Similarity=0.296  Sum_probs=54.3

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      .++|+|+|.|.+.+..+.                           +++++++.||||||||++||.+++..+....+   
T Consensus        74 ~~gf~pt~iQ~~ai~~il---------------------------~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Li  126 (1104)
T 4ddu_A           74 KFGKDLTGYQRLWAKRIV---------------------------QGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSAL  126 (1104)
T ss_dssp             HSSSCCCHHHHHHHHHHT---------------------------TTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEE
T ss_pred             hcCCCCCHHHHHHHHHHH---------------------------cCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEE
Confidence            468899999998877653                           25689999999999999999998777644432   


Q ss_pred             -----HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 -----LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 -----~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                           .|-.|+.+.    ++++.+..+++..+-|.
T Consensus       127 l~PtreLa~Q~~~~----l~~l~~~~i~v~~l~Gg  157 (1104)
T 4ddu_A          127 VFPTVTLVKQTLER----LQKLADEKVKIFGFYSS  157 (1104)
T ss_dssp             EESSHHHHHHHHHH----HHTTSCTTSCEEEECTT
T ss_pred             EechHHHHHHHHHH----HHHhhCCCCeEEEEeCC
Confidence                 566666543    33433556677666554

>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}

Probab=96.96  E-value=0.00057  Score=82.05  Aligned_cols=44  Identities=27%  Similarity=0.151  Sum_probs=34.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +++.|++.|.+.+.    .+.++.++++.+|||+|||++|++|++..+
T Consensus       245 ~~~~~r~~Q~~ai~----~il~g~~~ll~a~TGsGKTl~~~~~i~~~l  288 (936)
T 4a2w_A          245 ETKKARSYQIELAQ----PAINGKNALICAPTGSGKTFVSILICEHHF  288 (936)
T ss_dssp             ---CCCHHHHHHHH----HHHTTCCEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             CCCCCCHHHHHHHH----HHHcCCCEEEEeCCCchHHHHHHHHHHHHH
Confidence            47789999965554    445678999999999999999999987653

>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}

Probab=96.94  E-value=0.00056  Score=74.52  Aligned_cols=47  Identities=19%  Similarity=0.274  Sum_probs=37.0

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +.| .|+|.|.+.+..+.+   .                      .++++++.||||+|||++|++|++..+.
T Consensus       110 ~g~~~p~~~Q~~ai~~il~---~----------------------~~~~~l~~a~TGsGKT~~~~l~il~~l~  157 (479)
T 3fmp_B          110 MGFNRPSKIQENALPLMLA---E----------------------PPQNLIAQSQSGTGKTAAFVLAMLSQVE  157 (479)
T ss_dssp             TTCCSCCHHHHHHHHHHTS---B----------------------SCCEEEEECCSSSSHHHHHHHHHHTTCC
T ss_pred             cCCCCCCHHHHHHHHHHHc---C----------------------CCCcEEEEcCCCCchhHHHHHHHHHHHh
Confidence            455 589999998877632   1                      1478999999999999999999876543

>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

Probab=96.90  E-value=0.0016  Score=80.13  Aligned_cols=82  Identities=22%  Similarity=0.318  Sum_probs=57.5

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH--
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE--  321 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k--  321 (795)
                      ..|||+++|.|.+.+..+.+.+..+                     ...++++.||||+|||++++.+++..+...++  
T Consensus       598 ~~f~~~~t~~Q~~ai~~il~~~~~g---------------------~p~d~ll~~~TGsGKT~val~aa~~~~~~g~~vl  656 (1151)
T 2eyq_A          598 DSFPFETTPDQAQAINAVLSDMCQP---------------------LAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVA  656 (1151)
T ss_dssp             HTCCSCCCHHHHHHHHHHHHHHHSS---------------------SCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEE
T ss_pred             HhCCCCCCHHHHHHHHHHHHHHhcC---------------------CcCcEEEECCCCCCHHHHHHHHHHHHHHhCCeEE
Confidence            3689999999999999998877542                     12379999999999999999998776655433  


Q ss_pred             ------HHHHHHHhhhhhhhhh-cCCCCceEEEecc
Q psy3462         322 ------LVQQKMFEQRTQDLQK-IPFRKLKISRLKA  350 (795)
Q Consensus       322 ------~LQ~Ql~~kdip~l~~-i~~~~l~~~~~KG  350 (795)
                            .|-+|..+.    +.+ ..+.++++..+-|
T Consensus       657 vlvPt~~La~Q~~~~----~~~~~~~~~i~v~~l~~  688 (1151)
T 2eyq_A          657 VLVPTTLLAQQHYDN----FRDRFANWPVRIEMISR  688 (1151)
T ss_dssp             EECSSHHHHHHHHHH----HHHHSTTTTCCEEEEST
T ss_pred             EEechHHHHHHHHHH----HHHHhhcCCCeEEEEeC
Confidence                  455665543    222 2234555555543

>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*

Probab=96.90  E-value=0.00089  Score=72.66  Aligned_cols=41  Identities=20%  Similarity=0.089  Sum_probs=32.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      .+.|+|.|.+.+    +++.++.++++.+|||+|||++|+.++..
T Consensus        91 ~~~l~~~Q~~ai----~~i~~~~~~ll~~~TGsGKT~~~l~~i~~  131 (472)
T 2fwr_A           91 EISLRDYQEKAL----ERWLVDKRGCIVLPTGSGKTHVAMAAINE  131 (472)
T ss_dssp             CCCBCHHHHHHH----HHHTTTTEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHH----HHHHhcCCEEEEeCCCCCHHHHHHHHHHH
Confidence            457999995554    44555677999999999999999998764

>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*

Probab=96.88  E-value=0.00036  Score=78.33  Aligned_cols=43  Identities=30%  Similarity=0.553  Sum_probs=35.8

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      .|+| ++||.|.+.+..+.                           +++++++.||||+|||++|++|++.
T Consensus        20 ~~g~~~~r~~Q~~~i~~il---------------------------~g~d~lv~apTGsGKTl~~~lp~l~   63 (523)
T 1oyw_A           20 TFGYQQFRPGQEEIIDTVL---------------------------SGRDCLVVMPTGGGKSLCYQIPALL   63 (523)
T ss_dssp             TTCCSSCCTTHHHHHHHHH---------------------------TTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HhCCCCCCHHHHHHHHHHH---------------------------cCCCEEEECCCCcHHHHHHHHHHHH
Confidence            4777 58999998888764                           2468999999999999999999873

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

Probab=96.83  E-value=0.0012  Score=80.24  Aligned_cols=50  Identities=16%  Similarity=0.273  Sum_probs=41.9

Q ss_pred             eeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         243 KVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       243 ~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ...|||+++|.|.+.+..+.+                           ++++++.||||+|||++|+++++..+...
T Consensus        80 ~~~~~f~L~~~Q~eai~~l~~---------------------------g~~vLV~apTGSGKTlva~lai~~~l~~g  129 (1010)
T 2xgj_A           80 ARTYPFTLDPFQDTAISCIDR---------------------------GESVLVSAHTSAGKTVVAEYAIAQSLKNK  129 (1010)
T ss_dssp             SCCCSSCCCHHHHHHHHHHHH---------------------------TCEEEEECCTTSCHHHHHHHHHHHHHHTT
T ss_pred             HHhCCCCCCHHHHHHHHHHHc---------------------------CCCEEEECCCCCChHHHHHHHHHHHhccC
Confidence            557899999999999887532                           46799999999999999999988777554

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

Probab=96.83  E-value=0.0013  Score=72.05  Aligned_cols=56  Identities=13%  Similarity=0.106  Sum_probs=43.6

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh------
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK------  320 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~------  320 (795)
                      +++++|.|.+.+..+.+                           +..+++.+|||+|||++++.++...+...+      
T Consensus       111 ~~~l~~~Q~~ai~~~~~---------------------------~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl  163 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLV---------------------------NRRRILNLPTSAGRSLIQALLARYYLENYEGKILII  163 (510)
T ss_dssp             EECCCHHHHHHHHHHHH---------------------------HSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEE
T ss_pred             CCCCCHHHHHHHHHHHh---------------------------cCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEE
Confidence            67999999999888643                           256899999999999999998877765543      


Q ss_pred             ---HHHHHHHHh
Q psy3462         321 ---ELVQQKMFE  329 (795)
Q Consensus       321 ---k~LQ~Ql~~  329 (795)
                         ..|-+|..+
T Consensus       164 ~P~~~L~~Q~~~  175 (510)
T 2oca_A          164 VPTTALTTQMAD  175 (510)
T ss_dssp             ESSHHHHHHHHH
T ss_pred             ECcHHHHHHHHH
Confidence               256666654

>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*

Probab=96.82  E-value=0.0014  Score=79.77  Aligned_cols=52  Identities=15%  Similarity=0.105  Sum_probs=38.0

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      |.+......+|.| +.|.    +++.++.+++++++.||||+|||+ |++|++..+..
T Consensus        46 ~~~~~~~~~g~~p-~iQ~----~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~   97 (1054)
T 1gku_B           46 FVEFFRKCVGEPR-AIQK----MWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL   97 (1054)
T ss_dssp             HHHHHHTTTCSCC-HHHH----HHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT
T ss_pred             HHHHHHHhcCCCH-HHHH----HHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh
Confidence            3444433344459 9995    455555578999999999999998 99998887653

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

Probab=96.82  E-value=0.001  Score=80.67  Aligned_cols=54  Identities=13%  Similarity=0.134  Sum_probs=41.0

Q ss_pred             HHHHHHhC---CCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNE---PNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         8 ~~~~~~~~---~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .|.++..+   ..+|.|++.|    .+++.++.+++++++.||||+|||++|++|++....
T Consensus        24 ~f~~l~~~~~~~~~f~l~~~Q----~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~   80 (997)
T 4a4z_A           24 NFDELIPNPARSWPFELDTFQ----KEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR   80 (997)
T ss_dssp             THHHHCSSCSCCCSSCCCHHH----HHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH
T ss_pred             chhhhhHhHHHhCCCCCCHHH----HHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh
Confidence            35555333   3467789999    455667778899999999999999999999776543

>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

Probab=96.82  E-value=0.00022  Score=78.30  Aligned_cols=43  Identities=16%  Similarity=0.088  Sum_probs=31.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -.|.|+|    +.+-..+.++.++|+.||||+|||++|++|+|..+.
T Consensus         3 ~q~~~iq----~~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~   45 (451)
T 2jlq_A            3 AMGEPDY----EVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREAL   45 (451)
T ss_dssp             CCCSCCC----CCCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHH
T ss_pred             CCCCCcH----HHHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHH
Confidence            3567777    323333444555699999999999999999987643

>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

Probab=96.81  E-value=0.0013  Score=66.38  Aligned_cols=40  Identities=20%  Similarity=0.054  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL   61 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL   61 (795)
                      .+.|++.|.+.+.    .+.++.++++.+|||+|||++++.++.
T Consensus        91 ~~~l~~~Q~~ai~----~~~~~~~~ll~~~tG~GKT~~a~~~~~  130 (237)
T 2fz4_A           91 EISLRDYQEKALE----RWLVDKRGCIVLPTGSGKTHVAMAAIN  130 (237)
T ss_dssp             CCCCCHHHHHHHH----HHTTTSEEEEEESSSTTHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHH----HHHhCCCEEEEeCCCCCHHHHHHHHHH
Confidence            4578999965554    444556799999999999999887754

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

Probab=96.80  E-value=0.001  Score=80.72  Aligned_cols=51  Identities=14%  Similarity=0.195  Sum_probs=41.2

Q ss_pred             eeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         242 VKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       242 ~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ....|||+++|.|.+.+..+.                           +++++++.||||+|||++|+.+++..+...
T Consensus        32 ~~~~~~f~l~~~Q~~aI~~il---------------------------~g~~vlv~apTGsGKTlv~~~~i~~~~~~g   82 (997)
T 4a4z_A           32 PARSWPFELDTFQKEAVYHLE---------------------------QGDSVFVAAHTSAGKTVVAEYAIAMAHRNM   82 (997)
T ss_dssp             CSCCCSSCCCHHHHHHHHHHH---------------------------TTCEEEEECCTTSCSHHHHHHHHHHHHHTT
T ss_pred             HHHhCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEECCCCcHHHHHHHHHHHHHhcC
Confidence            344799999999998777653                           257899999999999999999987766544

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

Probab=96.78  E-value=0.00085  Score=73.58  Aligned_cols=43  Identities=14%  Similarity=0.060  Sum_probs=35.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+.|+|.|.+.+..+.+    +.++++.+|||+|||++|+.|++..+
T Consensus       111 ~~~l~~~Q~~ai~~~~~----~~~~ll~~~tGsGKT~~~~~~~~~~~  153 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLARYYL  153 (510)
T ss_dssp             EECCCHHHHHHHHHHHH----HSEEEEECCSTTTHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHh----cCCcEEEeCCCCCHHHHHHHHHHHHH
Confidence            45899999777666553    47899999999999999999877665

>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}

Probab=96.73  E-value=0.001  Score=81.48  Aligned_cols=62  Identities=13%  Similarity=0.247  Sum_probs=48.3

Q ss_pred             CeeeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh
Q psy3462         241 GVKVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK  320 (795)
Q Consensus       241 ~~~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~  320 (795)
                      .....|||+++|.|.+.+..+   +                        .++++++.||||+|||++|+.|++..+...+
T Consensus       176 ~~~~~~~f~ltp~Q~~AI~~i---~------------------------~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~  228 (1108)
T 3l9o_A          176 NEARTYPFTLDPFQDTAISCI---D------------------------RGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ  228 (1108)
T ss_dssp             SCSSCCSSCCCHHHHHHHHHH---T------------------------TTCCEEEECCSSSHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCCCCCHHHHHHHHHH---H------------------------cCCCEEEECCCCCChHHHHHHHHHHHHhcCC
Confidence            345579999999999888775   2                        2578999999999999999999988776543


Q ss_pred             H--------HHHHHHHh
Q psy3462         321 E--------LVQQKMFE  329 (795)
Q Consensus       321 k--------~LQ~Ql~~  329 (795)
                      +        .|-.|...
T Consensus       229 rvlvl~PtraLa~Q~~~  245 (1108)
T 3l9o_A          229 RVIYTSPIKALSNQKYR  245 (1108)
T ss_dssp             EEEEEESSHHHHHHHHH
T ss_pred             eEEEEcCcHHHHHHHHH
Confidence            3        56666553

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

Probab=96.73  E-value=0.0015  Score=74.40  Aligned_cols=48  Identities=27%  Similarity=0.299  Sum_probs=39.0

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .|+| +|||.|.+.+..+.                           .++++++.+|||+|||++|++|++..+...
T Consensus         8 ~~g~~~lr~~Q~~~i~~~l---------------------------~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~   56 (696)
T 2ykg_A            8 LYSPFKPRNYQLELALPAM---------------------------KGKNTIICAPTGCGKTFVSLLICEHHLKKF   56 (696)
T ss_dssp             TTC--CCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             ccCCCCccHHHHHHHHHHH---------------------------cCCCEEEEcCCCchHHHHHHHHHHHHHHhC
Confidence            4665 69999999987753                           246899999999999999999998877653

>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

Probab=96.68  E-value=0.0011  Score=69.66  Aligned_cols=42  Identities=26%  Similarity=0.331  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      +++||.|.+.+..+.+                           + ++++.+|||+|||++++.+++..+.
T Consensus         8 ~~l~~~Q~~~i~~~~~---------------------------~-~~ll~~~tG~GKT~~~~~~~~~~~~   49 (494)
T 1wp9_A            8 IQPRIYQEVIYAKCKE---------------------------T-NCLIVLPTGLGKTLIAMMIAEYRLT   49 (494)
T ss_dssp             HCCCHHHHHHHHHGGG---------------------------S-CEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHhh---------------------------C-CEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            7899999998877431                           3 7899999999999999999887765

>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*

Probab=96.66  E-value=0.0013  Score=78.37  Aligned_cols=40  Identities=23%  Similarity=0.112  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..||+.|    ....-++..|.  |.|++||||||+||++|++..+
T Consensus        73 ~~p~~VQ----~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~  112 (853)
T 2fsf_A           73 MRHFDVQ----LLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNA  112 (853)
T ss_dssp             CCCCHHH----HHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCChHH----HhhcccccCCe--eeeecCCchHHHHHHHHHHHHH
Confidence            5899999    44444566665  9999999999999999988543

>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

Probab=96.62  E-value=0.0013  Score=78.94  Aligned_cols=41  Identities=17%  Similarity=0.105  Sum_probs=33.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ++.||++|    ....-.+..|+  |.||+||+||||+|++|++..+
T Consensus       109 G~rP~~VQ----~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~a  149 (922)
T 1nkt_A          109 DQRPFDVQ----VMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNA  149 (922)
T ss_dssp             SCCCCHHH----HHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHH
T ss_pred             CCCCCHHH----HHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHH
Confidence            35999999    44445666665  9999999999999999987544

>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

Probab=96.55  E-value=0.0038  Score=63.56  Aligned_cols=43  Identities=14%  Similarity=0.098  Sum_probs=34.2

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ++++|.|.+.+..+.+                           ++.+++.+|||+|||++++.++...+.
T Consensus       112 ~~l~~~Q~~ai~~~l~---------------------------~~~~ll~~~tGsGKT~~~~~~~~~~~~  154 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLV---------------------------NRRRILNLPTSAGRSLIQALLARYYLE  154 (282)
T ss_dssp             CCCCHHHHHHHHHHHH---------------------------HSEEEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             cCccHHHHHHHHHHHh---------------------------cCCeEEEcCCCCCcHHHHHHHHHHHHH
Confidence            6899999998887543                           235688999999999999887665544

>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

Probab=96.55  E-value=0.00044  Score=79.68  Aligned_cols=43  Identities=16%  Similarity=0.148  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -.|.|+|..    ....+.+++++|+.||||||||++|++|+|..+.
T Consensus       170 ~~~lpiq~~----~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~  212 (618)
T 2whx_A          170 RIGEPDYEV----DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREAL  212 (618)
T ss_dssp             CCCCCCCCC----CGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHH
T ss_pred             ccCCCcccc----CHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            456777754    2778888999999999999999999999997754

>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*

Probab=96.54  E-value=0.0017  Score=70.37  Aligned_cols=44  Identities=20%  Similarity=0.197  Sum_probs=35.6

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      .++++++|.|.+.+..+.+                           ++.+++.+|||+|||+.|+.++...
T Consensus        89 ~~~~~l~~~Q~~ai~~i~~---------------------------~~~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A           89 DAEISLRDYQEKALERWLV---------------------------DKRGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             CCCCCBCHHHHHHHHHHTT---------------------------TTEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCcCHHHHHHHHHHHh---------------------------cCCEEEEeCCCCCHHHHHHHHHHHc
Confidence            4688999999998876531                           2459999999999999999886543

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

Probab=96.48  E-value=0.0029  Score=71.09  Aligned_cols=41  Identities=22%  Similarity=0.253  Sum_probs=34.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC-CcEEEECCCCCchHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKA-KNCLLESPTGSGKTLALLCS   59 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~-~~~llEAPTGTGKTLAyL~p   59 (795)
                      +.|++.|.+.+..+.+++.++ .++++.+|||+|||++++..
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~  218 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQI  218 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHH
Confidence            469999999999999998776 55899999999999996544

>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

Probab=96.40  E-value=0.0039  Score=79.65  Aligned_cols=54  Identities=24%  Similarity=0.367  Sum_probs=40.3

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHH-hcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGC-NKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al-~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      .|+++... .+..+.|.|    .+++.++ +.++++++.||||+|||+++.+|++..+..
T Consensus       915 ~~e~l~~~-~f~~fnpiQ----~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~  969 (1724)
T 4f92_B          915 AFESLYQD-KFPFFNPIQ----TQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQ  969 (1724)
T ss_dssp             HHHTTTTT-TCSBCCHHH----HHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-cCCCCCHHH----HHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHh
Confidence            45555544 344578999    4455555 567899999999999999999999877653

>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

Probab=96.40  E-value=0.0026  Score=81.17  Aligned_cols=45  Identities=27%  Similarity=0.271  Sum_probs=36.4

Q ss_pred             CCCCCHHHHHHHHHHHH-HHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQ-GCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~-al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      +-.+.+.|.    .+++ +++.++|+|+.||||+|||+++.+|++..+..
T Consensus        77 ~~~ln~iQs----~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~  122 (1724)
T 4f92_B           77 FKTLNRIQS----KLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGK  122 (1724)
T ss_dssp             CSBCCHHHH----HTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGG
T ss_pred             CCCCCHHHH----HHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHh
Confidence            445779994    4444 45778999999999999999999999987754

>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}

Probab=96.40  E-value=0.0027  Score=74.50  Aligned_cols=46  Identities=30%  Similarity=0.336  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      +++|+|.|.+.+..+.                           +++++++.+|||+|||++|++|++..+...
T Consensus       246 ~~~l~~~Q~~~i~~~l---------------------------~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~  291 (797)
T 4a2q_A          246 TKKARSYQIELAQPAI---------------------------NGKNALICAPTGSGKTFVSILICEHHFQNM  291 (797)
T ss_dssp             --CCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHH---------------------------hCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            3579999999887653                           246799999999999999999998887653

>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

Probab=96.37  E-value=0.0028  Score=63.82  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=33.5

Q ss_pred             eeccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHH
Q psy3462         243 KVEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSV  312 (795)
Q Consensus       243 ~~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~  312 (795)
                      .+.++++++|.|.+.+..+.   +                        ++.+++.+|||+|||+.++.++
T Consensus        87 ~~~~~~~l~~~Q~~ai~~~~---~------------------------~~~~ll~~~tG~GKT~~a~~~~  129 (237)
T 2fz4_A           87 YFDAEISLRDYQEKALERWL---V------------------------DKRGCIVLPTGSGKTHVAMAAI  129 (237)
T ss_dssp             CCCCCCCCCHHHHHHHHHHT---T------------------------TSEEEEEESSSTTHHHHHHHHH
T ss_pred             cccCCCCcCHHHHHHHHHHH---h------------------------CCCEEEEeCCCCCHHHHHHHHH
Confidence            34566899999999887642   2                        2458999999999999987764

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

Probab=96.32  E-value=0.0004  Score=80.93  Aligned_cols=46  Identities=15%  Similarity=0.084  Sum_probs=33.1

Q ss_pred             CCCHHHH-----HHHHHHH--HHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          20 LKYSSCK-----ILHLQVI--QGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        20 ~p~~~Q~-----~mm~~i~--~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .|+++|.     +-+..+.  +.+.+++++|+.||||+|||++|++|++..+.
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~  267 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAI  267 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHH
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            5778886     3332222  23347899999999999999999999987653

>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*

Probab=96.30  E-value=0.00096  Score=73.21  Aligned_cols=31  Identities=29%  Similarity=0.274  Sum_probs=27.2

Q ss_pred             HHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          35 GCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        35 al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ++.+++++++.||||+|||++|++|++..+.
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~   34 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECA   34 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHH
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4667899999999999999999999888653

>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

Probab=96.25  E-value=0.0022  Score=73.97  Aligned_cols=75  Identities=24%  Similarity=0.287  Sum_probs=49.5

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      ++| +++|.|.+.+..+.                           +++++++.||||+|||++++.+++..+...++   
T Consensus        21 ~g~~~l~~~Q~~~i~~i~---------------------------~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~   73 (702)
T 2p6r_A           21 EGIEELFPPQAEAVEKVF---------------------------SGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLY   73 (702)
T ss_dssp             C---CCCCCCHHHHHHHT---------------------------TCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CCCCCCCHHHHHHHHHHh---------------------------CCCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEE
Confidence            567 68999988877742                           25789999999999999999999876654332   


Q ss_pred             -----HHHHHHHhhhhhhhhhcCCCCceEEEeccc
Q psy3462         322 -----LVQQKMFEQRTQDLQKIPFRKLKISRLKAK  351 (795)
Q Consensus       322 -----~LQ~Ql~~kdip~l~~i~~~~l~~~~~KGr  351 (795)
                           .|-.|..+.    +++.....+++..+-|.
T Consensus        74 i~P~r~La~q~~~~----~~~~~~~g~~v~~~~G~  104 (702)
T 2p6r_A           74 VVPLRALAGEKYES----FKKWEKIGLRIGISTGD  104 (702)
T ss_dssp             EESSHHHHHHHHHH----HTTTTTTTCCEEEECSS
T ss_pred             EeCcHHHHHHHHHH----HHHHHhcCCEEEEEeCC
Confidence                 466665543    22222334566666554

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

Probab=96.24  E-value=0.0046  Score=69.52  Aligned_cols=44  Identities=23%  Similarity=0.178  Sum_probs=34.5

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l  313 (795)
                      +.+||.|.+.+..+.+.+.++                      ++.+++.+|||||||++.+..+.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~----------------------~~~~ll~~~TGsGKT~~~~~~~~  220 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQG----------------------KKRSLITMATGTGKTVVAFQISW  220 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTT----------------------CSEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHhcC----------------------CCceEEEecCCCChHHHHHHHHH
Confidence            479999999999998877542                      35689999999999999765443

>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*

Probab=96.12  E-value=0.0033  Score=72.62  Aligned_cols=46  Identities=28%  Similarity=0.345  Sum_probs=37.2

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ++| +++|.|.+.+..+   +                       .+++++++.||||+|||+++.++++..+.
T Consensus        19 ~g~~~l~~~Q~~~i~~~---~-----------------------~~~~~~lv~apTGsGKT~~~~l~il~~~~   65 (720)
T 2zj8_A           19 RGIESFYPPQAEALKSG---I-----------------------LEGKNALISIPTASGKTLIAEIAMVHRIL   65 (720)
T ss_dssp             TTCCBCCHHHHHHHTTT---G-----------------------GGTCEEEEECCGGGCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH---h-----------------------cCCCcEEEEcCCccHHHHHHHHHHHHHHH
Confidence            677 6899998877652   1                       13578999999999999999999987665

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

Probab=96.08  E-value=0.0041  Score=74.83  Aligned_cols=41  Identities=24%  Similarity=0.139  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ++.|+++|    ....-.+..|.  |.+|.||+|||++|++|++..+
T Consensus        77 G~~Pt~VQ----~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~a  117 (997)
T 2ipc_A           77 GMRHFDVQ----LIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNA  117 (997)
T ss_dssp             CCCCCHHH----HHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHH----HhhcccccCCc--eeeccCCCchHHHHHHHHHHHH
Confidence            45999999    44445666666  9999999999999999986544

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

Probab=96.08  E-value=0.0044  Score=71.35  Aligned_cols=46  Identities=30%  Similarity=0.408  Sum_probs=37.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ++| +++|.|.+.+..+   +                       .+++++++.||||+|||+++..+++..+.
T Consensus        26 ~g~~~l~~~Q~~~i~~~---~-----------------------~~~~~~lv~apTGsGKT~~~~l~il~~~~   72 (715)
T 2va8_A           26 RGIKKLNPPQTEAVKKG---L-----------------------LEGNRLLLTSPTGSGKTLIAEMGIISFLL   72 (715)
T ss_dssp             TSCCBCCHHHHHHHHTT---T-----------------------TTTCCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH---h-----------------------cCCCcEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            677 6899999887752   2                       13578999999999999999999987665

>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*

Probab=96.03  E-value=0.0034  Score=68.93  Aligned_cols=32  Identities=28%  Similarity=0.334  Sum_probs=27.5

Q ss_pred             ccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         288 CNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       288 l~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      +.+++++++.||||||||++|++|++..+...
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~   36 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECARR   36 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc
Confidence            45689999999999999999999998866544

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

Probab=96.03  E-value=0.0038  Score=68.74  Aligned_cols=32  Identities=25%  Similarity=0.249  Sum_probs=27.4

Q ss_pred             hccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         287 GCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       287 al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ++.+++++++.||||||||++|++|++..+..
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~   48 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ   48 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            35567899999999999999999999876653

>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}

Probab=95.83  E-value=0.0062  Score=73.17  Aligned_cols=45  Identities=31%  Similarity=0.358  Sum_probs=36.6

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      +++|||.|.+.+..+.                           +++++++.+|||+|||++|++|++..+..
T Consensus       246 ~~~~r~~Q~~ai~~il---------------------------~g~~~ll~a~TGsGKTl~~~~~i~~~l~~  290 (936)
T 4a2w_A          246 TKKARSYQIELAQPAI---------------------------NGKNALICAPTGSGKTFVSILICEHHFQN  290 (936)
T ss_dssp             --CCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHTTTTT
T ss_pred             CCCCCHHHHHHHHHHH---------------------------cCCCEEEEeCCCchHHHHHHHHHHHHHHh
Confidence            4689999999887763                           24679999999999999999998877654

>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

Probab=95.79  E-value=0.004  Score=68.34  Aligned_cols=35  Identities=20%  Similarity=0.193  Sum_probs=26.5

Q ss_pred             Hhhcc-ccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         285 IQGCN-KAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       285 i~al~-~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      |+.+. .+.++++.||||||||++|++|+|..+...
T Consensus        12 i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~   47 (451)
T 2jlq_A           12 DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR   47 (451)
T ss_dssp             CGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT
T ss_pred             HHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc
Confidence            44443 345569999999999999999998765443

>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*

Probab=95.79  E-value=0.0073  Score=73.60  Aligned_cols=44  Identities=16%  Similarity=0.135  Sum_probs=35.0

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ++|+| |.|.+.+..+.                           .++++++.||||||||+ |++|++..+..
T Consensus        54 ~g~~p-~iQ~~ai~~il---------------------------~g~dvlv~apTGSGKTl-~~lp~l~~~~~   97 (1054)
T 1gku_B           54 VGEPR-AIQKMWAKRIL---------------------------RKESFAATAPTGVGKTS-FGLAMSLFLAL   97 (1054)
T ss_dssp             TCSCC-HHHHHHHHHHH---------------------------TTCCEECCCCBTSCSHH-HHHHHHHHHHT
T ss_pred             cCCCH-HHHHHHHHHHH---------------------------hCCCEEEEcCCCCCHHH-HHHHHHHHHhh
Confidence            55667 88888877753                           25789999999999998 88888877654

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

Probab=95.75  E-value=0.0038  Score=68.22  Aligned_cols=26  Identities=23%  Similarity=0.272  Sum_probs=23.5

Q ss_pred             CCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          39 AKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        39 ~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ++++++.||||+|||++|++|++..+
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~   27 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREA   27 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            57899999999999999999998655

>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

Probab=95.75  E-value=0.0059  Score=70.38  Aligned_cols=35  Identities=23%  Similarity=0.238  Sum_probs=30.2

Q ss_pred             HhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         285 IQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       285 i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      ++.+.+++++++.||||||||++|++|+|..+...
T Consensus       180 i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~  214 (618)
T 2whx_A          180 EDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR  214 (618)
T ss_dssp             GGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT
T ss_pred             HHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC
Confidence            56677889999999999999999999998776543

>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}

Probab=95.70  E-value=0.0069  Score=60.25  Aligned_cols=34  Identities=18%  Similarity=0.283  Sum_probs=26.9

Q ss_pred             HHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         283 QVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       283 ~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ++++++.+++++++.||||+|||..+.++++...
T Consensus        68 ~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~  101 (235)
T 3llm_A           68 EILEAISQNSVVIIRGATGCGKTTQVPQFILDDF  101 (235)
T ss_dssp             HHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcch
Confidence            4555666788999999999999998887765543

>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

Probab=95.54  E-value=0.009  Score=71.40  Aligned_cols=42  Identities=21%  Similarity=0.158  Sum_probs=32.9

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ..|.|+|.|..-+-.+.                           .|+  +.||+||+|||++|++|++..+
T Consensus        80 lG~~pt~VQ~~~ip~ll---------------------------~G~--Iaea~TGeGKTlaf~LP~~l~a  121 (844)
T 1tf5_A           80 TGMFPFKVQLMGGVALH---------------------------DGN--IAEMKTGEGKTLTSTLPVYLNA  121 (844)
T ss_dssp             HSCCCCHHHHHHHHHHH---------------------------TTS--EEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHhhHHHh---------------------------CCC--EEEccCCcHHHHHHHHHHHHHH
Confidence            45689999987665442                           244  8899999999999999997443

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

Probab=95.41  E-value=0.0087  Score=65.41  Aligned_cols=39  Identities=26%  Similarity=0.394  Sum_probs=29.8

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHHHHhh---------HHHHHHHHh
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQRKEK---------ELVQQKMFE  329 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~~~~~---------k~LQ~Ql~~  329 (795)
                      ++++++.||||+|||++|+.|++..+...+         +.|-+|+.+
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~   49 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYE   49 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHH
Confidence            578999999999999999999985544433         256666654

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

Probab=95.07  E-value=0.011  Score=68.93  Aligned_cols=31  Identities=23%  Similarity=0.306  Sum_probs=26.6

Q ss_pred             cccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         289 NKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       289 ~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .+++++++.||||||||++|++|++..+...
T Consensus       239 ~~g~dvlv~apTGSGKTl~~ll~il~~l~~~  269 (673)
T 2wv9_A          239 KKRQLTVLDLHPGAGKTRRILPQIIKDAIQK  269 (673)
T ss_dssp             STTCEEEECCCTTTTTTTTHHHHHHHHHHHT
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC
Confidence            3678999999999999999999998775443

>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*

Probab=94.91  E-value=0.018  Score=70.30  Aligned_cols=44  Identities=16%  Similarity=0.099  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhc----------CCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNK----------AKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~----------~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ..|||.|.+.+..+.+.+..          +.++++.+|||||||+++ ++++..
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~l  323 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARL  323 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHH
Confidence            46999999999999888753          367999999999999997 565544

>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

Probab=94.68  E-value=0.041  Score=60.08  Aligned_cols=40  Identities=15%  Similarity=-0.118  Sum_probs=33.9

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHH
Q psy3462          20 LKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCS   59 (795)
Q Consensus        20 ~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~p   59 (795)
                      .+||.|.+.+..+......+.++|+-+|||+|||+..+..
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~   76 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAV   76 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHH
Confidence            5889999988877777777889999999999999886543

>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*

Probab=94.47  E-value=0.028  Score=67.24  Aligned_cols=42  Identities=21%  Similarity=0.209  Sum_probs=32.3

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ....|+|.|..-+-.+.                           .|+  +.||+||||||++|++|++..+
T Consensus        71 lg~~p~~VQ~~~i~~ll---------------------------~G~--Iaem~TGsGKTlaf~LP~l~~~  112 (853)
T 2fsf_A           71 FGMRHFDVQLLGGMVLN---------------------------ERC--IAEMRTGEGKTLTATLPAYLNA  112 (853)
T ss_dssp             HSCCCCHHHHHHHHHHH---------------------------SSE--EEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCCChHHHhhccccc---------------------------CCe--eeeecCCchHHHHHHHHHHHHH
Confidence            45788999987665431                           244  8999999999999999997544

>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

Probab=94.43  E-value=0.026  Score=67.91  Aligned_cols=43  Identities=19%  Similarity=0.213  Sum_probs=33.0

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR  317 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~  317 (795)
                      ..+.|+|.|..-+-.+.                           .|+  +.||+||+|||+++++|++..+.
T Consensus       108 lG~rP~~VQ~~~ip~Ll---------------------------~G~--Iaem~TGeGKTLa~~LP~~l~aL  150 (922)
T 1nkt_A          108 LDQRPFDVQVMGAAALH---------------------------LGN--VAEMKTGEGKTLTCVLPAYLNAL  150 (922)
T ss_dssp             HSCCCCHHHHHHHHHHH---------------------------TTE--EEECCTTSCHHHHTHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHhHh---------------------------cCC--EEEecCCCccHHHHHHHHHHHHH
Confidence            45789999987665432                           233  99999999999999999965443

>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 ...

Probab=93.72  E-value=0.006  Score=71.30  Aligned_cols=33  Identities=24%  Similarity=0.191  Sum_probs=28.2

Q ss_pred             HHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          30 LQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        30 ~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      +++..++.+++++++.||||+|||++|++|++.
T Consensus       223 ~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~  255 (666)
T 3o8b_A          223 SSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA  255 (666)
T ss_dssp             CSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH
T ss_pred             HHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH
Confidence            556677778889999999999999999998764

>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*

Probab=93.57  E-value=0.043  Score=64.87  Aligned_cols=39  Identities=18%  Similarity=0.158  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      ..|.+.|+   +++..++.+++++++.||||+|||+  ++|.+.
T Consensus        92 ~lP~~~q~---~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll  130 (773)
T 2xau_A           92 ELPVHAQR---DEFLKLYQNNQIMVFVGETGSGKTT--QIPQFV  130 (773)
T ss_dssp             TSGGGGGH---HHHHHHHHHCSEEEEECCTTSSHHH--HHHHHH
T ss_pred             cCChHHHH---HHHHHHHhCCCeEEEECCCCCCHHH--HHHHHH
Confidence            46777774   4556667788899999999999998  788763

>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}

Probab=93.53  E-value=0.13  Score=56.45  Aligned_cols=64  Identities=14%  Similarity=0.128  Sum_probs=43.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCC-cEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccccc
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAK-NCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDF   96 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~-~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~   96 (795)
                      +-.+.+.|++.+..+...+.++. +++|.||.|||||. .+...+.++...                +...++.|+-|+.
T Consensus        23 ~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~-ll~~~~~~l~~~----------------~~~~il~~a~T~~   85 (459)
T 3upu_A           23 FDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATT-LTKFIIEALIST----------------GETGIILAAPTHA   85 (459)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHH-HHHHHHHHHHHT----------------TCCCEEEEESSHH
T ss_pred             cccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHH-HHHHHHHHHHhc----------------CCceEEEecCcHH
Confidence            33455899999999988888766 89999999999993 333333333322                1245777777765


Q ss_pred             cc
Q psy3462          97 FL   98 (795)
Q Consensus        97 ~l   98 (795)
                      ..
T Consensus        86 Aa   87 (459)
T 3upu_A           86 AK   87 (459)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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

Probab=93.08  E-value=0.11  Score=56.56  Aligned_cols=45  Identities=20%  Similarity=0.191  Sum_probs=34.2

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSV  312 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~  312 (795)
                      .+..++||.|.+.+..+......                       +..+++..|||+|||+..+..+
T Consensus        33 ~~~~~L~~~Q~~~v~~l~~~~~~-----------------------~~~~ilad~~GlGKT~~ai~~i   77 (500)
T 1z63_A           33 NIKANLRPYQIKGFSWMRFMNKL-----------------------GFGICLADDMGLGKTLQTIAVF   77 (500)
T ss_dssp             SCSSCCCHHHHHHHHHHHHHHHT-----------------------TCCEEECCCTTSCHHHHHHHHH
T ss_pred             hhhccchHHHHHHHHHHHHHhhC-----------------------CCCEEEEeCCCCcHHHHHHHHH
Confidence            34567999999998877544432                       4678999999999999876543

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

Probab=92.66  E-value=0.077  Score=64.15  Aligned_cols=42  Identities=24%  Similarity=0.255  Sum_probs=32.6

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ..|.|+|.|..-+-.+.                           .|.  +.||.||+|||+++++|++..+
T Consensus        76 lG~~Pt~VQ~~~ip~Ll---------------------------qG~--IaeakTGeGKTLvf~Lp~~L~a  117 (997)
T 2ipc_A           76 LGMRHFDVQLIGGAVLH---------------------------EGK--IAEMKTGEGKTLVATLAVALNA  117 (997)
T ss_dssp             TCCCCCHHHHHHHHHHH---------------------------TTS--EEECCSTHHHHHHHHHHHHHHH
T ss_pred             hCCCCcHHHHhhccccc---------------------------CCc--eeeccCCCchHHHHHHHHHHHH
Confidence            56799999987765432                           244  8999999999999999995433

>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*

Probab=92.52  E-value=0.11  Score=61.84  Aligned_cols=43  Identities=21%  Similarity=0.160  Sum_probs=33.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          17 NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        17 ~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      -+..||+.|  +|-.+  +|+.|+  |.|..||.||||++.+|++..+.
T Consensus        72 lg~r~~dvQ--ligg~--~L~~G~--iaEM~TGEGKTLva~lp~~lnAL  114 (822)
T 3jux_A           72 LGMRPFDVQ--VMGGI--ALHEGK--VAEMKTGEGKTLAATMPIYLNAL  114 (822)
T ss_dssp             TSCCCCHHH--HHHHH--HHHTTC--EEECCTTSCHHHHTHHHHHHHHT
T ss_pred             hCCCCcHHH--HHHHH--HHhCCC--hhhccCCCCccHHHHHHHHHHHh
Confidence            366899999  44443  566665  99999999999999999876554

>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 ...

Probab=91.93  E-value=0.048  Score=63.76  Aligned_cols=31  Identities=26%  Similarity=0.223  Sum_probs=25.6

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      +++++.+++++++.||||+|||++++.+++.
T Consensus       225 i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~  255 (666)
T 3o8b_A          225 PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA  255 (666)
T ss_dssp             CCCCCSSCEEEEEECCTTSCTTTHHHHHHHH
T ss_pred             HHHHHHcCCeEEEEeCCchhHHHHHHHHHHH
Confidence            4455667889999999999999999987653

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

Probab=91.61  E-value=0.22  Score=57.13  Aligned_cols=56  Identities=20%  Similarity=0.343  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      +.|.   ++|..++......||.||.|||||-.. +-++.++               +.  .+.+|+.|+-||..+.
T Consensus       192 ~~Q~---~AV~~al~~~~~~lI~GPPGTGKT~ti-~~~I~~l---------------~~--~~~~ILv~a~TN~AvD  247 (646)
T 4b3f_X          192 TSQK---EAVLFALSQKELAIIHGPPGTGKTTTV-VEIILQA---------------VK--QGLKVLCCAPSNIAVD  247 (646)
T ss_dssp             HHHH---HHHHHHHHCSSEEEEECCTTSCHHHHH-HHHHHHH---------------HH--TTCCEEEEESSHHHHH
T ss_pred             HHHH---HHHHHHhcCCCceEEECCCCCCHHHHH-HHHHHHH---------------Hh--CCCeEEEEcCchHHHH
Confidence            6774   466667777778999999999999542 2222221               11  2468999999998763

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

Probab=91.22  E-value=0.17  Score=46.63  Aligned_cols=27  Identities=15%  Similarity=0.160  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      ++.+.+..+...+.+++|.+|+|||||
T Consensus        12 ~~~~~~~~~a~~~~~vll~G~~GtGKt   38 (145)
T 3n70_A           12 QYRRRLQQLSETDIAVWLYGAPGTGRM   38 (145)
T ss_dssp             HHHHHHHHHTTCCSCEEEESSTTSSHH
T ss_pred             HHHHHHHHHhCCCCCEEEECCCCCCHH
Confidence            444555555567789999999999999

>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*

Probab=91.16  E-value=0.14  Score=62.60  Aligned_cols=55  Identities=18%  Similarity=0.135  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ..|||.|...+..+.+.+....             ..-..-..++.+++.+|||||||++. ++++.++
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~-------------~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll  324 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSF-------------TAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLA  324 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHH-------------HHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcc-------------cccccccCCCCEEEEecCCCCHHHHH-HHHHHHH
Confidence            4699999999999887664210             00000012357999999999999997 5544443

>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*

Probab=90.77  E-value=0.17  Score=58.00  Aligned_cols=57  Identities=16%  Similarity=0.132  Sum_probs=39.0

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEECCCCCchH--HHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccccccc
Q psy3462          22 YSSCKILHLQVIQGCNKAKNCLLESPTGSGKT--LALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFL   98 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKT--LAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l   98 (795)
                      .+.|++.+..    +..+..+++.||+|||||  ++++++.+...                ....+.+++.|+.|+...
T Consensus       151 ~~~Q~~Ai~~----~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~----------------~~~~~~~vll~APTg~AA  209 (608)
T 1w36_D          151 INWQKVAAAV----ALTRRISVISGGPGTGKTTTVAKLLAALIQM----------------ADGERCRIRLAAPTGKAA  209 (608)
T ss_dssp             CCHHHHHHHH----HHTBSEEEEECCTTSTHHHHHHHHHHHHHHT----------------CSSCCCCEEEEBSSHHHH
T ss_pred             CHHHHHHHHH----HhcCCCEEEEeCCCCCHHHHHHHHHHHHHHh----------------hhcCCCeEEEEeCChhHH
Confidence            4678554443    335789999999999999  88888876532                112345777887776643

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

Probab=90.67  E-value=0.12  Score=53.48  Aligned_cols=45  Identities=22%  Similarity=0.231  Sum_probs=34.4

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      .++..+......  ..-+|.+.+..+..++..+.+++|.||+|||||
T Consensus        16 ~~~~~~~~~~~~--~i~g~~~~~~~l~~~l~~~~~vll~G~pGtGKT   60 (331)
T 2r44_A           16 NKIKEVIDEVGK--VVVGQKYMINRLLIGICTGGHILLEGVPGLAKT   60 (331)
T ss_dssp             HHHHHHHHHHTT--TCCSCHHHHHHHHHHHHHTCCEEEESCCCHHHH
T ss_pred             HHHHHHHHHhcc--ceeCcHHHHHHHHHHHHcCCeEEEECCCCCcHH
Confidence            445555554332  345677888888888888999999999999999

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

Probab=90.64  E-value=0.17  Score=46.58  Aligned_cols=27  Identities=15%  Similarity=0.197  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      ++.+.+..+...+.+++|.+|+|||||
T Consensus        15 ~l~~~~~~~~~~~~~vll~G~~GtGKt   41 (143)
T 3co5_A           15 EMNREVEAAAKRTSPVFLTGEAGSPFE   41 (143)
T ss_dssp             HHHHHHHHHHTCSSCEEEEEETTCCHH
T ss_pred             HHHHHHHHHhCCCCcEEEECCCCccHH
Confidence            344455555566789999999999999

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

Probab=90.32  E-value=0.3  Score=59.09  Aligned_cols=44  Identities=18%  Similarity=0.038  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      .+.|+|.|.+.+..+..  .....+|+-+|||+|||+.++..+...
T Consensus       151 ~~~LrpyQ~eav~~~l~--~~~~~~LLad~tGlGKTi~Ai~~i~~l  194 (968)
T 3dmq_A          151 RTSLIPHQLNIAHDVGR--RHAPRVLLADEVGLGKTIEAGMILHQQ  194 (968)
T ss_dssp             SSCCCHHHHHHHHHHHH--SSSCEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHH--hcCCCEEEECCCCCcHHHHHHHHHHHH
Confidence            46799999876665544  224578999999999999987775444

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

Probab=90.21  E-value=0.28  Score=46.81  Aligned_cols=32  Identities=19%  Similarity=0.020  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHhcC------CcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKA------KNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~------~~~llEAPTGTGKTL   54 (795)
                      +.|.+.++.+.+.+.+.      .+++|.+|+|||||.
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~   69 (202)
T 2w58_A           32 DGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTY   69 (202)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHH
T ss_pred             hhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHH
Confidence            46767777777777654      689999999999994

>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*

Probab=89.32  E-value=0.37  Score=45.36  Aligned_cols=36  Identities=19%  Similarity=0.132  Sum_probs=26.9

Q ss_pred             CCCC-CHHHHHHHHHHHHHHh-----cCCcEEEECCCCCchH
Q psy3462          18 YFLK-YSSCKILHLQVIQGCN-----KAKNCLLESPTGSGKT   53 (795)
Q Consensus        18 ~~~p-~~~Q~~mm~~i~~al~-----~~~~~llEAPTGTGKT   53 (795)
                      .|.| .+.|.+.++.+.+.+.     .+..++|.+|+|||||
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKT   52 (180)
T 3ec2_A           11 TYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKT   52 (180)
T ss_dssp             SCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHH
T ss_pred             cccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHH
Confidence            4445 4678777777666553     3678999999999999

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

Probab=88.92  E-value=0.28  Score=44.80  Aligned_cols=34  Identities=24%  Similarity=0.128  Sum_probs=24.7

Q ss_pred             CCHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          21 KYSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      ..-++.+.++.+.+.+..+  .+++|.||+|||||.
T Consensus        23 ~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~   58 (195)
T 1jbk_A           23 PVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTA   58 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHH
T ss_pred             ccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHH
Confidence            3344455667777777654  579999999999993

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

Probab=88.40  E-value=0.57  Score=55.24  Aligned_cols=43  Identities=16%  Similarity=-0.060  Sum_probs=37.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHH
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL   61 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL   61 (795)
                      ..+||.|.+-+..+......+.++||-.+||+|||+..+..+.
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~  277 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFIS  277 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHH
Confidence            4678999999998888888999999999999999988766543

>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

Probab=88.38  E-value=0.55  Score=54.00  Aligned_cols=44  Identities=14%  Similarity=0.171  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHHHh-----cCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          20 LKYSSCKILHLQVIQGCN-----KAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        20 ~p~~~Q~~mm~~i~~al~-----~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      .+||.|.+-+..+++.+.     ++..+|+-.+||+|||+..+..+...
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l  103 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTL  103 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHH
Confidence            578999999998888874     45679999999999998877665443

>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}

Probab=88.28  E-value=0.67  Score=50.85  Aligned_cols=51  Identities=16%  Similarity=0.208  Sum_probs=37.5

Q ss_pred             cCCC-CCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPVK-AYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy~-~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .+|. .-+.|.+.+..+.+.+.++                      .++.++.||.|||||. .+...+.++...
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~----------------------~~~~li~G~aGTGKT~-ll~~~~~~l~~~   72 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEK----------------------KHHVTINGPAGTGATT-LTKFIIEALIST   72 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSS----------------------SCEEEEECCTTSCHHH-HHHHHHHHHHHT
T ss_pred             CccccCCHHHHHHHHHHHHHHhcC----------------------CCEEEEEeCCCCCHHH-HHHHHHHHHHhc
Confidence            3453 6789999999988877642                      3489999999999995 445556666543

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

Probab=87.93  E-value=0.5  Score=57.13  Aligned_cols=49  Identities=20%  Similarity=0.223  Sum_probs=36.8

Q ss_pred             cCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         246 FPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       246 fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .++++||.|.+.+..+..   +                      .+..+++.+|||+|||+.++..+.......
T Consensus       150 ~~~~LrpyQ~eav~~~l~---~----------------------~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g  198 (968)
T 3dmq_A          150 QRTSLIPHQLNIAHDVGR---R----------------------HAPRVLLADEVGLGKTIEAGMILHQQLLSG  198 (968)
T ss_dssp             CSSCCCHHHHHHHHHHHH---S----------------------SSCEEEECCCTTSCHHHHHHHHHHHHHHTS
T ss_pred             CCCCCcHHHHHHHHHHHH---h----------------------cCCCEEEECCCCCcHHHHHHHHHHHHHHhC
Confidence            458899999998776543   2                      135689999999999999988765555433

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

Probab=87.52  E-value=0.26  Score=55.68  Aligned_cols=45  Identities=9%  Similarity=0.044  Sum_probs=34.6

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      +.+..+.+.+..  -.-+|.+.++.+..++..+.+++|.||+|||||
T Consensus        11 ~~~~~l~~~l~~--~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT   55 (500)
T 3nbx_X           11 ERISRLSSSLEK--GLYERSHAIRLCLLAALSGESVFLLGPPGIAKS   55 (500)
T ss_dssp             HHHHHHHHHHHT--TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHH
T ss_pred             HHHHHHHHHHHh--hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHH
Confidence            445555554432  234677888999999999999999999999999

>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*

Probab=87.42  E-value=0.29  Score=46.09  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKAK---NCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~---~~llEAPTGTGKTL   54 (795)
                      -++.+.++.+...+..+.   .++|.||+|||||.
T Consensus        26 ~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~   60 (250)
T 1njg_A           26 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTS   60 (250)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHH
T ss_pred             hCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHH
Confidence            445566777777777765   58999999999993

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

Probab=87.35  E-value=0.3  Score=44.76  Aligned_cols=32  Identities=25%  Similarity=0.176  Sum_probs=23.7

Q ss_pred             CHHHHHHHHHHHHHHhc--CCcEEEECCCCCchH
Q psy3462          22 YSSCKILHLQVIQGCNK--AKNCLLESPTGSGKT   53 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~--~~~~llEAPTGTGKT   53 (795)
                      .-++...++.+.+.+..  ..+++|.+|+|||||
T Consensus        24 ~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT   57 (187)
T 2p65_A           24 VIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKT   57 (187)
T ss_dssp             CCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHH
T ss_pred             hhcchHHHHHHHHHHhCCCCCceEEECCCCCCHH
Confidence            33445556677777755  457999999999999

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=87.34  E-value=0.75  Score=48.17  Aligned_cols=30  Identities=20%  Similarity=0.165  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHhc-----CCcEEEECCCCCchH
Q psy3462          24 SCKILHLQVIQGCNK-----AKNCLLESPTGSGKT   53 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~-----~~~~llEAPTGTGKT   53 (795)
                      .+.+.++.+.+.+.+     +.+++|.||||||||
T Consensus       132 ~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT  166 (308)
T 2qgz_A          132 SRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKS  166 (308)
T ss_dssp             HHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHH
T ss_pred             HHHHHHHHHHHHHHhccccCCceEEEECCCCCCHH
Confidence            555566666666664     578999999999999

>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*

Probab=87.13  E-value=0.59  Score=43.96  Aligned_cols=41  Identities=17%  Similarity=0.127  Sum_probs=29.5

Q ss_pred             CCC-CHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhH
Q psy3462         248 VKA-YPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       248 y~~-yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTl  306 (795)
                      |.+ .+.|...+..+.+.++.-                  .+..+.++++-||+|||||.
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~------------------~~~~g~~~~l~G~~G~GKTt   53 (180)
T 3ec2_A           12 YHPKNVSQNRALLTIRVFVHNF------------------NPEEGKGLTFVGSPGVGKTH   53 (180)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHSC------------------CGGGCCEEEECCSSSSSHHH
T ss_pred             ccCCCHHHHHHHHHHHHHHHhc------------------cccCCCEEEEECCCCCCHHH
Confidence            544 578888888877666531                  01246789999999999995

>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

Probab=86.96  E-value=0.76  Score=52.70  Aligned_cols=57  Identities=18%  Similarity=0.226  Sum_probs=36.2

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          22 YSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      -+.|.+.+..+   + .+...+|.||+|||||.... .++.++.                ...+.+++.|+-||....
T Consensus       182 n~~Q~~av~~~---l-~~~~~li~GppGTGKT~~~~-~~i~~l~----------------~~~~~~ilv~a~tn~A~~  238 (624)
T 2gk6_A          182 NHSQVYAVKTV---L-QRPLSLIQGPPGTGKTVTSA-TIVYHLA----------------RQGNGPVLVCAPSNIAVD  238 (624)
T ss_dssp             CHHHHHHHHHH---H-TCSEEEEECCTTSCHHHHHH-HHHHHHH----------------TSSSCCEEEEESSHHHHH
T ss_pred             CHHHHHHHHHH---h-cCCCeEEECCCCCCHHHHHH-HHHHHHH----------------HcCCCeEEEEeCcHHHHH
Confidence            37785555443   3 35689999999999995322 1222111                114578999999987754

>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}

Probab=86.55  E-value=0.39  Score=44.91  Aligned_cols=32  Identities=19%  Similarity=0.260  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      -++.+.++.+.+.+..+  .+++|.||+|||||.
T Consensus        20 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~   53 (226)
T 2chg_A           20 VGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTA   53 (226)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHH
T ss_pred             cCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHH
Confidence            34556677777777765  359999999999993

>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*

Probab=86.32  E-value=0.39  Score=48.34  Aligned_cols=15  Identities=60%  Similarity=0.860  Sum_probs=13.8

Q ss_pred             CCcEEEECCCCCchH
Q psy3462          39 AKNCLLESPTGSGKT   53 (795)
Q Consensus        39 ~~~~llEAPTGTGKT   53 (795)
                      ..+++|.||+|||||
T Consensus        50 ~~~vll~G~~GtGKT   64 (310)
T 1ofh_A           50 PKNILMIGPTGVGKT   64 (310)
T ss_dssp             CCCEEEECCTTSSHH
T ss_pred             CceEEEECCCCCCHH
Confidence            567999999999999

>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

Probab=86.21  E-value=0.42  Score=50.45  Aligned_cols=17  Identities=65%  Similarity=0.827  Sum_probs=14.6

Q ss_pred             cCCcEEEECCCCCchHH
Q psy3462          38 KAKNCLLESPTGSGKTL   54 (795)
Q Consensus        38 ~~~~~llEAPTGTGKTL   54 (795)
                      ...+++|.+|+|||||.
T Consensus        50 ~~~~vll~GppGtGKT~   66 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTL   66 (363)
T ss_dssp             CCCCEEEECCTTSSHHH
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            34679999999999994

>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*

Probab=86.13  E-value=0.4  Score=56.74  Aligned_cols=29  Identities=21%  Similarity=0.242  Sum_probs=22.3

Q ss_pred             HHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         284 VIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       284 ~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      +..++..++++++.||||+|||+  ++|.+.
T Consensus       102 i~~~l~~~~~vii~gpTGSGKTt--llp~ll  130 (773)
T 2xau_A          102 FLKLYQNNQIMVFVGETGSGKTT--QIPQFV  130 (773)
T ss_dssp             HHHHHHHCSEEEEECCTTSSHHH--HHHHHH
T ss_pred             HHHHHhCCCeEEEECCCCCCHHH--HHHHHH
Confidence            44445567889999999999999  566653

>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*

Probab=86.06  E-value=0.5  Score=47.24  Aligned_cols=27  Identities=26%  Similarity=0.207  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      ++.+.+..+...+.+++|.||+|||||
T Consensus        17 ~~~~~~~~~~~~~~~vll~G~~GtGKt   43 (265)
T 2bjv_A           17 EVLEQVSHLAPLDKPVLIIGERGTGKE   43 (265)
T ss_dssp             HHHHHHHHHTTSCSCEEEECCTTSCHH
T ss_pred             HHHHHHHHHhCCCCCEEEECCCCCcHH
Confidence            444555555566788999999999999

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

Probab=85.88  E-value=0.44  Score=43.43  Aligned_cols=17  Identities=35%  Similarity=0.395  Sum_probs=14.6

Q ss_pred             cCcEEEeCCCCCChhHH
Q psy3462         291 AKNCLLESPTGSGKTLA  307 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTla  307 (795)
                      ..++++.||+|||||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46799999999999953

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

Probab=85.60  E-value=0.72  Score=42.36  Aligned_cols=17  Identities=18%  Similarity=0.282  Sum_probs=15.0

Q ss_pred             ccCcEEEeCCCCCChhH
Q psy3462         290 KAKNCLLESPTGSGKTL  306 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTl  306 (795)
                      .+.++++.||+|||||.
T Consensus        23 ~~~~vll~G~~GtGKt~   39 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMT   39 (145)
T ss_dssp             CCSCEEEESSTTSSHHH
T ss_pred             CCCCEEEECCCCCCHHH
Confidence            45789999999999995

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

Probab=85.42  E-value=0.4  Score=56.08  Aligned_cols=27  Identities=19%  Similarity=0.151  Sum_probs=21.7

Q ss_pred             HHHHHHhccCccccccCc--eeEEEEeec
Q psy3462         624 AYRALNQALGRCIRHRYD--WGAILLVDQ  650 (795)
Q Consensus       624 AmRaVNQAIGRvIRHknD--yGaIiLlD~  650 (795)
                      ......|.+||+=|...+  -|.++++..
T Consensus       415 s~~~~~QR~GRAGR~g~~g~~G~v~~l~~  443 (677)
T 3rc3_A          415 TTSQALQIAGRAGRFSSRFKEGEVTTMNH  443 (677)
T ss_dssp             CHHHHHHHHTTBTCTTSSCSSEEEEESST
T ss_pred             CHHHHHHHhcCCCCCCCCCCCEEEEEEec
Confidence            356778999999999876  578888864

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=85.39  E-value=0.58  Score=44.83  Aligned_cols=29  Identities=21%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHhc--CCcEEEECCCCCchH
Q psy3462          25 CKILHLQVIQGCNK--AKNCLLESPTGSGKT   53 (795)
Q Consensus        25 Q~~mm~~i~~al~~--~~~~llEAPTGTGKT   53 (795)
                      +.+.++.+...+..  +..++|.||+|||||
T Consensus        36 ~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT   66 (242)
T 3bos_A           36 NDELIGALKSAASGDGVQAIYLWGPVKSGRT   66 (242)
T ss_dssp             CHHHHHHHHHHHHTCSCSEEEEECSTTSSHH
T ss_pred             CHHHHHHHHHHHhCCCCCeEEEECCCCCCHH
Confidence            34566666666654  567999999999999

>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*

Probab=85.29  E-value=0.49  Score=54.29  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=20.0

Q ss_pred             cCcEEEeCCCCCChh--HHHHHHHHH
Q psy3462         291 AKNCLLESPTGSGKT--LALLCSVLA  314 (795)
Q Consensus       291 ~~~~l~EaPTGTGKT--layL~~~l~  314 (795)
                      ++++++.||+|||||  ++++++.+.
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l~  189 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAALI  189 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            578999999999999  777777654

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

Probab=85.00  E-value=0.49  Score=55.37  Aligned_cols=17  Identities=41%  Similarity=0.509  Sum_probs=15.4

Q ss_pred             cCCcEEEECCCCCchHH
Q psy3462          38 KAKNCLLESPTGSGKTL   54 (795)
Q Consensus        38 ~~~~~llEAPTGTGKTL   54 (795)
                      +++++++.||||+|||+
T Consensus       154 ~rk~vlv~apTGSGKT~  170 (677)
T 3rc3_A          154 QRKIIFHSGPTNSGKTY  170 (677)
T ss_dssp             CCEEEEEECCTTSSHHH
T ss_pred             CCCEEEEEcCCCCCHHH
Confidence            56789999999999997

>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

Probab=84.45  E-value=0.66  Score=46.91  Aligned_cols=33  Identities=18%  Similarity=0.247  Sum_probs=27.1

Q ss_pred             CHHHHHHHHHHHHHHhcCC--cEEEECCCCCchHH
Q psy3462          22 YSSCKILHLQVIQGCNKAK--NCLLESPTGSGKTL   54 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKTL   54 (795)
                      .-+|.+.++.+...+..+.  +++|.||+|||||.
T Consensus        27 ~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~   61 (327)
T 1iqp_A           27 IVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTT   61 (327)
T ss_dssp             CCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHH
T ss_pred             hhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHH
Confidence            3567777888888887765  79999999999993

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

Probab=83.50  E-value=0.48  Score=43.38  Aligned_cols=16  Identities=38%  Similarity=0.451  Sum_probs=14.2

Q ss_pred             cCcEEEeCCCCCChhH
Q psy3462         291 AKNCLLESPTGSGKTL  306 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTl  306 (795)
                      ..++++.||+|||||.
T Consensus        43 ~~~vll~G~~G~GKT~   58 (187)
T 2p65_A           43 KNNPILLGDPGVGKTA   58 (187)
T ss_dssp             SCEEEEESCGGGCHHH
T ss_pred             CCceEEECCCCCCHHH
Confidence            4678999999999995

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

Probab=82.73  E-value=0.51  Score=47.80  Aligned_cols=31  Identities=29%  Similarity=0.282  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHhcC-----------CcEEEECCCCCchHH
Q psy3462          24 SCKILHLQVIQGCNKA-----------KNCLLESPTGSGKTL   54 (795)
Q Consensus        24 ~Q~~mm~~i~~al~~~-----------~~~llEAPTGTGKTL   54 (795)
                      +|...++.+..++...           .+++|.+|+|||||.
T Consensus        21 G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~   62 (311)
T 4fcw_A           21 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTE   62 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHH
Confidence            4555556666655543           469999999999993

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=82.11  E-value=0.51  Score=48.46  Aligned_cols=33  Identities=21%  Similarity=0.231  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          22 YSSCKILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      .-+|.+.++.+...+..+  .+++|.||+|||||.
T Consensus        39 i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~   73 (353)
T 1sxj_D           39 VTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTS   73 (353)
T ss_dssp             CCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHH
T ss_pred             hhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHH
Confidence            356667788888888887  679999999999993

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

Probab=81.93  E-value=0.7  Score=42.45  Aligned_cols=17  Identities=18%  Similarity=0.225  Sum_probs=14.8

Q ss_pred             ccCcEEEeCCCCCChhH
Q psy3462         290 KAKNCLLESPTGSGKTL  306 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTl  306 (795)
                      .+.++++.||+|||||.
T Consensus        26 ~~~~vll~G~~GtGKt~   42 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFET   42 (143)
T ss_dssp             CSSCEEEEEETTCCHHH
T ss_pred             CCCcEEEECCCCccHHH
Confidence            35789999999999995

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=81.80  E-value=0.91  Score=47.32  Aligned_cols=28  Identities=21%  Similarity=0.315  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHhcCCcEEEECCCCCchHH
Q psy3462          27 ILHLQVIQGCNKAKNCLLESPTGSGKTL   54 (795)
Q Consensus        27 ~mm~~i~~al~~~~~~llEAPTGTGKTL   54 (795)
                      ++++.+..+...+.+++|.+|||||||+
T Consensus        13 ~~~~~~~~~a~~~~~vLi~Ge~GtGKt~   40 (304)
T 1ojl_A           13 HLLNEIAMVAPSDATVLIHGDSGTGKEL   40 (304)
T ss_dssp             HHHHHHHHHCSTTSCEEEESCTTSCHHH
T ss_pred             HHHHHHHHHhCCCCcEEEECCCCchHHH
Confidence            4444455555567789999999999994

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

Probab=81.50  E-value=0.85  Score=48.68  Aligned_cols=32  Identities=13%  Similarity=0.022  Sum_probs=23.4

Q ss_pred             HHHH-HHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          23 SSCK-ILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~-~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      ..|. ++...+..++..+  .+++|-||+|||||.
T Consensus        26 e~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~   60 (318)
T 3te6_A           26 VEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQ   60 (318)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHH
Confidence            4454 5555777777554  569999999999993

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=81.48  E-value=0.68  Score=47.78  Aligned_cols=32  Identities=19%  Similarity=0.197  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHhc----C---CcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNK----A---KNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~----~---~~~llEAPTGTGKTL   54 (795)
                      -+|...++.+...+..    +   .+++|.||+|||||.
T Consensus        32 iG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~   70 (338)
T 3pfi_A           32 IGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTT   70 (338)
T ss_dssp             CSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHH
T ss_pred             CChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHH
Confidence            3455555555555543    2   479999999999994

>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}

Probab=81.23  E-value=0.93  Score=42.30  Aligned_cols=15  Identities=40%  Similarity=0.724  Sum_probs=13.4

Q ss_pred             CcEEEeCCCCCChhH
Q psy3462         292 KNCLLESPTGSGKTL  306 (795)
Q Consensus       292 ~~~l~EaPTGTGKTl  306 (795)
                      .++++.||+|||||.
T Consensus        39 ~~~ll~G~~G~GKT~   53 (226)
T 2chg_A           39 PHLLFSGPPGTGKTA   53 (226)
T ss_dssp             CCEEEECSTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            469999999999995

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

Probab=80.89  E-value=2.6  Score=48.23  Aligned_cols=58  Identities=10%  Similarity=-0.024  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEeccccccc
Q psy3462          19 FLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFL   98 (795)
Q Consensus        19 ~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l   98 (795)
                      +...+.|++.+.    .+..+..++|.||.|||||..  +-++....               . ..+.+|+.|+.|+...
T Consensus       188 ~~L~~~Q~~Av~----~~~~~~~~~I~G~pGTGKTt~--i~~l~~~l---------------~-~~g~~Vl~~ApT~~Aa  245 (574)
T 3e1s_A          188 KGLSEEQASVLD----QLAGHRLVVLTGGPGTGKSTT--TKAVADLA---------------E-SLGLEVGLCAPTGKAA  245 (574)
T ss_dssp             TTCCHHHHHHHH----HHTTCSEEEEECCTTSCHHHH--HHHHHHHH---------------H-HTTCCEEEEESSHHHH
T ss_pred             CCCCHHHHHHHH----HHHhCCEEEEEcCCCCCHHHH--HHHHHHHH---------------H-hcCCeEEEecCcHHHH
Confidence            345588855444    344568899999999999932  22222111               0 1346788888777554

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

Probab=80.87  E-value=1.1  Score=42.71  Aligned_cols=15  Identities=40%  Similarity=0.512  Sum_probs=13.8

Q ss_pred             CcEEEeCCCCCChhH
Q psy3462         292 KNCLLESPTGSGKTL  306 (795)
Q Consensus       292 ~~~l~EaPTGTGKTl  306 (795)
                      ..+++.||+|||||.
T Consensus        55 ~~~~l~G~~GtGKT~   69 (202)
T 2w58_A           55 KGLYLHGSFGVGKTY   69 (202)
T ss_dssp             CEEEEECSTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            679999999999996

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

Probab=80.71  E-value=2.2  Score=50.71  Aligned_cols=56  Identities=23%  Similarity=0.306  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccCCceeEEecccccccc
Q psy3462          23 SSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKELVQQKMFEQRTQDLQKTSFVFCGRSDFFLL   99 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~~~~~vq~~~~~~~~~~~~~~~~~yc~rth~~l~   99 (795)
                      +.|.+.+..+    ..+...+|.||.|||||... .-++.++...                .+.+++.|+-||....
T Consensus       363 ~~Q~~Av~~~----l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~----------------~~~~ILv~a~tn~A~d  418 (802)
T 2xzl_A          363 SSQSNAVSHV----LQRPLSLIQGPPGTGKTVTS-ATIVYHLSKI----------------HKDRILVCAPSNVAVD  418 (802)
T ss_dssp             HHHHHHHHHH----TTCSEEEEECSTTSSHHHHH-HHHHHHHHHH----------------HCCCEEEEESSHHHHH
T ss_pred             HHHHHHHHHH----hcCCCEEEECCCCCCHHHHH-HHHHHHHHhC----------------CCCeEEEEcCcHHHHH
Confidence            7885544433    23567999999999999542 2222222110                3468888988887753

>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*

Probab=80.08  E-value=1.7  Score=45.65  Aligned_cols=33  Identities=12%  Similarity=0.225  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCC--c-EEEECCCCCchH
Q psy3462          21 KYSSCKILHLQVIQGCNKAK--N-CLLESPTGSGKT   53 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~~--~-~llEAPTGTGKT   53 (795)
                      .||.|.+.++.+.+++.+++  + .++.||.|||||
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt   38 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDD   38 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHH
Confidence            48999999999999998875  3 899999999999

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	795
d1vqox1	82	d.29.1.1 (X:7-88) Ribosomal protein L31e {Archaeon	2e-22

>d1vqox1 d.29.1.1 (X:7-88) Ribosomal protein L31e {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L31e
superfamily: Ribosomal protein L31e
family: Ribosomal protein L31e
domain: Ribosomal protein L31e
species: Archaeon Haloarcula marismortui [TaxId: 2238]

 Score = 89.7 bits (223), Expect = 2e-22
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 126 RDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTED--VRIDTRLNKHIWSKGINN 182
           R  TI + +        KRA +A+ ++R  + K    ++  VR+D  +N+  W++G  N
Sbjct: 2   RVVTIPL-RDARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWARGRAN 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	795
d1vqox1	82	Ribosomal protein L31e {Archaeon Haloarcula marism	99.91
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.56
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.53
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.5
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.44
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.43
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.35
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.31
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.29
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	98.14
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.07
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	98.05
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.02
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.93
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	97.89
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	97.87
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.73
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	97.73
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	97.69
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	97.67
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	97.65
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	97.56
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.54
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.54
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.29
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.01
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.99
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	96.99
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.9
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.73
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.6
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.48
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.39
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.38
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	95.78
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	95.61
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.6
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	95.18
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	93.17
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	91.73
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	91.52
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	91.03
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	90.72
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.72
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	90.01
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	89.55
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	88.81
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	88.58
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	88.51
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	87.54
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	86.3
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	86.16
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	85.81
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	85.56
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	85.41
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	85.2
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	84.58
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	84.55
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	84.24
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	83.59
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	83.16
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	83.07
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	82.98
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	82.7
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	82.67
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	81.98
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	81.91
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	81.29

>d1vqox1 d.29.1.1 (X:7-88) Ribosomal protein L31e {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein L31e
superfamily: Ribosomal protein L31e
family: Ribosomal protein L31e
domain: Ribosomal protein L31e
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=99.91  E-value=1.6e-25  Score=194.30  Aligned_cols=69  Identities=23%  Similarity=0.374  Sum_probs=66.1

Q ss_pred             eeEEEEecCccccccCCCCcchHHHHHHHHHHHhhhCCCC--eEeCccchHHHHhcCCCCCCCceEEEeccc
Q psy3462         125 TRDYTIHMHKRLHKVGFKKRAPRAIKVVRAFVKKQMGTED--VRIDTRLNKHIWSKGINNHTLGTAYFDSAA  194 (795)
Q Consensus       125 treyTInL~K~v~g~~fkkRAprAik~IrkFa~K~mkt~d--VrID~~LNk~IWsrGirnpP~rirV~~s~~  194 (795)
                      +|+|||||++ +++++++||||+||++||+||+|||||+|  |+|||+||++||++|++|||++|+|+++..
T Consensus         1 Er~yTI~Lr~-~~~~~~~kRA~rAik~Ir~f~~khmkt~d~~V~ID~~lN~~IWsrGi~~pP~rIRVr~~r~   71 (82)
T d1vqox1           1 ERVVTIPLRD-ARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWARGRANTPSKIRVRAARF   71 (82)
T ss_dssp             CEEEEEECGG-GGGSCGGGHHHHHHHHHHHHHHHHTTCCGGGEEECHHHHHHHTTTCTTCCCSEEEEEEEEE
T ss_pred             CeEEEEEcHH-hhCCCcccccHHHHHHHHHHHHHHhCCCCCeEEECcHHHHHHHhccCcCCCCeEEEEEEEe
Confidence            5899999988 89999999999999999999999999997  999999999999999999999999998764

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

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 DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.56  E-value=2.6e-08  Score=95.27  Aligned_cols=50  Identities=20%  Similarity=0.287  Sum_probs=41.5

Q ss_pred             HHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462          11 TYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus        11 ~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +.++..++-.|+|+|    ..++.++.+|+++++.||||||||+||++|++...
T Consensus        14 ~~l~~~g~~~pt~iQ----~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~   63 (209)
T d1q0ua_          14 EAIKTLRFYKPTEIQ----ERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKI   63 (209)
T ss_dssp             HHHHHTTCCSCCHHH----HHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHC
T ss_pred             HHHHHCCCCCCCHHH----HHHHHHHHCCCCeEeecccccccceeeeeeecccc
Confidence            334445777899999    66667777899999999999999999999987654

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

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: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.53  E-value=5.5e-08  Score=94.31  Aligned_cols=52  Identities=17%  Similarity=0.121  Sum_probs=42.9

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+.+ ...++-.|+|+|    ..++..+.+|+++++.||||||||+||++|++...
T Consensus        14 l~~~l-~~~g~~~pt~iQ----~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~   65 (206)
T d1veca_          14 LLMGI-FEMGWEKPSPIQ----EESIPIALSGRDILARAKNGTGKSGAYLIPLLERL   65 (206)
T ss_dssp             HHHHH-HTTTCCSCCHHH----HHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHC
T ss_pred             HHHHH-HHCCCCCCCHHH----HHHHHHHHcCCCEEeeccCccccccccccchhhcc
Confidence            33444 455888999999    66677788999999999999999999999998753

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

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: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.50  E-value=6.8e-08  Score=93.74  Aligned_cols=50  Identities=14%  Similarity=0.179  Sum_probs=42.3

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      .+.+. ..++..|+|.|    ..++.++.+|+++++.||||||||+||++|++..
T Consensus        13 ~~~l~-~~g~~~pt~iQ----~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~   62 (207)
T d1t6na_          13 LRAIV-DCGFEHPSEVQ----HECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ   62 (207)
T ss_dssp             HHHHH-HTTCCCCCHHH----HHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHH-HCCCCCCCHHH----HHHHHHHHcCCCeEEEeccccccccccccceeee
Confidence            34444 45788999999    7777778889999999999999999999998765

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

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: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=98.44  E-value=9e-08  Score=94.99  Aligned_cols=49  Identities=20%  Similarity=0.160  Sum_probs=41.9

Q ss_pred             hCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHHH
Q psy3462          14 NEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK   66 (795)
Q Consensus        14 ~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~~   66 (795)
                      ...++-.|+|.|    .+++.++.+|+++++.||||||||+|||+|+|..+..
T Consensus        37 ~~~g~~~pt~iQ----~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~   85 (238)
T d1wrba1          37 LLASYQRPTPIQ----KNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVC   85 (238)
T ss_dssp             TTTTCCSCCHHH----HHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             HHCCCCCCCHHH----HHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHh
Confidence            344677899999    6666777789999999999999999999999987654

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

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=98.43  E-value=9.4e-08  Score=94.36  Aligned_cols=52  Identities=19%  Similarity=0.225  Sum_probs=42.8

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.+. +.++..|+|+|    ..++.++.+|+++++.||||||||+||++|++..+.
T Consensus        29 ~~~L~-~~g~~~pt~IQ----~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~   80 (222)
T d2j0sa1          29 LRGIY-AYGFEKPSAIQ----QRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLD   80 (222)
T ss_dssp             HHHHH-HHTCCSCCHHH----HHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCC
T ss_pred             HHHHH-HCCCCCCCHHH----HHHHHHHHCCCCeEEEcCcchhhhhhhccccccccc
Confidence            34444 44788999999    666777778999999999999999999999987654

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

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: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=1.9e-07  Score=91.64  Aligned_cols=52  Identities=17%  Similarity=0.246  Sum_probs=42.5

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..+.+ .+.++-.|+|+|    ..++..+.+|+++++.||||||||+||++|++..+
T Consensus        23 l~~~L-~~~g~~~pt~iQ----~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i   74 (218)
T d2g9na1          23 LLRGI-YAYGFEKPSAIQ----QRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI   74 (218)
T ss_dssp             HHHHH-HHHTCCSCCHHH----HHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HHHHH-HHCCCCCCCHHH----HHHHHHHHcCCCEEEEcccchhhhhhhhhhhhhee
Confidence            33444 344777899999    66667777899999999999999999999988664

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

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: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.31  E-value=4e-07  Score=87.57  Aligned_cols=53  Identities=15%  Similarity=0.192  Sum_probs=43.3

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      +..+.+.+ .++-.|+|.|    ..++.++.+|+++++.||||||||+||++|++...
T Consensus        11 ~l~~~L~~-~g~~~pt~iQ----~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~   63 (206)
T d1s2ma1          11 ELLMGIFE-AGFEKPSPIQ----EEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKV   63 (206)
T ss_dssp             HHHHHHHH-TTCCSCCHHH----HHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHH-CCCCCCCHHH----HHHHHHHHcCCCEEEecCCcchhhhhhcccccccc
Confidence            34445544 4788999999    66777788899999999999999999999988653

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

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: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.29  E-value=3.3e-07  Score=89.32  Aligned_cols=52  Identities=13%  Similarity=0.126  Sum_probs=43.5

Q ss_pred             HHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           9 FKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         9 ~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      .+.+. +.++-.|+|.|    ..++.++..|+++++.||||||||+||++|++..+.
T Consensus        22 ~~~L~-~~g~~~pt~iQ----~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~   73 (212)
T d1qdea_          22 LRGVF-GYGFEEPSAIQ----QRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRID   73 (212)
T ss_dssp             HHHHH-HHTCCSCCHHH----HHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             HHHHH-HCCCCCCCHHH----HHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhh
Confidence            34443 45788999999    777777888999999999999999999999988753

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=98.14  E-value=9.2e-07  Score=83.96  Aligned_cols=48  Identities=27%  Similarity=0.418  Sum_probs=36.6

Q ss_pred             HHHhCC-CCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHH
Q psy3462          11 TYLNEP-NYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA   62 (795)
Q Consensus        11 ~~~~~~-~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~   62 (795)
                      +++.+. ++..+||.|.+    +++++.+++++++.||||+|||++|.+|++.
T Consensus        15 ~~l~~~fg~~~~rp~Q~~----ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~   63 (206)
T d1oywa2          15 QVLQETFGYQQFRPGQEE----IIDTVLSGRDCLVVMPTGGGKSLCYQIPALL   63 (206)
T ss_dssp             HHHHHTTCCSSCCTTHHH----HHHHHHTTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCCHHHHH----HHHHHHcCCCEEEEcCCCCCCcchhhhhhhh
Confidence            444444 45578899954    4455667889999999999999999999753

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

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: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.07  E-value=1.3e-06  Score=84.61  Aligned_cols=43  Identities=19%  Similarity=0.187  Sum_probs=34.8

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      ..| .|.|.|...+-.+.                           +|+++++.||||||||+||++|++..
T Consensus        19 ~g~~~pt~iQ~~aip~il---------------------------~g~dvl~~A~TGsGKTla~~lp~l~~   62 (207)
T d1t6na_          19 CGFEHPSEVQHECIPQAI---------------------------LGMDVLCQAKSGMGKTAVFVLATLQQ   62 (207)
T ss_dssp             TTCCCCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHH---------------------------cCCCeEEEeccccccccccccceeee
Confidence            355 48999987766643                           46899999999999999999998654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.05  E-value=1.6e-06  Score=84.27  Aligned_cols=53  Identities=19%  Similarity=0.095  Sum_probs=41.3

Q ss_pred             HHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           7 DIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         7 ~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      ..|.++... .+..|+++|+    .+++.+..|+++++.||||+|||+++++|++..+
T Consensus        31 ~~~~~~~~~-~~~~p~~~Q~----~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~   83 (237)
T d1gkub1          31 KEFVEFFRK-CVGEPRAIQK----MWAKRILRKESFAATAPTGVGKTSFGLAMSLFLA   83 (237)
T ss_dssp             HHHHHHHHT-TTCSCCHHHH----HHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-ccCCCCHHHH----HHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHH
Confidence            346666666 3558999994    4455566789999999999999999999987553

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

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: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=98.02  E-value=3.5e-06  Score=83.31  Aligned_cols=46  Identities=22%  Similarity=0.286  Sum_probs=37.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ..| .|.|.|...+..+.                           +|+++++.||||||||+|||+|+|..+..
T Consensus        39 ~g~~~pt~iQ~~~ip~il---------------------------~g~dvvi~a~TGsGKTlayllp~l~~l~~   85 (238)
T d1wrba1          39 ASYQRPTPIQKNAIPAIL---------------------------EHRDIMACAQTGSGKTAAFLIPIINHLVC   85 (238)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHhhhhh---------------------------CCCCEEEECCCCCCcceeeHHHHHHHHHh
Confidence            456 48999988776653                           36899999999999999999999977643

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

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: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=2e-06  Score=83.12  Aligned_cols=44  Identities=23%  Similarity=0.253  Sum_probs=35.6

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ..| .|.|.|...+-.+.                           +|+++++.||||||||+||++|++..+
T Consensus        21 ~g~~~pt~iQ~~aip~il---------------------------~g~dvl~~a~TGsGKTlayllP~l~~~   65 (206)
T d1veca_          21 MGWEKPSPIQEESIPIAL---------------------------SGRDILARAKNGTGKSGAYLIPLLERL   65 (206)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCSSSTTHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHH---------------------------cCCCEEeeccCccccccccccchhhcc
Confidence            456 48999987776542                           468999999999999999999987653

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

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: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.93  E-value=2.3e-06  Score=81.27  Aligned_cols=55  Identities=24%  Similarity=0.206  Sum_probs=41.1

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHHH
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ   64 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~~   64 (795)
                      .+.....+++.++-.|||.|    .++++.+.+++++++.||||+|||.+++++++...
T Consensus        11 ~~~~~~~l~~~g~~~l~~~Q----~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~   65 (202)
T d2p6ra3          11 SSYAVGILKEEGIEELFPPQ----AEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREA   65 (202)
T ss_dssp             HHHHHHHHHCC---CCCCCC----HHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHcCCCCCCHHH----HHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHh
Confidence            34455667776777899999    55566667789999999999999999988877654

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

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 DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.89  E-value=3.5e-06  Score=80.17  Aligned_cols=44  Identities=23%  Similarity=0.257  Sum_probs=35.5

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ..| .|.|.|.+.+..+.                           +|+++++.||||||||+||++|++...
T Consensus        19 ~g~~~pt~iQ~~aip~~l---------------------------~G~dvii~a~TGSGKTlayllp~l~~~   63 (209)
T d1q0ua_          19 LRFYKPTEIQERIIPGAL---------------------------RGESMVGQSQTGTGKTHAYLLPIMEKI   63 (209)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------HTCCEEEECCSSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHH---------------------------CCCCeEeecccccccceeeeeeecccc
Confidence            456 48999987776543                           368899999999999999999987653

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

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: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.87  E-value=6.3e-06  Score=79.38  Aligned_cols=51  Identities=22%  Similarity=0.231  Sum_probs=37.6

Q ss_pred             HHHHHHhCCCCCCCCHHHHHHHHHHHHHH-hcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462           8 IFKTYLNEPNYFLKYSSCKILHLQVIQGC-NKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus         8 ~~~~~~~~~~~~~p~~~Q~~mm~~i~~al-~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      ..+.+. ..++-.|+|.|.    .++..+ .++.++++.||||+|||+||++|++..
T Consensus        15 l~~~l~-~~g~~~pt~iQ~----~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~   66 (208)
T d1hv8a1          15 ILNAIR-NKGFEKPTDIQM----KVIPLFLNDEYNIVAQARTGSGKTASFAIPLIEL   66 (208)
T ss_dssp             HHHHHH-HHTCCSCCHHHH----HHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             HHHHHH-HCCCCCCCHHHH----HHHHHHHcCCCCeeeechhcccccceeecccccc
Confidence            334433 346778999994    444444 444699999999999999999998753

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

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: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.73  E-value=7.3e-06  Score=76.61  Aligned_cols=41  Identities=24%  Similarity=0.307  Sum_probs=31.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      .+.||+.|.+.++.+    . ++++|+.||||+|||+++++++...
T Consensus         7 ~~~pr~~Q~~~~~~~----~-~~n~lv~~pTGsGKT~i~~~~~~~~   47 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKC----K-ETNCLIVLPTGLGKTLIAMMIAEYR   47 (200)
T ss_dssp             HHCCCHHHHHHHHHG----G-GSCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHH----h-cCCeEEEeCCCCcHHHHHHHHHHHH
Confidence            457999997766544    2 4579999999999999888876543

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

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=97.73  E-value=1.1e-05  Score=79.13  Aligned_cols=27  Identities=33%  Similarity=0.505  Sum_probs=24.1

Q ss_pred             ccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         290 KAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      +++++++.||||||||+||++|++..+
T Consensus        53 ~g~dvi~~a~TGSGKTlayllPil~~l   79 (222)
T d2j0sa1          53 KGRDVIAQSQSGTGKTATFSISVLQCL   79 (222)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHHHHTC
T ss_pred             CCCCeEEEcCcchhhhhhhcccccccc
Confidence            478999999999999999999987654

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

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: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.69  E-value=1.6e-05  Score=77.52  Aligned_cols=45  Identities=20%  Similarity=0.258  Sum_probs=35.4

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ...| .|.|.|...+-.+.                           .++++++.||||||||+||++|++..+
T Consensus        29 ~~g~~~pt~iQ~~aip~il---------------------------~g~dvl~~a~TGsGKTlayllp~l~~i   74 (218)
T d2g9na1          29 AYGFEKPSAIQQRAILPCI---------------------------KGYDVIAQAQSGTGKTATFAISILQQI   74 (218)
T ss_dssp             HHTCCSCCHHHHHHHHHHH---------------------------HTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcccchhhhhhhhhhhhhee
Confidence            3566 48999976665532                           368899999999999999999987554

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.67  E-value=1.5e-05  Score=77.22  Aligned_cols=55  Identities=24%  Similarity=0.218  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH-------
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE-------  321 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k-------  321 (795)
                      +|+|.|.+.+..+   |                        .++.+++.||||+|||++++++++..+...++       
T Consensus        43 ~p~~~Q~~~i~~~---l------------------------~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt   95 (237)
T d1gkub1          43 EPRAIQKMWAKRI---L------------------------RKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPT   95 (237)
T ss_dssp             SCCHHHHHHHHHH---H------------------------TTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESC
T ss_pred             CCCHHHHHHHHHH---H------------------------CCCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEecc
Confidence            5788888776654   2                        36789999999999999999998876655443       


Q ss_pred             -HHHHHHHhh
Q psy3462         322 -LVQQKMFEQ  330 (795)
Q Consensus       322 -~LQ~Ql~~k  330 (795)
                       .|-+|..++
T Consensus        96 ~~La~Q~~~~  105 (237)
T d1gkub1          96 SLLVIQAAET  105 (237)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence             566666543

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=97.65  E-value=8e-06  Score=77.29  Aligned_cols=42  Identities=31%  Similarity=0.576  Sum_probs=34.8

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVL  313 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l  313 (795)
                      .|+| .+||.|.+.+..+.                           .++++++.||||+|||++|.+|++
T Consensus        20 ~fg~~~~rp~Q~~ai~~~l---------------------------~g~~vlv~apTGsGKT~~~~~~~~   62 (206)
T d1oywa2          20 TFGYQQFRPGQEEIIDTVL---------------------------SGRDCLVVMPTGGGKSLCYQIPAL   62 (206)
T ss_dssp             TTCCSSCCTTHHHHHHHHH---------------------------TTCCEEEECSCHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHH---------------------------cCCCEEEEcCCCCCCcchhhhhhh
Confidence            5788 47999999887753                           256899999999999999998865

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

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: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.56  E-value=2.5e-05  Score=75.70  Aligned_cols=45  Identities=16%  Similarity=0.228  Sum_probs=36.6

Q ss_pred             ccCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         245 EFPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       245 ~fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ...| .|.|.|...+..+.                           .|+++++.||||||||+||++|++..+
T Consensus        27 ~~g~~~pt~iQ~~aip~il---------------------------~g~dvl~~a~TGsGKT~a~~lp~i~~l   72 (212)
T d1qdea_          27 GYGFEEPSAIQQRAIMPII---------------------------EGHDVLAQAQSGTGKTGTFSIAALQRI   72 (212)
T ss_dssp             HHTCCSCCHHHHHHHHHHH---------------------------TTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             HCCCCCCCHHHHHHHHHHH---------------------------cCCCEEeecccccchhhhhHhhhHhhh
Confidence            3566 48999988777653                           368899999999999999999987754

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

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: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.54  E-value=3.4e-05  Score=71.92  Aligned_cols=43  Identities=28%  Similarity=0.311  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHH
Q psy3462         248 VKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRK  318 (795)
Q Consensus       248 y~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~  318 (795)
                      ++||+.|.+.++.+   .                         ++++++.||||+|||+.++.++...+..
T Consensus         8 ~~pr~~Q~~~~~~~---~-------------------------~~n~lv~~pTGsGKT~i~~~~~~~~~~~   50 (200)
T d1wp9a1           8 IQPRIYQEVIYAKC---K-------------------------ETNCLIVLPTGLGKTLIAMMIAEYRLTK   50 (200)
T ss_dssp             HCCCHHHHHHHHHG---G-------------------------GSCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH---h-------------------------cCCeEEEeCCCCcHHHHHHHHHHHHHHh
Confidence            47999999987753   2                         3578999999999999888776555544

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

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: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.54  E-value=3.6e-05  Score=73.56  Aligned_cols=43  Identities=23%  Similarity=0.275  Sum_probs=34.4

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAW  315 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~  315 (795)
                      ..| .|.|.|...+-.+.                           +++++++.||||||||+||++|++..
T Consensus        19 ~g~~~pt~iQ~~aip~il---------------------------~g~dvi~~a~tGsGKTlay~lp~i~~   62 (206)
T d1s2ma1          19 AGFEKPSPIQEEAIPVAI---------------------------TGRDILARAKNGTGKTAAFVIPTLEK   62 (206)
T ss_dssp             TTCCSCCHHHHHHHHHHH---------------------------HTCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHH---------------------------cCCCEEEecCCcchhhhhhccccccc
Confidence            455 48889887776543                           36789999999999999999997653

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

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: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.29  E-value=0.00043  Score=68.78  Aligned_cols=108  Identities=19%  Similarity=0.257  Sum_probs=75.7

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH---
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE---  321 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k---  321 (795)
                      .|||+.-+.|...+++|.+.+..+                     ...+.|+.|.||+|||..|+.++...+...++   
T Consensus        51 ~lP~~lt~~Q~~~~~~i~~~~~~~---------------------~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~  109 (233)
T d2eyqa3          51 SFPFETTPDQAQAINAVLSDMCQP---------------------LAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAV  109 (233)
T ss_dssp             TCCSCCCHHHHHHHHHHHHHHHSS---------------------SCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEE
T ss_pred             ccccccchhHHHHHHHHHHHHhcc---------------------CccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEE
Confidence            699999999999999999999864                     23578999999999999999998887766544   


Q ss_pred             -----HHHHHHHhhhhhhhhh-cCCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceeeeccc
Q psy3462         322 -----LVQQKMFEQRTQDLQK-IPFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNGR  395 (795)
Q Consensus       322 -----~LQ~Ql~~kdip~l~~-i~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~l~sR  395 (795)
                           .|-.|+...    +++ ..+.+++++++-|..                +..+..+.+..+.+.   ..-.++|-|
T Consensus       110 l~Pt~~La~Q~~~~----~~~~~~~~~~~v~~l~~~~----------------~~~~~~~~~~~~~~g---~~~iviGth  166 (233)
T d2eyqa3         110 LVPTTLLAQQHYDN----FRDRFANWPVRIEMISRFR----------------SAKEQTQILAEVAEG---KIDILIGTH  166 (233)
T ss_dssp             ECSSHHHHHHHHHH----HHHHSTTTTCCEEEESTTS----------------CHHHHHHHHHHHHTT---CCSEEEECT
T ss_pred             EccHHHhHHHHHHH----HHHHHhhCCCEEEeccCcc----------------cchhHHHHHHHHhCC---CCCEEEeeh
Confidence                 577777654    333 234566666665542                223334445555543   123577888


Q ss_pred             c
Q psy3462         396 S  396 (795)
Q Consensus       396 ~  396 (795)
                      +
T Consensus       167 s  167 (233)
T d2eyqa3         167 K  167 (233)
T ss_dssp             H
T ss_pred             h
Confidence            7

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=97.01  E-value=0.00016  Score=70.78  Aligned_cols=43  Identities=23%  Similarity=0.248  Sum_probs=31.8

Q ss_pred             hccccCcEEEeCCCCCChhHHHHHHHHHHHHHhh---------HHHHHHHHh
Q psy3462         287 GCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEK---------ELVQQKMFE  329 (795)
Q Consensus       287 al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~---------k~LQ~Ql~~  329 (795)
                      .+..++++++.||||+|||++||.+++.-....+         +.|-+|+.+
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~   56 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEE   56 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHH
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHH
Confidence            3567899999999999999999888775444322         256666654

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.99  E-value=7.5e-05  Score=73.23  Aligned_cols=29  Identities=21%  Similarity=0.249  Sum_probs=24.7

Q ss_pred             HHhcCCcEEEECCCCCchHHHHHHHHHHH
Q psy3462          35 GCNKAKNCLLESPTGSGKTLALLCSVLAW   63 (795)
Q Consensus        35 al~~~~~~llEAPTGTGKTLAyL~paL~~   63 (795)
                      .+..++++++.||||+|||++||.|++..
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~   33 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVRE   33 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHH
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHH
Confidence            45678899999999999999998887654

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

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: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.99  E-value=0.00034  Score=66.91  Aligned_cols=43  Identities=21%  Similarity=0.249  Sum_probs=32.7

Q ss_pred             cCC-CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHH
Q psy3462         246 FPV-KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLA  314 (795)
Q Consensus       246 fpy-~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~  314 (795)
                      ..| .|.|.|.+.+..+.   .                       .+.++++.||||||||++|++|++.
T Consensus        22 ~g~~~pt~iQ~~~ip~~l---~-----------------------g~~d~iv~a~TGsGKT~~~~l~~~~   65 (208)
T d1hv8a1          22 KGFEKPTDIQMKVIPLFL---N-----------------------DEYNIVAQARTGSGKTASFAIPLIE   65 (208)
T ss_dssp             HTCCSCCHHHHHHHHHHH---H-----------------------TCSEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHH---c-----------------------CCCCeeeechhcccccceeeccccc
Confidence            456 48899977665542   2                       1357999999999999999999765

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

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: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.90  E-value=0.00036  Score=65.64  Aligned_cols=30  Identities=37%  Similarity=0.379  Sum_probs=24.5

Q ss_pred             ccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         290 KAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      +++++++.||||+|||.+++++++..+...
T Consensus        39 ~~~~~il~apTGsGKT~~a~l~i~~~~~~~   68 (202)
T d2p6ra3          39 SGKNLLLAMPTAAGKTLLAEMAMVREAIKG   68 (202)
T ss_dssp             TCSCEEEECSSHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCEEEEcCCCCchhHHHHHHHHHHhhcc
Confidence            357899999999999999988877665544

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=96.73  E-value=0.00047  Score=59.11  Aligned_cols=31  Identities=29%  Similarity=0.360  Sum_probs=25.1

Q ss_pred             cccCcEEEeCCCCCChhHHHHHHHHHHHHHh
Q psy3462         289 NKAKNCLLESPTGSGKTLALLCSVLAWQRKE  319 (795)
Q Consensus       289 ~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~  319 (795)
                      .++++++|.||||+|||+.++..++......
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~   35 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR   35 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc
Confidence            4578999999999999998877766666544

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=96.60  E-value=0.00035  Score=59.92  Aligned_cols=30  Identities=30%  Similarity=0.321  Sum_probs=24.2

Q ss_pred             HhcCCcEEEECCCCCchHHHHHHHHHHHHH
Q psy3462          36 CNKAKNCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus        36 l~~~~~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      |.++++++|.||||+|||+.++..++....
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~   33 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECA   33 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHH
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhh
Confidence            567899999999999999887766555543

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

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: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.48  E-value=0.0034  Score=63.22  Aligned_cols=109  Identities=17%  Similarity=0.157  Sum_probs=75.3

Q ss_pred             eccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHHHHHHHHHHhhH--
Q psy3462         244 VEFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLCSVLAWQRKEKE--  321 (795)
Q Consensus       244 ~~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~~~l~~~~~~~k--  321 (795)
                      -.+||+.-+.|...+++|.+.+..+                     ...+.|+.|.||+|||..|+.+++..+....+  
T Consensus        78 ~~LPFeLT~~Q~~ai~ei~~d~~~~---------------------~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~  136 (264)
T d1gm5a3          78 KSLPFKLTNAQKRAHQEIRNDMISE---------------------KPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTA  136 (264)
T ss_dssp             HHSSSCCCHHHHHHHHHHHHHHHSS---------------------SCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEE
T ss_pred             hhccccCCchHHHHHHHHHHHhhcc---------------------CcceeeeeccccccccHHHHHHHHHHHhccccee
Confidence            3699999999999999999988753                     24578999999999999999999888776644  


Q ss_pred             ------HHHHHHHhhhhhhhhhc-CCCCceEEEecccccccccchhhHHHHHHhHHHHHHHHHHHHhhcccccceeeecc
Q psy3462         322 ------LVQQKMFEQRTQDLQKI-PFRKLKISRLKAKDFSTNNGMEQQLLTCITTINQQEDELRQSTKKTRVDKLKVLNG  394 (795)
Q Consensus       322 ------~LQ~Ql~~kdip~l~~i-~~~~l~~~~~KGr~~~~~~~~~~~L~~~~rt~~q~e~el~~~~~~~~~~~~~~l~s  394 (795)
                            .|-.|....    +.+. .+..++++++-|..                +-.+.++.+..+...   ..-.++|.
T Consensus       137 ~m~Pt~~La~Qh~~~----~~~~f~~~~~~v~~l~~~~----------------~~~~r~~~~~~~~~g---~~~iiIGT  193 (264)
T d1gm5a3         137 FMVPTSILAIQHYRR----TVESFSKFNIHVALLIGAT----------------TPSEKEKIKSGLRNG---QIDVVIGT  193 (264)
T ss_dssp             EECSCHHHHHHHHHH----HHHHHTCSSCCEEECCSSS----------------CHHHHHHHHHHHHSS---CCCEEEEC
T ss_pred             EEeehHhhhHHHHHH----HHHhhhhccccceeecccc----------------chHHHHHHHHHHHCC---CCCEEEee
Confidence                  455565543    3332 33456666666653                223444555555542   12367788


Q ss_pred             cc
Q psy3462         395 RS  396 (795)
Q Consensus       395 R~  396 (795)
                      |+
T Consensus       194 hs  195 (264)
T d1gm5a3         194 HA  195 (264)
T ss_dssp             TT
T ss_pred             hH
Confidence            87

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

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: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.39  E-value=0.0025  Score=63.13  Aligned_cols=61  Identities=11%  Similarity=0.080  Sum_probs=51.4

Q ss_pred             hhHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCC--cEEEECCCCCchHHHHHHHHHHHHH
Q psy3462           4 KSSDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAK--NCLLESPTGSGKTLALLCSVLAWQR   65 (795)
Q Consensus         4 ~~~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKTLAyL~paL~~~~   65 (795)
                      ...+.++.+.+. .+|.+.+.|++-+++|.+.+..+.  +-++.|.||+|||..|+..+...+.
T Consensus        40 ~~~~~~~~~~~~-lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~  102 (233)
T d2eyqa3          40 HDREQYQLFCDS-FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD  102 (233)
T ss_dssp             CCHHHHHHHHHT-CCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT
T ss_pred             CCHHHHHhhhhc-cccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH
Confidence            356777788877 456899999999999999998876  6899999999999999999776654

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

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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.38  E-value=0.0014  Score=62.25  Aligned_cols=36  Identities=22%  Similarity=0.044  Sum_probs=27.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      .+.+|+.|.+.++    .+.++..+++.+|||+|||+..+
T Consensus        68 ~~~Lr~yQ~eav~----~~~~~~~~ll~~~tG~GKT~~a~  103 (206)
T d2fz4a1          68 EISLRDYQEKALE----RWLVDKRGCIVLPTGSGKTHVAM  103 (206)
T ss_dssp             CCCCCHHHHHHHH----HHTTTSEEEEEESSSTTHHHHHH
T ss_pred             CCCcCHHHHHHHH----HHHhCCCcEEEeCCCCCceehHH
Confidence            4578999966544    44456788999999999997544

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

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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.78  E-value=0.0034  Score=59.51  Aligned_cols=38  Identities=24%  Similarity=0.257  Sum_probs=28.6

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL  309 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL  309 (795)
                      ..++++||.|.+.++.+   ++                        ++.+++.+|||+|||+..+
T Consensus        66 ~~~~~Lr~yQ~eav~~~---~~------------------------~~~~ll~~~tG~GKT~~a~  103 (206)
T d2fz4a1          66 DAEISLRDYQEKALERW---LV------------------------DKRGCIVLPTGSGKTHVAM  103 (206)
T ss_dssp             CCCCCCCHHHHHHHHHH---TT------------------------TSEEEEEESSSTTHHHHHH
T ss_pred             CCCCCcCHHHHHHHHHH---Hh------------------------CCCcEEEeCCCCCceehHH
Confidence            34578999999877653   32                        3567899999999998644

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.61  E-value=0.0068  Score=60.70  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=30.0

Q ss_pred             ccCCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHHH
Q psy3462         245 EFPVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLC  310 (795)
Q Consensus       245 ~fpy~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL~  310 (795)
                      ..|++||+-|.+.+..+   +.                        ++.+++.+|||+|||+.-+.
T Consensus       109 ~~~~~~rdyQ~~av~~~---l~------------------------~~~~il~~pTGsGKT~i~~~  147 (282)
T d1rifa_         109 NKRIEPHWYQKDAVFEG---LV------------------------NRRRILNLPTSAGRSLIQAL  147 (282)
T ss_dssp             TEECCCCHHHHHHHHHH---HH------------------------HSEEEECCCTTSCHHHHHHH
T ss_pred             CCccccchHHHHHHHHH---Hh------------------------cCCceeEEEcccCccHHHHH
Confidence            45799999998777664   32                        35689999999999986443

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

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: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.60  E-value=0.0083  Score=60.29  Aligned_cols=61  Identities=21%  Similarity=0.247  Sum_probs=49.8

Q ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCC--cEEEECCCCCchHHHHHHHHHHHHHHh
Q psy3462           6 SDIFKTYLNEPNYFLKYSSCKILHLQVIQGCNKAK--NCLLESPTGSGKTLALLCSVLAWQRKE   67 (795)
Q Consensus         6 ~~~~~~~~~~~~~~~p~~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKTLAyL~paL~~~~~~   67 (795)
                      .+.++...+.+ +|.+.+.|++-+++|.+.+.++.  +-++.|-||+|||..|+..++..+...
T Consensus        70 ~~l~~~f~~~L-PFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g  132 (264)
T d1gm5a3          70 GKLAEEFIKSL-PFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG  132 (264)
T ss_dssp             THHHHHHHHHS-SSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHhhc-cccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcc
Confidence            34566666664 45899999999999999998765  689999999999999999987766543

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.18  E-value=0.015  Score=58.19  Aligned_cols=36  Identities=17%  Similarity=0.085  Sum_probs=26.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          18 YFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        18 ~~~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      .+.||+.|.+.+..+   +.+ +.+++.+|||+|||+..+
T Consensus       111 ~~~~rdyQ~~av~~~---l~~-~~~il~~pTGsGKT~i~~  146 (282)
T d1rifa_         111 RIEPHWYQKDAVFEG---LVN-RRRILNLPTSAGRSLIQA  146 (282)
T ss_dssp             ECCCCHHHHHHHHHH---HHH-SEEEECCCTTSCHHHHHH
T ss_pred             ccccchHHHHHHHHH---Hhc-CCceeEEEcccCccHHHH
Confidence            478999996555443   433 579999999999997644

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=93.17  E-value=0.02  Score=49.80  Aligned_cols=18  Identities=39%  Similarity=0.551  Sum_probs=15.7

Q ss_pred             ccCcEEEeCCCCCChhHH
Q psy3462         290 KAKNCLLESPTGSGKTLA  307 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTla  307 (795)
                      +.+.+++.||||+|||+.
T Consensus         7 ~~~~~ll~apTGsGKT~~   24 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTK   24 (136)
T ss_dssp             SCEEEEEECCTTSCTTTH
T ss_pred             CCCEEEEEeCCCCCHHHH
Confidence            457899999999999964

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=91.73  E-value=0.03  Score=48.64  Aligned_cols=17  Identities=41%  Similarity=0.581  Sum_probs=14.3

Q ss_pred             CCcEEEECCCCCchHHH
Q psy3462          39 AKNCLLESPTGSGKTLA   55 (795)
Q Consensus        39 ~~~~llEAPTGTGKTLA   55 (795)
                      .+.++|.||||+|||+.
T Consensus         8 ~~~~ll~apTGsGKT~~   24 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTK   24 (136)
T ss_dssp             CEEEEEECCTTSCTTTH
T ss_pred             CCEEEEEeCCCCCHHHH
Confidence            35689999999999953

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.52  E-value=0.064  Score=50.06  Aligned_cols=31  Identities=26%  Similarity=0.307  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHhcCC--cEEEECCCCCchH
Q psy3462          23 SSCKILHLQVIQGCNKAK--NCLLESPTGSGKT   53 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKT   53 (795)
                      =+|.+..+.+...+.++.  +++|.||+|||||
T Consensus        17 vg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKt   49 (227)
T d1sxjc2          17 YGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT   49 (227)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHH
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCChh
Confidence            345666777777777765  5999999999999

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=91.03  E-value=0.079  Score=49.90  Aligned_cols=43  Identities=19%  Similarity=0.251  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhH
Q psy3462         247 PVKAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       247 py~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTl  306 (795)
                      -|+++..|..+...+...+....                 +....+.+++-||+|||||.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~P~~ilL~GpPGtGKT~   47 (273)
T d1gvnb_           5 NFTDKQFENRLNDNLEELIQGKK-----------------AVESPTAFLLGGQPGSGKTS   47 (273)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCC-----------------CCSSCEEEEEECCTTSCTHH
T ss_pred             ccChHHHHHHHHHHHHHHHhccc-----------------CCCCCEEEEEECCCCCCHHH
Confidence            36778888888888877765420                 11234568899999999995

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=90.72  E-value=0.11  Score=48.36  Aligned_cols=14  Identities=36%  Similarity=0.480  Sum_probs=13.2

Q ss_pred             CcEEEECCCCCchH
Q psy3462          40 KNCLLESPTGSGKT   53 (795)
Q Consensus        40 ~~~llEAPTGTGKT   53 (795)
                      .+++|.||+|||||
T Consensus        44 ~~lll~GppGtGKT   57 (276)
T d1fnna2          44 PRATLLGRPGTGKT   57 (276)
T ss_dssp             CEEEEECCTTSSHH
T ss_pred             CceEEECCCCCCHH
Confidence            57999999999999

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=90.72  E-value=0.12  Score=48.52  Aligned_cols=38  Identities=26%  Similarity=0.158  Sum_probs=28.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCC------cEEEECCCCCchH
Q psy3462          16 PNYFLKYSSCKILHLQVIQGCNKAK------NCLLESPTGSGKT   53 (795)
Q Consensus        16 ~~~~~p~~~Q~~mm~~i~~al~~~~------~~llEAPTGTGKT   53 (795)
                      +-.|.++..|..+.+.+...+....      .+++-||+|||||
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT   46 (273)
T d1gvnb_           3 IVNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKT   46 (273)
T ss_dssp             TTCCCHHHHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTH
T ss_pred             CcccChHHHHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHH
Confidence            3456778888777777766654432      3889999999999

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=90.01  E-value=0.15  Score=47.26  Aligned_cols=17  Identities=29%  Similarity=0.399  Sum_probs=14.7

Q ss_pred             cCcEEEeCCCCCChhHH
Q psy3462         291 AKNCLLESPTGSGKTLA  307 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTla  307 (795)
                      ..+++|.||+|||||..
T Consensus        43 ~~~lll~GppGtGKT~l   59 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVT   59 (276)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            36899999999999954

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=89.55  E-value=0.088  Score=52.77  Aligned_cols=15  Identities=60%  Similarity=0.860  Sum_probs=13.5

Q ss_pred             CCcEEEECCCCCchH
Q psy3462          39 AKNCLLESPTGSGKT   53 (795)
Q Consensus        39 ~~~~llEAPTGTGKT   53 (795)
                      ...+++.+|||||||
T Consensus        49 ~~~iLl~GPpG~GKT   63 (309)
T d1ofha_          49 PKNILMIGPTGVGKT   63 (309)
T ss_dssp             CCCEEEECCTTSSHH
T ss_pred             CceEEEECCCCCCHH
Confidence            467999999999999

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.81  E-value=0.12  Score=48.11  Aligned_cols=33  Identities=27%  Similarity=0.454  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhH
Q psy3462         253 SQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTL  306 (795)
Q Consensus       253 ~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTl  306 (795)
                      +|.+..+.+.+.++++                     .-.++++.||+|||||.
T Consensus        18 g~~~~~~~L~~~i~~~---------------------~~~~lLl~Gp~G~GKtt   50 (227)
T d1sxjc2          18 GQNEVITTVRKFVDEG---------------------KLPHLLFYGPPGTGKTS   50 (227)
T ss_dssp             SCHHHHHHHHHHHHTT---------------------CCCCEEEECSSSSSHHH
T ss_pred             CcHHHHHHHHHHHHcC---------------------CCCeEEEECCCCCChhH
Confidence            3456667777777643                     12468999999999994

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=88.58  E-value=0.1  Score=48.99  Aligned_cols=15  Identities=47%  Similarity=0.740  Sum_probs=13.5

Q ss_pred             CcEEEECCCCCchHH
Q psy3462          40 KNCLLESPTGSGKTL   54 (795)
Q Consensus        40 ~~~llEAPTGTGKTL   54 (795)
                      .++||.||+|||||.
T Consensus        36 ~~~L~~GPpGtGKT~   50 (238)
T d1in4a2          36 DHVLLAGPPGLGKTT   50 (238)
T ss_dssp             CCEEEESSTTSSHHH
T ss_pred             CeEEEECCCCCcHHH
Confidence            469999999999994

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.51  E-value=0.12  Score=48.43  Aligned_cols=32  Identities=19%  Similarity=0.255  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHhcC--CcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKA--KNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~--~~~llEAPTGTGKTL   54 (795)
                      =+|.+..+.+...+.++  .+++|.||+|||||.
T Consensus        27 ig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTt   60 (231)
T d1iqpa2          27 VGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTT   60 (231)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHH
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHH
Confidence            46777778888888776  569999999999983

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=87.54  E-value=0.18  Score=47.01  Aligned_cols=33  Identities=15%  Similarity=-0.060  Sum_probs=21.3

Q ss_pred             HHHH-HHHHHHHHHHhcCC-------cEEEECCCCCchHHH
Q psy3462          23 SSCK-ILHLQVIQGCNKAK-------NCLLESPTGSGKTLA   55 (795)
Q Consensus        23 ~~Q~-~mm~~i~~al~~~~-------~~llEAPTGTGKTLA   55 (795)
                      ..|. +++..+...+.++.       .+++.||+|||||..
T Consensus        22 e~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l   62 (287)
T d1w5sa2          22 RGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTL   62 (287)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHH
Confidence            4555 44555556665543       245679999999943

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=86.30  E-value=0.23  Score=46.55  Aligned_cols=16  Identities=44%  Similarity=0.571  Sum_probs=13.9

Q ss_pred             CcEEEECCCCCchHHH
Q psy3462          40 KNCLLESPTGSGKTLA   55 (795)
Q Consensus        40 ~~~llEAPTGTGKTLA   55 (795)
                      .++||.||+|||||..
T Consensus        36 ~~~Ll~GPpG~GKTtl   51 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTL   51 (239)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4799999999999943

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=86.16  E-value=0.33  Score=45.53  Aligned_cols=41  Identities=12%  Similarity=0.240  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHHHH
Q psy3462         249 KAYPSQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL  309 (795)
Q Consensus       249 ~~yp~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTlayL  309 (795)
                      ..||+|....+++.+.+...+                    -....++.||.|+|||....
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~--------------------l~h~lLl~Gp~G~GKtt~a~   42 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGR--------------------GHHALLIQALPGMGDDALIY   42 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTC--------------------CCSEEEEECCTTSCHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHcCC--------------------cCeEEEEECCCCCcHHHHHH
Confidence            468999999999988887531                    01237899999999986443

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

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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=85.81  E-value=0.39  Score=45.83  Aligned_cols=31  Identities=23%  Similarity=0.167  Sum_probs=21.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          21 KYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      ..|.|++.++    .  ...+++|.||.|||||-..+
T Consensus         2 L~~eQ~~av~----~--~~~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1           2 LNPGQQQAVE----F--VTGPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             CCHHHHHHHH----C--CSSEEEECCCTTSCHHHHHH
T ss_pred             cCHHHHHHHh----C--CCCCEEEEeeCCccHHHHHH
Confidence            3477855443    2  34679999999999996544

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.56  E-value=0.28  Score=42.49  Aligned_cols=24  Identities=29%  Similarity=0.472  Sum_probs=17.5

Q ss_pred             CcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         292 KNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       292 ~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      ++++|-||.|||||- ++-.++..+
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHH
Confidence            579999999999997 444434333

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=85.41  E-value=0.15  Score=54.10  Aligned_cols=15  Identities=60%  Similarity=0.860  Sum_probs=13.6

Q ss_pred             CCcEEEECCCCCchH
Q psy3462          39 AKNCLLESPTGSGKT   53 (795)
Q Consensus        39 ~~~~llEAPTGTGKT   53 (795)
                      .+|+|+.+|||||||
T Consensus        49 ksNILliGPTGvGKT   63 (443)
T d1g41a_          49 PKNILMIGPTGVGKT   63 (443)
T ss_dssp             CCCEEEECCTTSSHH
T ss_pred             cccEEEECCCCCCHH
Confidence            358999999999999

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=85.20  E-value=0.24  Score=50.24  Aligned_cols=28  Identities=32%  Similarity=0.360  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHhcCCcEEEECCCCCchH
Q psy3462          26 KILHLQVIQGCNKAKNCLLESPTGSGKT   53 (795)
Q Consensus        26 ~~mm~~i~~al~~~~~~llEAPTGTGKT   53 (795)
                      .+|+..+..++..+.++++-+|||+|||
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKT  180 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKT  180 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHH
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccch
Confidence            4566777888889999999999999999

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=84.58  E-value=0.23  Score=46.45  Aligned_cols=16  Identities=44%  Similarity=0.669  Sum_probs=14.2

Q ss_pred             CcEEEeCCCCCChhHH
Q psy3462         292 KNCLLESPTGSGKTLA  307 (795)
Q Consensus       292 ~~~l~EaPTGTGKTla  307 (795)
                      .++||.||+|||||..
T Consensus        36 ~~~L~~GPpGtGKT~l   51 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTL   51 (238)
T ss_dssp             CCEEEESSTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            5799999999999973

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=84.55  E-value=0.23  Score=51.22  Aligned_cols=14  Identities=71%  Similarity=0.945  Sum_probs=13.1

Q ss_pred             CcEEEECCCCCchH
Q psy3462          40 KNCLLESPTGSGKT   53 (795)
Q Consensus        40 ~~~llEAPTGTGKT   53 (795)
                      .+.++.+|||+|||
T Consensus        69 ~niLfiGPTGvGKT   82 (364)
T d1um8a_          69 SNILLIGPTGSGKT   82 (364)
T ss_dssp             CCEEEECCTTSSHH
T ss_pred             cceeeeCCCCccHH
Confidence            56999999999999

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=84.24  E-value=0.17  Score=53.67  Aligned_cols=17  Identities=53%  Similarity=0.706  Sum_probs=15.0

Q ss_pred             ccCcEEEeCCCCCChhH
Q psy3462         290 KAKNCLLESPTGSGKTL  306 (795)
Q Consensus       290 ~~~~~l~EaPTGTGKTl  306 (795)
                      .++|+|+-||||||||+
T Consensus        48 ~ksNILliGPTGvGKTl   64 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTE   64 (443)
T ss_dssp             CCCCEEEECCTTSSHHH
T ss_pred             ccccEEEECCCCCCHHH
Confidence            35799999999999995

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=83.59  E-value=0.23  Score=46.33  Aligned_cols=34  Identities=24%  Similarity=0.403  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHhcCCccccccchhhhhHHHHHhhccccCcEEEeCCCCCChhHH
Q psy3462         253 SQISMMNQVSNLFEQPNHFLKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLA  307 (795)
Q Consensus       253 ~Q~~mm~~i~~~l~~~~~~~~~~~~~~~~~~~i~al~~~~~~l~EaPTGTGKTla  307 (795)
                      +|....+.+.+.++..                     ...+.+|.||+|||||..
T Consensus        28 g~~~~~~~l~~~i~~~---------------------~~~~lll~Gp~G~GKTtl   61 (231)
T d1iqpa2          28 GQEHIVKRLKHYVKTG---------------------SMPHLLFAGPPGVGKTTA   61 (231)
T ss_dssp             SCHHHHHHHHHHHHHT---------------------CCCEEEEESCTTSSHHHH
T ss_pred             CcHHHHHHHHHHHHcC---------------------CCCeEEEECCCCCcHHHH
Confidence            4566677777777643                     235799999999999853

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=83.16  E-value=0.2  Score=50.02  Aligned_cols=16  Identities=56%  Similarity=0.748  Sum_probs=14.0

Q ss_pred             cCcEEEeCCCCCChhH
Q psy3462         291 AKNCLLESPTGSGKTL  306 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTl  306 (795)
                      .+.+|+.||||||||+
T Consensus        49 ~~~iLl~GPpG~GKT~   64 (309)
T d1ofha_          49 PKNILMIGPTGVGKTE   64 (309)
T ss_dssp             CCCEEEECCTTSSHHH
T ss_pred             CceEEEECCCCCCHHH
Confidence            4678899999999995

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.07  E-value=0.36  Score=44.93  Aligned_cols=32  Identities=19%  Similarity=0.141  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHhcCC--cEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCNKAK--NCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~~~~--~~llEAPTGTGKTL   54 (795)
                      =+|.+..+.+...+.++.  +++|.||.|+|||.
T Consensus        18 ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt   51 (224)
T d1sxjb2          18 VGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTT   51 (224)
T ss_dssp             CSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchh
Confidence            345566677777777764  69999999999993

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=82.98  E-value=0.56  Score=43.91  Aligned_cols=33  Identities=12%  Similarity=0.248  Sum_probs=27.8

Q ss_pred             CHHHHHHHHHHHHHHhcCC--c-EEEECCCCCchHH
Q psy3462          22 YSSCKILHLQVIQGCNKAK--N-CLLESPTGSGKTL   54 (795)
Q Consensus        22 ~~~Q~~mm~~i~~al~~~~--~-~llEAPTGTGKTL   54 (795)
                      ||.|....+.+.+.+.+++  + +++.||.|+|||.
T Consensus         4 yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt   39 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDA   39 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHH
T ss_pred             CcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHH
Confidence            5788888888888888865  3 8999999999994

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

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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=82.70  E-value=0.5  Score=45.03  Aligned_cols=25  Identities=32%  Similarity=0.465  Sum_probs=18.4

Q ss_pred             cCcEEEeCCCCCChhHHHHHHHHHHH
Q psy3462         291 AKNCLLESPTGSGKTLALLCSVLAWQ  316 (795)
Q Consensus       291 ~~~~l~EaPTGTGKTlayL~~~l~~~  316 (795)
                      .+++++.||.|||||..++-= ++++
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~r-v~~l   38 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNK-IAHL   38 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHH-HHHH
T ss_pred             CCCEEEEeeCCccHHHHHHHH-HHHH
Confidence            357889999999999876543 3443

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

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: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=82.67  E-value=0.59  Score=45.17  Aligned_cols=32  Identities=22%  Similarity=0.092  Sum_probs=22.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHHH
Q psy3462          21 KYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALLC   58 (795)
Q Consensus        21 p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL~   58 (795)
                      ..+.|++.++    +  .+.+++|.||.|||||...+-
T Consensus        12 L~~eQ~~~v~----~--~~g~~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          12 LNKEQQEAVR----T--TEGPLLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             SCHHHHHHHH----C--CSSCEEEEECTTSCHHHHHHH
T ss_pred             CCHHHHHHHh----C--CCCCEEEEecCCccHHHHHHH
Confidence            4577855443    2  356799999999999965543

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

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: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=81.98  E-value=0.98  Score=42.23  Aligned_cols=38  Identities=16%  Similarity=-0.120  Sum_probs=31.1

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEECCCCCchHHHHH
Q psy3462          20 LKYSSCKILHLQVIQGCNKAKNCLLESPTGSGKTLALL   57 (795)
Q Consensus        20 ~p~~~Q~~mm~~i~~al~~~~~~llEAPTGTGKTLAyL   57 (795)
                      ..+|.|.+-+.-++........+|+--++|+|||+..+
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i   49 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI   49 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH
Confidence            46899998887777777777778998999999997654

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.91  E-value=0.38  Score=41.59  Aligned_cols=15  Identities=40%  Similarity=0.767  Sum_probs=13.7

Q ss_pred             CcEEEECCCCCchHH
Q psy3462          40 KNCLLESPTGSGKTL   54 (795)
Q Consensus        40 ~~~llEAPTGTGKTL   54 (795)
                      ++++|-+|+|||||-
T Consensus         2 k~v~ItG~~GtGKTt   16 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT   16 (189)
T ss_dssp             CCEEEESCCSSCHHH
T ss_pred             cEEEEECCCCCcHHH
Confidence            689999999999994

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=81.29  E-value=0.31  Score=48.46  Aligned_cols=32  Identities=16%  Similarity=0.197  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHh--cCCcEEEECCCCCchHH
Q psy3462          23 SSCKILHLQVIQGCN--KAKNCLLESPTGSGKTL   54 (795)
Q Consensus        23 ~~Q~~mm~~i~~al~--~~~~~llEAPTGTGKTL   54 (795)
                      -+|.++-.++.-++.  .+.|+++++|.|||||.
T Consensus        10 ~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~   43 (333)
T d1g8pa_          10 VGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKST   43 (333)
T ss_dssp             CSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTH
T ss_pred             cCcHHHHHHHHHHHhccCCCeEEEECCCCccHHH
Confidence            567655554443332  45689999999999993